Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.
Identifieur interne : 000002 ( PubMed/Corpus ); précédent : 000001; suivant : 000003Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.
Auteurs : Marc F. Lensink ; Sameer Velankar ; Andriy Kryshtafovych ; Shen-You Huang ; Dina Schneidman-Duhovny ; Andrej Sali ; Joan Segura ; Narcis Fernandez-Fuentes ; Shruthi Viswanath ; Ron Elber ; Sergei Grudinin ; Petr Popov ; Emilie Neveu ; Hasup Lee ; Minkyung Baek ; Sangwoo Park ; Lim Heo ; Gyu Rie Lee ; Chaok Seok ; Sanbo Qin ; Huan-Xiang Zhou ; David W. Ritchie ; Bernard Maigret ; Marie-Dominique Devignes ; Anisah Ghoorah ; Mieczyslaw Torchala ; Raphaël A G. Chaleil ; Paul A. Bates ; Efrat Ben-Zeev ; Miriam Eisenstein ; Surendra S. Negi ; Zhiping Weng ; Thom Vreven ; Brian G. Pierce ; Tyler M. Borrman ; Jinchao Yu ; Françoise Ochsenbein ; Raphaël Guerois ; Anna Vangone ; João P G L M. Rodrigues ; Gydo Van Zundert ; Mehdi Nellen ; Li Xue ; Ezgi Karaca ; Adrien S J. Melquiond ; Koen Visscher ; Panagiotis L. Kastritis ; Alexandre M J J. Bonvin ; Xianjin Xu ; Liming Qiu ; Chengfei Yan ; Jilong Li ; Zhiwei Ma ; Jianlin Cheng ; Xiaoqin Zou ; Yang Shen ; Lenna X. Peterson ; Hyung-Rae Kim ; Amit Roy ; Xusi Han ; Juan Esquivel-Rodriguez ; Daisuke Kihara ; Xiaofeng Yu ; Neil J. Bruce ; Jonathan C. Fuller ; Rebecca C. Wade ; Ivan Anishchenko ; Petras J. Kundrotas ; Ilya A. Vakser ; Kenichiro Imai ; Kazunori Yamada ; Toshiyuki Oda ; Tsukasa Nakamura ; Kentaro Tomii ; Chiara Pallara ; Miguel Romero-Durana ; Brian Jiménez-García ; Iain H. Moal ; Juan Férnandez-Recio ; Jong Young Joung ; Jong Yun Kim ; Keehyoung Joo ; Jooyoung Lee ; Dima Kozakov ; Sandor Vajda ; Scott Mottarella ; David R. Hall ; Dmitri Beglov ; Artem Mamonov ; Bing Xia ; Tanggis Bohnuud ; Carlos A. Del Carpio ; Eichiro Ichiishi ; Nicholas Marze ; Daisuke Kuroda ; Shourya S. Roy Burman ; Jeffrey J. Gray ; Edrisse Chermak ; Luigi Cavallo ; Romina Oliva ; Andrey Tovchigrechko ; Shoshana J. WodakSource :
- Proteins [ 1097-0134 ] ; 2016.
Abstract
We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. This article is protected by copyright. All rights reserved.
DOI: 10.1002/prot.25007
PubMed: 27122118
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.</title><author><name sortKey="Lensink, Marc F" sort="Lensink, Marc F" uniqKey="Lensink M" first="Marc F" last="Lensink">Marc F. Lensink</name><affiliation><nlm:affiliation>University Lille, CNRS UMR8576 UGSF, F-59000, Lille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Velankar, Sameer" sort="Velankar, Sameer" uniqKey="Velankar S" first="Sameer" last="Velankar">Sameer Velankar</name><affiliation><nlm:affiliation>European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Kryshtafovych, Andriy" sort="Kryshtafovych, Andriy" uniqKey="Kryshtafovych A" first="Andriy" last="Kryshtafovych">Andriy Kryshtafovych</name><affiliation><nlm:affiliation>Genome Center, University of California, Davis, CA, 95616, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Huang, Shen You" sort="Huang, Shen You" uniqKey="Huang S" first="Shen-You" last="Huang">Shen-You Huang</name><affiliation><nlm:affiliation>Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Schneidman Duhovny, Dina" sort="Schneidman Duhovny, Dina" uniqKey="Schneidman Duhovny D" first="Dina" last="Schneidman-Duhovny">Dina Schneidman-Duhovny</name><affiliation><nlm:affiliation>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sali, Andrej" sort="Sali, Andrej" uniqKey="Sali A" first="Andrej" last="Sali">Andrej Sali</name><affiliation><nlm:affiliation>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Segura, Joan" sort="Segura, Joan" uniqKey="Segura J" first="Joan" last="Segura">Joan Segura</name><affiliation><nlm:affiliation>GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC), 28049, Madrid, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Fernandez Fuentes, Narcis" sort="Fernandez Fuentes, Narcis" uniqKey="Fernandez Fuentes N" first="Narcis" last="Fernandez-Fuentes">Narcis Fernandez-Fuentes</name><affiliation><nlm:affiliation>Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY233FG, Aberystwyth, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Viswanath, Shruthi" sort="Viswanath, Shruthi" uniqKey="Viswanath S" first="Shruthi" last="Viswanath">Shruthi Viswanath</name><affiliation><nlm:affiliation>Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Elber, Ron" sort="Elber, Ron" uniqKey="Elber R" first="Ron" last="Elber">Ron Elber</name><affiliation><nlm:affiliation>Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, 78712, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Grudinin, Sergei" sort="Grudinin, Sergei" uniqKey="Grudinin S" first="Sergei" last="Grudinin">Sergei Grudinin</name><affiliation><nlm:affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</nlm:affiliation></affiliation></author><author><name sortKey="Popov, Petr" sort="Popov, Petr" uniqKey="Popov P" first="Petr" last="Popov">Petr Popov</name><affiliation><nlm:affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</nlm:affiliation></affiliation></author><author><name sortKey="Neveu, Emilie" sort="Neveu, Emilie" uniqKey="Neveu E" first="Emilie" last="Neveu">Emilie Neveu</name><affiliation><nlm:affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Hasup" sort="Lee, Hasup" uniqKey="Lee H" first="Hasup" last="Lee">Hasup Lee</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Baek, Minkyung" sort="Baek, Minkyung" uniqKey="Baek M" first="Minkyung" last="Baek">Minkyung Baek</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Park, Sangwoo" sort="Park, Sangwoo" uniqKey="Park S" first="Sangwoo" last="Park">Sangwoo Park</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Heo, Lim" sort="Heo, Lim" uniqKey="Heo L" first="Lim" last="Heo">Lim Heo</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Rie Lee, Gyu" sort="Rie Lee, Gyu" uniqKey="Rie Lee G" first="Gyu" last="Rie Lee">Gyu Rie Lee</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Seok, Chaok" sort="Seok, Chaok" uniqKey="Seok C" first="Chaok" last="Seok">Chaok Seok</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Qin, Sanbo" sort="Qin, Sanbo" uniqKey="Qin S" first="Sanbo" last="Qin">Sanbo Qin</name><affiliation><nlm:affiliation>Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Huan Xiang" sort="Zhou, Huan Xiang" uniqKey="Zhou H" first="Huan-Xiang" last="Zhou">Huan-Xiang Zhou</name><affiliation><nlm:affiliation>Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W" last="Ritchie">David W. 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Chaleil</name><affiliation><nlm:affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Bates, Paul A" sort="Bates, Paul A" uniqKey="Bates P" first="Paul A" last="Bates">Paul A. Bates</name><affiliation><nlm:affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Ben Zeev, Efrat" sort="Ben Zeev, Efrat" uniqKey="Ben Zeev E" first="Efrat" last="Ben-Zeev">Efrat Ben-Zeev</name><affiliation><nlm:affiliation>G-INCPM, Weizmann Institute of Science, Rehovot, 7610001, Israel.</nlm:affiliation></affiliation></author><author><name sortKey="Eisenstein, Miriam" sort="Eisenstein, Miriam" uniqKey="Eisenstein M" first="Miriam" last="Eisenstein">Miriam Eisenstein</name><affiliation><nlm:affiliation>Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.</nlm:affiliation></affiliation></author><author><name sortKey="Negi, Surendra S" sort="Negi, Surendra S" uniqKey="Negi S" first="Surendra S" last="Negi">Surendra S. Negi</name><affiliation><nlm:affiliation>Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0857, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Weng, Zhiping" sort="Weng, Zhiping" uniqKey="Weng Z" first="Zhiping" last="Weng">Zhiping Weng</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vreven, Thom" sort="Vreven, Thom" uniqKey="Vreven T" first="Thom" last="Vreven">Thom Vreven</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Pierce, Brian G" sort="Pierce, Brian G" uniqKey="Pierce B" first="Brian G" last="Pierce">Brian G. 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Rodrigues</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Van Zundert, Gydo" sort="Van Zundert, Gydo" uniqKey="Van Zundert G" first="Gydo" last="Van Zundert">Gydo Van Zundert</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Nellen, Mehdi" sort="Nellen, Mehdi" uniqKey="Nellen M" first="Mehdi" last="Nellen">Mehdi Nellen</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Xue, Li" sort="Xue, Li" uniqKey="Xue L" first="Li" last="Xue">Li Xue</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Karaca, Ezgi" sort="Karaca, Ezgi" uniqKey="Karaca E" first="Ezgi" last="Karaca">Ezgi Karaca</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Melquiond, Adrien S J" sort="Melquiond, Adrien S J" uniqKey="Melquiond A" first="Adrien S J" last="Melquiond">Adrien S J. Melquiond</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Visscher, Koen" sort="Visscher, Koen" uniqKey="Visscher K" first="Koen" last="Visscher">Koen Visscher</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Kastritis, Panagiotis L" sort="Kastritis, Panagiotis L" uniqKey="Kastritis P" first="Panagiotis L" last="Kastritis">Panagiotis L. Kastritis</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Bonvin, Alexandre M J J" sort="Bonvin, Alexandre M J J" uniqKey="Bonvin A" first="Alexandre M J J" last="Bonvin">Alexandre M J J. Bonvin</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Xianjin" sort="Xu, Xianjin" uniqKey="Xu X" first="Xianjin" last="Xu">Xianjin Xu</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Qiu, Liming" sort="Qiu, Liming" uniqKey="Qiu L" first="Liming" last="Qiu">Liming Qiu</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Yan, Chengfei" sort="Yan, Chengfei" uniqKey="Yan C" first="Chengfei" last="Yan">Chengfei Yan</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Jilong" sort="Li, Jilong" uniqKey="Li J" first="Jilong" last="Li">Jilong Li</name><affiliation><nlm:affiliation>Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ma, Zhiwei" sort="Ma, Zhiwei" uniqKey="Ma Z" first="Zhiwei" last="Ma">Zhiwei Ma</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name><affiliation><nlm:affiliation>Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zou, Xiaoqin" sort="Zou, Xiaoqin" uniqKey="Zou X" first="Xiaoqin" last="Zou">Xiaoqin Zou</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Shen, Yang" sort="Shen, Yang" uniqKey="Shen Y" first="Yang" last="Shen">Yang Shen</name><affiliation><nlm:affiliation>Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Peterson, Lenna X" sort="Peterson, Lenna X" uniqKey="Peterson L" first="Lenna X" last="Peterson">Lenna X. Peterson</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Hyung Rae" sort="Kim, Hyung Rae" uniqKey="Kim H" first="Hyung-Rae" last="Kim">Hyung-Rae Kim</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Roy, Amit" sort="Roy, Amit" uniqKey="Roy A" first="Amit" last="Roy">Amit Roy</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Xusi" sort="Han, Xusi" uniqKey="Han X" first="Xusi" last="Han">Xusi Han</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Esquivel Rodriguez, Juan" sort="Esquivel Rodriguez, Juan" uniqKey="Esquivel Rodriguez J" first="Juan" last="Esquivel-Rodriguez">Juan Esquivel-Rodriguez</name><affiliation><nlm:affiliation>Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, 59840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Kihara, Daisuke" sort="Kihara, Daisuke" uniqKey="Kihara D" first="Daisuke" last="Kihara">Daisuke Kihara</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Xiaofeng" sort="Yu, Xiaofeng" uniqKey="Yu X" first="Xiaofeng" last="Yu">Xiaofeng Yu</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bruce, Neil J" sort="Bruce, Neil J" uniqKey="Bruce N" first="Neil J" last="Bruce">Neil J. Bruce</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Fuller, Jonathan C" sort="Fuller, Jonathan C" uniqKey="Fuller J" first="Jonathan C" last="Fuller">Jonathan C. Fuller</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wade, Rebecca C" sort="Wade, Rebecca C" uniqKey="Wade R" first="Rebecca C" last="Wade">Rebecca C. Wade</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Anishchenko, Ivan" sort="Anishchenko, Ivan" uniqKey="Anishchenko I" first="Ivan" last="Anishchenko">Ivan Anishchenko</name><affiliation><nlm:affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Kundrotas, Petras J" sort="Kundrotas, Petras J" uniqKey="Kundrotas P" first="Petras J" last="Kundrotas">Petras J. Kundrotas</name><affiliation><nlm:affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Vakser, Ilya A" sort="Vakser, Ilya A" uniqKey="Vakser I" first="Ilya A" last="Vakser">Ilya A. Vakser</name><affiliation><nlm:affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Imai, Kenichiro" sort="Imai, Kenichiro" uniqKey="Imai K" first="Kenichiro" last="Imai">Kenichiro Imai</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yamada, Kazunori" sort="Yamada, Kazunori" uniqKey="Yamada K" first="Kazunori" last="Yamada">Kazunori Yamada</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Oda, Toshiyuki" sort="Oda, Toshiyuki" uniqKey="Oda T" first="Toshiyuki" last="Oda">Toshiyuki Oda</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Nakamura, Tsukasa" sort="Nakamura, Tsukasa" uniqKey="Nakamura T" first="Tsukasa" last="Nakamura">Tsukasa Nakamura</name><affiliation><nlm:affiliation>Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Tomii, Kentaro" sort="Tomii, Kentaro" uniqKey="Tomii K" first="Kentaro" last="Tomii">Kentaro Tomii</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Pallara, Chiara" sort="Pallara, Chiara" uniqKey="Pallara C" first="Chiara" last="Pallara">Chiara Pallara</name><affiliation><nlm:affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Romero Durana, Miguel" sort="Romero Durana, Miguel" uniqKey="Romero Durana M" first="Miguel" last="Romero-Durana">Miguel Romero-Durana</name><affiliation><nlm:affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Jimenez Garcia, Brian" sort="Jimenez Garcia, Brian" uniqKey="Jimenez Garcia B" first="Brian" last="Jiménez-García">Brian Jiménez-García</name><affiliation><nlm:affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Moal, Iain H" sort="Moal, Iain H" uniqKey="Moal I" first="Iain H" last="Moal">Iain H. Moal</name><affiliation><nlm:affiliation>Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034, Barcelona, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Fernandez Recio, Juan" sort="Fernandez Recio, Juan" uniqKey="Fernandez Recio J" first="Juan" last="Férnandez-Recio">Juan Férnandez-Recio</name><affiliation><nlm:affiliation>Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034, Barcelona, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Joung, Jong Young" sort="Joung, Jong Young" uniqKey="Joung J" first="Jong Young" last="Joung">Jong Young Joung</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Jong Yun" sort="Kim, Jong Yun" uniqKey="Kim J" first="Jong Yun" last="Kim">Jong Yun Kim</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Joo, Keehyoung" sort="Joo, Keehyoung" uniqKey="Joo K" first="Keehyoung" last="Joo">Keehyoung Joo</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Jooyoung" sort="Lee, Jooyoung" uniqKey="Lee J" first="Jooyoung" last="Lee">Jooyoung Lee</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kozakov, Dima" sort="Kozakov, Dima" uniqKey="Kozakov D" first="Dima" last="Kozakov">Dima Kozakov</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vajda, Sandor" sort="Vajda, Sandor" uniqKey="Vajda S" first="Sandor" last="Vajda">Sandor Vajda</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mottarella, Scott" sort="Mottarella, Scott" uniqKey="Mottarella S" first="Scott" last="Mottarella">Scott Mottarella</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Hall, David R" sort="Hall, David R" uniqKey="Hall D" first="David R" last="Hall">David R. Hall</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Beglov, Dmitri" sort="Beglov, Dmitri" uniqKey="Beglov D" first="Dmitri" last="Beglov">Dmitri Beglov</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mamonov, Artem" sort="Mamonov, Artem" uniqKey="Mamonov A" first="Artem" last="Mamonov">Artem Mamonov</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Xia, Bing" sort="Xia, Bing" uniqKey="Xia B" first="Bing" last="Xia">Bing Xia</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bohnuud, Tanggis" sort="Bohnuud, Tanggis" uniqKey="Bohnuud T" first="Tanggis" last="Bohnuud">Tanggis Bohnuud</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Del Carpio, Carlos A" sort="Del Carpio, Carlos A" uniqKey="Del Carpio C" first="Carlos A" last="Del Carpio">Carlos A. Del Carpio</name><affiliation><nlm:affiliation>Institute of Biological Diversity, International Pacific Institute of Indiana, PO Box 7304, Bloomington, IN, 47401, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ichiishi, Eichiro" sort="Ichiishi, Eichiro" uniqKey="Ichiishi E" first="Eichiro" last="Ichiishi">Eichiro Ichiishi</name><affiliation><nlm:affiliation>International University of Health and Welfare Hospital (IUHW Hospital), 537 Iguchi, Asushiobara-city, Tochigi Pref., 329-2763, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Marze, Nicholas" sort="Marze, Nicholas" uniqKey="Marze N" first="Nicholas" last="Marze">Nicholas Marze</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Kuroda, Daisuke" sort="Kuroda, Daisuke" uniqKey="Kuroda D" first="Daisuke" last="Kuroda">Daisuke Kuroda</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Roy Burman, Shourya S" sort="Roy Burman, Shourya S" uniqKey="Roy Burman S" first="Shourya S" last="Roy Burman">Shourya S. Roy Burman</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Gray, Jeffrey J" sort="Gray, Jeffrey J" uniqKey="Gray J" first="Jeffrey J" last="Gray">Jeffrey J. Gray</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Chermak, Edrisse" sort="Chermak, Edrisse" uniqKey="Chermak E" first="Edrisse" last="Chermak">Edrisse Chermak</name><affiliation><nlm:affiliation>King Abdullah University of Science and Technology, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Cavallo, Luigi" sort="Cavallo, Luigi" uniqKey="Cavallo L" first="Luigi" last="Cavallo">Luigi Cavallo</name><affiliation><nlm:affiliation>King Abdullah University of Science and Technology, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Oliva, Romina" sort="Oliva, Romina" uniqKey="Oliva R" first="Romina" last="Oliva">Romina Oliva</name><affiliation><nlm:affiliation>University of Naples "Parthenope", Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Tovchigrechko, Andrey" sort="Tovchigrechko, Andrey" uniqKey="Tovchigrechko A" first="Andrey" last="Tovchigrechko">Andrey Tovchigrechko</name><affiliation><nlm:affiliation>J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wodak, Shoshana J" sort="Wodak, Shoshana J" uniqKey="Wodak S" first="Shoshana J" last="Wodak">Shoshana J. 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Lensink</name><affiliation><nlm:affiliation>University Lille, CNRS UMR8576 UGSF, F-59000, Lille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Velankar, Sameer" sort="Velankar, Sameer" uniqKey="Velankar S" first="Sameer" last="Velankar">Sameer Velankar</name><affiliation><nlm:affiliation>European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Kryshtafovych, Andriy" sort="Kryshtafovych, Andriy" uniqKey="Kryshtafovych A" first="Andriy" last="Kryshtafovych">Andriy Kryshtafovych</name><affiliation><nlm:affiliation>Genome Center, University of California, Davis, CA, 95616, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Huang, Shen You" sort="Huang, Shen You" uniqKey="Huang S" first="Shen-You" last="Huang">Shen-You Huang</name><affiliation><nlm:affiliation>Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Schneidman Duhovny, Dina" sort="Schneidman Duhovny, Dina" uniqKey="Schneidman Duhovny D" first="Dina" last="Schneidman-Duhovny">Dina Schneidman-Duhovny</name><affiliation><nlm:affiliation>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sali, Andrej" sort="Sali, Andrej" uniqKey="Sali A" first="Andrej" last="Sali">Andrej Sali</name><affiliation><nlm:affiliation>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Segura, Joan" sort="Segura, Joan" uniqKey="Segura J" first="Joan" last="Segura">Joan Segura</name><affiliation><nlm:affiliation>GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC), 28049, Madrid, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Fernandez Fuentes, Narcis" sort="Fernandez Fuentes, Narcis" uniqKey="Fernandez Fuentes N" first="Narcis" last="Fernandez-Fuentes">Narcis Fernandez-Fuentes</name><affiliation><nlm:affiliation>Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY233FG, Aberystwyth, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Viswanath, Shruthi" sort="Viswanath, Shruthi" uniqKey="Viswanath S" first="Shruthi" last="Viswanath">Shruthi Viswanath</name><affiliation><nlm:affiliation>Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Elber, Ron" sort="Elber, Ron" uniqKey="Elber R" first="Ron" last="Elber">Ron Elber</name><affiliation><nlm:affiliation>Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, 78712, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Grudinin, Sergei" sort="Grudinin, Sergei" uniqKey="Grudinin S" first="Sergei" last="Grudinin">Sergei Grudinin</name><affiliation><nlm:affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</nlm:affiliation></affiliation></author><author><name sortKey="Popov, Petr" sort="Popov, Petr" uniqKey="Popov P" first="Petr" last="Popov">Petr Popov</name><affiliation><nlm:affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</nlm:affiliation></affiliation></author><author><name sortKey="Neveu, Emilie" sort="Neveu, Emilie" uniqKey="Neveu E" first="Emilie" last="Neveu">Emilie Neveu</name><affiliation><nlm:affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Hasup" sort="Lee, Hasup" uniqKey="Lee H" first="Hasup" last="Lee">Hasup Lee</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Baek, Minkyung" sort="Baek, Minkyung" uniqKey="Baek M" first="Minkyung" last="Baek">Minkyung Baek</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Park, Sangwoo" sort="Park, Sangwoo" uniqKey="Park S" first="Sangwoo" last="Park">Sangwoo Park</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Heo, Lim" sort="Heo, Lim" uniqKey="Heo L" first="Lim" last="Heo">Lim Heo</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Rie Lee, Gyu" sort="Rie Lee, Gyu" uniqKey="Rie Lee G" first="Gyu" last="Rie Lee">Gyu Rie Lee</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Seok, Chaok" sort="Seok, Chaok" uniqKey="Seok C" first="Chaok" last="Seok">Chaok Seok</name><affiliation><nlm:affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Qin, Sanbo" sort="Qin, Sanbo" uniqKey="Qin S" first="Sanbo" last="Qin">Sanbo Qin</name><affiliation><nlm:affiliation>Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Huan Xiang" sort="Zhou, Huan Xiang" uniqKey="Zhou H" first="Huan-Xiang" last="Zhou">Huan-Xiang Zhou</name><affiliation><nlm:affiliation>Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W" last="Ritchie">David W. Ritchie</name><affiliation><nlm:affiliation>INRIA Nancy - Grand Est, 54600, Villers-lès-Nancy, France.</nlm:affiliation></affiliation></author><author><name sortKey="Maigret, Bernard" sort="Maigret, Bernard" uniqKey="Maigret B" first="Bernard" last="Maigret">Bernard Maigret</name><affiliation><nlm:affiliation>CNRS, LORIA, Campus Scientifique, BP 239, 54506, Vandœuvre-lès-Nancy, France.</nlm:affiliation></affiliation></author><author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name><affiliation><nlm:affiliation>CNRS, LORIA, Campus Scientifique, BP 239, 54506, Vandœuvre-lès-Nancy, France.</nlm:affiliation></affiliation></author><author><name sortKey="Ghoorah, Anisah" sort="Ghoorah, Anisah" uniqKey="Ghoorah A" first="Anisah" last="Ghoorah">Anisah Ghoorah</name><affiliation><nlm:affiliation>Department of Computer Science and Engineering, University of Mauritius, Reduit, Mauritius.</nlm:affiliation></affiliation></author><author><name sortKey="Torchala, Mieczyslaw" sort="Torchala, Mieczyslaw" uniqKey="Torchala M" first="Mieczyslaw" last="Torchala">Mieczyslaw Torchala</name><affiliation><nlm:affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Chaleil, Raphael A G" sort="Chaleil, Raphael A G" uniqKey="Chaleil R" first="Raphaël A G" last="Chaleil">Raphaël A G. Chaleil</name><affiliation><nlm:affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Bates, Paul A" sort="Bates, Paul A" uniqKey="Bates P" first="Paul A" last="Bates">Paul A. Bates</name><affiliation><nlm:affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Ben Zeev, Efrat" sort="Ben Zeev, Efrat" uniqKey="Ben Zeev E" first="Efrat" last="Ben-Zeev">Efrat Ben-Zeev</name><affiliation><nlm:affiliation>G-INCPM, Weizmann Institute of Science, Rehovot, 7610001, Israel.</nlm:affiliation></affiliation></author><author><name sortKey="Eisenstein, Miriam" sort="Eisenstein, Miriam" uniqKey="Eisenstein M" first="Miriam" last="Eisenstein">Miriam Eisenstein</name><affiliation><nlm:affiliation>Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.</nlm:affiliation></affiliation></author><author><name sortKey="Negi, Surendra S" sort="Negi, Surendra S" uniqKey="Negi S" first="Surendra S" last="Negi">Surendra S. Negi</name><affiliation><nlm:affiliation>Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0857, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Weng, Zhiping" sort="Weng, Zhiping" uniqKey="Weng Z" first="Zhiping" last="Weng">Zhiping Weng</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vreven, Thom" sort="Vreven, Thom" uniqKey="Vreven T" first="Thom" last="Vreven">Thom Vreven</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Pierce, Brian G" sort="Pierce, Brian G" uniqKey="Pierce B" first="Brian G" last="Pierce">Brian G. Pierce</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Borrman, Tyler M" sort="Borrman, Tyler M" uniqKey="Borrman T" first="Tyler M" last="Borrman">Tyler M. Borrman</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Jinchao" sort="Yu, Jinchao" uniqKey="Yu J" first="Jinchao" last="Yu">Jinchao Yu</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ochsenbein, Francoise" sort="Ochsenbein, Francoise" uniqKey="Ochsenbein F" first="Françoise" last="Ochsenbein">Françoise Ochsenbein</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Guerois, Raphael" sort="Guerois, Raphael" uniqKey="Guerois R" first="Raphaël" last="Guerois">Raphaël Guerois</name><affiliation><nlm:affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vangone, Anna" sort="Vangone, Anna" uniqKey="Vangone A" first="Anna" last="Vangone">Anna Vangone</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Rodrigues, Joao P G L M" sort="Rodrigues, Joao P G L M" uniqKey="Rodrigues J" first="João P G L M" last="Rodrigues">João P G L M. Rodrigues</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Van Zundert, Gydo" sort="Van Zundert, Gydo" uniqKey="Van Zundert G" first="Gydo" last="Van Zundert">Gydo Van Zundert</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Nellen, Mehdi" sort="Nellen, Mehdi" uniqKey="Nellen M" first="Mehdi" last="Nellen">Mehdi Nellen</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Xue, Li" sort="Xue, Li" uniqKey="Xue L" first="Li" last="Xue">Li Xue</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Karaca, Ezgi" sort="Karaca, Ezgi" uniqKey="Karaca E" first="Ezgi" last="Karaca">Ezgi Karaca</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Melquiond, Adrien S J" sort="Melquiond, Adrien S J" uniqKey="Melquiond A" first="Adrien S J" last="Melquiond">Adrien S J. Melquiond</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Visscher, Koen" sort="Visscher, Koen" uniqKey="Visscher K" first="Koen" last="Visscher">Koen Visscher</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Kastritis, Panagiotis L" sort="Kastritis, Panagiotis L" uniqKey="Kastritis P" first="Panagiotis L" last="Kastritis">Panagiotis L. Kastritis</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Bonvin, Alexandre M J J" sort="Bonvin, Alexandre M J J" uniqKey="Bonvin A" first="Alexandre M J J" last="Bonvin">Alexandre M J J. Bonvin</name><affiliation><nlm:affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Xianjin" sort="Xu, Xianjin" uniqKey="Xu X" first="Xianjin" last="Xu">Xianjin Xu</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Qiu, Liming" sort="Qiu, Liming" uniqKey="Qiu L" first="Liming" last="Qiu">Liming Qiu</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Yan, Chengfei" sort="Yan, Chengfei" uniqKey="Yan C" first="Chengfei" last="Yan">Chengfei Yan</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Jilong" sort="Li, Jilong" uniqKey="Li J" first="Jilong" last="Li">Jilong Li</name><affiliation><nlm:affiliation>Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ma, Zhiwei" sort="Ma, Zhiwei" uniqKey="Ma Z" first="Zhiwei" last="Ma">Zhiwei Ma</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name><affiliation><nlm:affiliation>Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zou, Xiaoqin" sort="Zou, Xiaoqin" uniqKey="Zou X" first="Xiaoqin" last="Zou">Xiaoqin Zou</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Shen, Yang" sort="Shen, Yang" uniqKey="Shen Y" first="Yang" last="Shen">Yang Shen</name><affiliation><nlm:affiliation>Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Peterson, Lenna X" sort="Peterson, Lenna X" uniqKey="Peterson L" first="Lenna X" last="Peterson">Lenna X. Peterson</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Hyung Rae" sort="Kim, Hyung Rae" uniqKey="Kim H" first="Hyung-Rae" last="Kim">Hyung-Rae Kim</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Roy, Amit" sort="Roy, Amit" uniqKey="Roy A" first="Amit" last="Roy">Amit Roy</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Xusi" sort="Han, Xusi" uniqKey="Han X" first="Xusi" last="Han">Xusi Han</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Esquivel Rodriguez, Juan" sort="Esquivel Rodriguez, Juan" uniqKey="Esquivel Rodriguez J" first="Juan" last="Esquivel-Rodriguez">Juan Esquivel-Rodriguez</name><affiliation><nlm:affiliation>Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, 59840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Kihara, Daisuke" sort="Kihara, Daisuke" uniqKey="Kihara D" first="Daisuke" last="Kihara">Daisuke Kihara</name><affiliation><nlm:affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Xiaofeng" sort="Yu, Xiaofeng" uniqKey="Yu X" first="Xiaofeng" last="Yu">Xiaofeng Yu</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bruce, Neil J" sort="Bruce, Neil J" uniqKey="Bruce N" first="Neil J" last="Bruce">Neil J. Bruce</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Fuller, Jonathan C" sort="Fuller, Jonathan C" uniqKey="Fuller J" first="Jonathan C" last="Fuller">Jonathan C. Fuller</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wade, Rebecca C" sort="Wade, Rebecca C" uniqKey="Wade R" first="Rebecca C" last="Wade">Rebecca C. Wade</name><affiliation><nlm:affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Anishchenko, Ivan" sort="Anishchenko, Ivan" uniqKey="Anishchenko I" first="Ivan" last="Anishchenko">Ivan Anishchenko</name><affiliation><nlm:affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Kundrotas, Petras J" sort="Kundrotas, Petras J" uniqKey="Kundrotas P" first="Petras J" last="Kundrotas">Petras J. Kundrotas</name><affiliation><nlm:affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Vakser, Ilya A" sort="Vakser, Ilya A" uniqKey="Vakser I" first="Ilya A" last="Vakser">Ilya A. Vakser</name><affiliation><nlm:affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Imai, Kenichiro" sort="Imai, Kenichiro" uniqKey="Imai K" first="Kenichiro" last="Imai">Kenichiro Imai</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yamada, Kazunori" sort="Yamada, Kazunori" uniqKey="Yamada K" first="Kazunori" last="Yamada">Kazunori Yamada</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Oda, Toshiyuki" sort="Oda, Toshiyuki" uniqKey="Oda T" first="Toshiyuki" last="Oda">Toshiyuki Oda</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Nakamura, Tsukasa" sort="Nakamura, Tsukasa" uniqKey="Nakamura T" first="Tsukasa" last="Nakamura">Tsukasa Nakamura</name><affiliation><nlm:affiliation>Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Tomii, Kentaro" sort="Tomii, Kentaro" uniqKey="Tomii K" first="Kentaro" last="Tomii">Kentaro Tomii</name><affiliation><nlm:affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Pallara, Chiara" sort="Pallara, Chiara" uniqKey="Pallara C" first="Chiara" last="Pallara">Chiara Pallara</name><affiliation><nlm:affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Romero Durana, Miguel" sort="Romero Durana, Miguel" uniqKey="Romero Durana M" first="Miguel" last="Romero-Durana">Miguel Romero-Durana</name><affiliation><nlm:affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Jimenez Garcia, Brian" sort="Jimenez Garcia, Brian" uniqKey="Jimenez Garcia B" first="Brian" last="Jiménez-García">Brian Jiménez-García</name><affiliation><nlm:affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Moal, Iain H" sort="Moal, Iain H" uniqKey="Moal I" first="Iain H" last="Moal">Iain H. Moal</name><affiliation><nlm:affiliation>Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034, Barcelona, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Fernandez Recio, Juan" sort="Fernandez Recio, Juan" uniqKey="Fernandez Recio J" first="Juan" last="Férnandez-Recio">Juan Férnandez-Recio</name><affiliation><nlm:affiliation>Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034, Barcelona, Spain.</nlm:affiliation></affiliation></author><author><name sortKey="Joung, Jong Young" sort="Joung, Jong Young" uniqKey="Joung J" first="Jong Young" last="Joung">Jong Young Joung</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Jong Yun" sort="Kim, Jong Yun" uniqKey="Kim J" first="Jong Yun" last="Kim">Jong Yun Kim</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Joo, Keehyoung" sort="Joo, Keehyoung" uniqKey="Joo K" first="Keehyoung" last="Joo">Keehyoung Joo</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Jooyoung" sort="Lee, Jooyoung" uniqKey="Lee J" first="Jooyoung" last="Lee">Jooyoung Lee</name><affiliation><nlm:affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kozakov, Dima" sort="Kozakov, Dima" uniqKey="Kozakov D" first="Dima" last="Kozakov">Dima Kozakov</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vajda, Sandor" sort="Vajda, Sandor" uniqKey="Vajda S" first="Sandor" last="Vajda">Sandor Vajda</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mottarella, Scott" sort="Mottarella, Scott" uniqKey="Mottarella S" first="Scott" last="Mottarella">Scott Mottarella</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Hall, David R" sort="Hall, David R" uniqKey="Hall D" first="David R" last="Hall">David R. Hall</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Beglov, Dmitri" sort="Beglov, Dmitri" uniqKey="Beglov D" first="Dmitri" last="Beglov">Dmitri Beglov</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mamonov, Artem" sort="Mamonov, Artem" uniqKey="Mamonov A" first="Artem" last="Mamonov">Artem Mamonov</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Xia, Bing" sort="Xia, Bing" uniqKey="Xia B" first="Bing" last="Xia">Bing Xia</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bohnuud, Tanggis" sort="Bohnuud, Tanggis" uniqKey="Bohnuud T" first="Tanggis" last="Bohnuud">Tanggis Bohnuud</name><affiliation><nlm:affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Del Carpio, Carlos A" sort="Del Carpio, Carlos A" uniqKey="Del Carpio C" first="Carlos A" last="Del Carpio">Carlos A. Del Carpio</name><affiliation><nlm:affiliation>Institute of Biological Diversity, International Pacific Institute of Indiana, PO Box 7304, Bloomington, IN, 47401, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ichiishi, Eichiro" sort="Ichiishi, Eichiro" uniqKey="Ichiishi E" first="Eichiro" last="Ichiishi">Eichiro Ichiishi</name><affiliation><nlm:affiliation>International University of Health and Welfare Hospital (IUHW Hospital), 537 Iguchi, Asushiobara-city, Tochigi Pref., 329-2763, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Marze, Nicholas" sort="Marze, Nicholas" uniqKey="Marze N" first="Nicholas" last="Marze">Nicholas Marze</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Kuroda, Daisuke" sort="Kuroda, Daisuke" uniqKey="Kuroda D" first="Daisuke" last="Kuroda">Daisuke Kuroda</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Roy Burman, Shourya S" sort="Roy Burman, Shourya S" uniqKey="Roy Burman S" first="Shourya S" last="Roy Burman">Shourya S. Roy Burman</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Gray, Jeffrey J" sort="Gray, Jeffrey J" uniqKey="Gray J" first="Jeffrey J" last="Gray">Jeffrey J. Gray</name><affiliation><nlm:affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Chermak, Edrisse" sort="Chermak, Edrisse" uniqKey="Chermak E" first="Edrisse" last="Chermak">Edrisse Chermak</name><affiliation><nlm:affiliation>King Abdullah University of Science and Technology, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Cavallo, Luigi" sort="Cavallo, Luigi" uniqKey="Cavallo L" first="Luigi" last="Cavallo">Luigi Cavallo</name><affiliation><nlm:affiliation>King Abdullah University of Science and Technology, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Oliva, Romina" sort="Oliva, Romina" uniqKey="Oliva R" first="Romina" last="Oliva">Romina Oliva</name><affiliation><nlm:affiliation>University of Naples "Parthenope", Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Tovchigrechko, Andrey" sort="Tovchigrechko, Andrey" uniqKey="Tovchigrechko A" first="Andrey" last="Tovchigrechko">Andrey Tovchigrechko</name><affiliation><nlm:affiliation>J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wodak, Shoshana J" sort="Wodak, Shoshana J" uniqKey="Wodak S" first="Shoshana J" last="Wodak">Shoshana J. Wodak</name><affiliation><nlm:affiliation>Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Proteins</title><idno type="eISSN">1097-0134</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. This article is protected by copyright. All rights reserved.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">27122118</PMID><DateCreated><Year>2016</Year><Month>4</Month><Day>28</Day></DateCreated><DateRevised><Year>2016</Year><Month>4</Month><Day>29</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1097-0134</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2016</Year><Month>Apr</Month><Day>28</Day></PubDate></JournalIssue><Title>Proteins</Title><ISOAbbreviation>Proteins</ISOAbbreviation></Journal><ArticleTitle>Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.</ArticleTitle><Pagination><MedlinePgn></MedlinePgn></Pagination><ELocationID EIdType="doi">10.1002/prot.25007</ELocationID><Abstract><AbstractText NlmCategory="UNASSIGNED">We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. This article is protected by copyright. All rights reserved.</AbstractText><CopyrightInformation>© 2016 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList><Author><LastName>Lensink</LastName><ForeName>Marc F</ForeName><Initials>MF</Initials><AffiliationInfo><Affiliation>University Lille, CNRS UMR8576 UGSF, F-59000, Lille, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Velankar</LastName><ForeName>Sameer</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.</Affiliation></AffiliationInfo></Author><Author><LastName>Kryshtafovych</LastName><ForeName>Andriy</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Genome Center, University of California, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Huang</LastName><ForeName>Shen-You</ForeName><Initials>SY</Initials><AffiliationInfo><Affiliation>Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Schneidman-Duhovny</LastName><ForeName>Dina</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Sali</LastName><ForeName>Andrej</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, 94158, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Segura</LastName><ForeName>Joan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC), 28049, Madrid, Spain.</Affiliation></AffiliationInfo></Author><Author><LastName>Fernandez-Fuentes</LastName><ForeName>Narcis</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY233FG, Aberystwyth, United Kingdom.</Affiliation></AffiliationInfo></Author><Author><LastName>Viswanath</LastName><ForeName>Shruthi</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, 78712, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Elber</LastName><ForeName>Ron</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, 78712, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Grudinin</LastName><ForeName>Sergei</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>INRIA, 38000, Grenoble, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Popov</LastName><ForeName>Petr</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>INRIA, 38000, Grenoble, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.</Affiliation></AffiliationInfo></Author><Author><LastName>Neveu</LastName><ForeName>Emilie</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>LJK, University Grenoble Alpes, CNRS, 38000, Grenoble, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>INRIA, 38000, Grenoble, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Lee</LastName><ForeName>Hasup</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Baek</LastName><ForeName>Minkyung</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Park</LastName><ForeName>Sangwoo</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Heo</LastName><ForeName>Lim</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Rie Lee</LastName><ForeName>Gyu</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Seok</LastName><ForeName>Chaok</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Qin</LastName><ForeName>Sanbo</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Zhou</LastName><ForeName>Huan-Xiang</ForeName><Initials>HX</Initials><AffiliationInfo><Affiliation>Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Ritchie</LastName><ForeName>David W</ForeName><Initials>DW</Initials><AffiliationInfo><Affiliation>INRIA Nancy - Grand Est, 54600, Villers-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Maigret</LastName><ForeName>Bernard</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>CNRS, LORIA, Campus Scientifique, BP 239, 54506, Vandœuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Devignes</LastName><ForeName>Marie-Dominique</ForeName><Initials>MD</Initials><AffiliationInfo><Affiliation>CNRS, LORIA, Campus Scientifique, BP 239, 54506, Vandœuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Ghoorah</LastName><ForeName>Anisah</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Engineering, University of Mauritius, Reduit, Mauritius.</Affiliation></AffiliationInfo></Author><Author><LastName>Torchala</LastName><ForeName>Mieczyslaw</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</Affiliation></AffiliationInfo></Author><Author><LastName>Chaleil</LastName><ForeName>Raphaël A G</ForeName><Initials>RA</Initials><AffiliationInfo><Affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</Affiliation></AffiliationInfo></Author><Author><LastName>Bates</LastName><ForeName>Paul A</ForeName><Initials>PA</Initials><AffiliationInfo><Affiliation>Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.</Affiliation></AffiliationInfo></Author><Author><LastName>Ben-Zeev</LastName><ForeName>Efrat</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>G-INCPM, Weizmann Institute of Science, Rehovot, 7610001, Israel.</Affiliation></AffiliationInfo></Author><Author><LastName>Eisenstein</LastName><ForeName>Miriam</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.</Affiliation></AffiliationInfo></Author><Author><LastName>Negi</LastName><ForeName>Surendra S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0857, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Weng</LastName><ForeName>Zhiping</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Vreven</LastName><ForeName>Thom</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Pierce</LastName><ForeName>Brian G</ForeName><Initials>BG</Initials><AffiliationInfo><Affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Borrman</LastName><ForeName>Tyler M</ForeName><Initials>TM</Initials><AffiliationInfo><Affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Yu</LastName><ForeName>Jinchao</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Ochsenbein</LastName><ForeName>Françoise</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Guerois</LastName><ForeName>Raphaël</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Vangone</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Rodrigues</LastName><ForeName>João P G L M</ForeName><Initials>JP</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>van Zundert</LastName><ForeName>Gydo</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Nellen</LastName><ForeName>Mehdi</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Xue</LastName><ForeName>Li</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Karaca</LastName><ForeName>Ezgi</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Melquiond</LastName><ForeName>Adrien S J</ForeName><Initials>AS</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Visscher</LastName><ForeName>Koen</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Kastritis</LastName><ForeName>Panagiotis L</ForeName><Initials>PL</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Bonvin</LastName><ForeName>Alexandre M J J</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author><LastName>Xu</LastName><ForeName>Xianjin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</Affiliation></AffiliationInfo></Author><Author><LastName>Qiu</LastName><ForeName>Liming</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</Affiliation></AffiliationInfo></Author><Author><LastName>Yan</LastName><ForeName>Chengfei</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Li</LastName><ForeName>Jilong</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Ma</LastName><ForeName>Zhiwei</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Cheng</LastName><ForeName>Jianlin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Zou</LastName><ForeName>Xiaoqin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of science - Chemistry, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Shen</LastName><ForeName>Yang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Peterson</LastName><ForeName>Lenna X</ForeName><Initials>LX</Initials><AffiliationInfo><Affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Kim</LastName><ForeName>Hyung-Rae</ForeName><Initials>HR</Initials><AffiliationInfo><Affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Roy</LastName><ForeName>Amit</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Han</LastName><ForeName>Xusi</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Esquivel-Rodriguez</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, 59840, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Kihara</LastName><ForeName>Daisuke</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, IL, 60637, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, 59840, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Yu</LastName><ForeName>Xiaofeng</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Bruce</LastName><ForeName>Neil J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Fuller</LastName><ForeName>Jonathan C</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Wade</LastName><ForeName>Rebecca C</ForeName><Initials>RC</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.</Affiliation></AffiliationInfo></Author><Author><LastName>Anishchenko</LastName><ForeName>Ivan</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</Affiliation></AffiliationInfo></Author><Author><LastName>Kundrotas</LastName><ForeName>Petras J</ForeName><Initials>PJ</Initials><AffiliationInfo><Affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</Affiliation></AffiliationInfo></Author><Author><LastName>Vakser</LastName><ForeName>Ilya A</ForeName><Initials>IA</Initials><AffiliationInfo><Affiliation>Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Imai</LastName><ForeName>Kenichiro</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Yamada</LastName><ForeName>Kazunori</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Oda</LastName><ForeName>Toshiyuki</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Nakamura</LastName><ForeName>Tsukasa</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Japan.</Affiliation></AffiliationInfo></Author><Author><LastName>Tomii</LastName><ForeName>Kentaro</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66047, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Japan.</Affiliation></AffiliationInfo></Author><Author><LastName>Pallara</LastName><ForeName>Chiara</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</Affiliation></AffiliationInfo></Author><Author><LastName>Romero-Durana</LastName><ForeName>Miguel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</Affiliation></AffiliationInfo></Author><Author><LastName>Jiménez-García</LastName><ForeName>Brian</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.</Affiliation></AffiliationInfo></Author><Author><LastName>Moal</LastName><ForeName>Iain H</ForeName><Initials>IH</Initials><AffiliationInfo><Affiliation>Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034, Barcelona, Spain.</Affiliation></AffiliationInfo></Author><Author><LastName>Férnandez-Recio</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034, Barcelona, Spain.</Affiliation></AffiliationInfo></Author><Author><LastName>Joung</LastName><ForeName>Jong Young</ForeName><Initials>JY</Initials><AffiliationInfo><Affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Kim</LastName><ForeName>Jong Yun</ForeName><Initials>JY</Initials><AffiliationInfo><Affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Joo</LastName><ForeName>Keehyoung</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Advanced Computation, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Lee</LastName><ForeName>Jooyoung</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Center for In-Silico Protein Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Computational Science, Korea Institute for Advanced Study, 130-722, Seoul, Korea.</Affiliation></AffiliationInfo></Author><Author><LastName>Kozakov</LastName><ForeName>Dima</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Vajda</LastName><ForeName>Sandor</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Chemistry, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Mottarella</LastName><ForeName>Scott</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Hall</LastName><ForeName>David R</ForeName><Initials>DR</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Beglov</LastName><ForeName>Dmitri</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Mamonov</LastName><ForeName>Artem</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Xia</LastName><ForeName>Bing</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Bohnuud</LastName><ForeName>Tanggis</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Boston University, Boston, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Del Carpio</LastName><ForeName>Carlos A</ForeName><Initials>CA</Initials><AffiliationInfo><Affiliation>Institute of Biological Diversity, International Pacific Institute of Indiana, PO Box 7304, Bloomington, IN, 47401, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Drosophila Genetic Resource Center, Kyoto Institute of Technology, Saga Ippongi-cho, Ukyo-ku, 616-8354, Japan.</Affiliation></AffiliationInfo></Author><Author><LastName>Ichiishi</LastName><ForeName>Eichiro</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>International University of Health and Welfare Hospital (IUHW Hospital), 537 Iguchi, Asushiobara-city, Tochigi Pref., 329-2763, Japan.</Affiliation></AffiliationInfo></Author><Author><LastName>Marze</LastName><ForeName>Nicholas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Kuroda</LastName><ForeName>Daisuke</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Roy Burman</LastName><ForeName>Shourya S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Gray</LastName><ForeName>Jeffrey J</ForeName><Initials>JJ</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Chermak</LastName><ForeName>Edrisse</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>King Abdullah University of Science and Technology, Saudi Arabia.</Affiliation></AffiliationInfo></Author><Author><LastName>Cavallo</LastName><ForeName>Luigi</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>King Abdullah University of Science and Technology, Saudi Arabia.</Affiliation></AffiliationInfo></Author><Author><LastName>Oliva</LastName><ForeName>Romina</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>University of Naples "Parthenope", Italy.</Affiliation></AffiliationInfo></Author><Author><LastName>Tovchigrechko</LastName><ForeName>Andrey</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA.</Affiliation></AffiliationInfo></Author><Author><LastName>Wodak</LastName><ForeName>Shoshana J</ForeName><Initials>SJ</Initials><AffiliationInfo><Affiliation>Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>VIB Structural Biology Research Center, VUB Pleinlaan 2, 1050, Brussels, Belgium.</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="">JOURNAL ARTICLE</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>4</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><MedlineTA>Proteins</MedlineTA><NlmUniqueID>8700181</NlmUniqueID><ISSNLinking>0887-3585</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">CAPRI</Keyword><Keyword MajorTopicYN="N">CASP</Keyword><Keyword MajorTopicYN="N">Oligomer state</Keyword><Keyword MajorTopicYN="N">blind prediction</Keyword><Keyword MajorTopicYN="N">protein docking</Keyword><Keyword MajorTopicYN="N">protein interaction</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>5</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>12</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>2</Month><Day>2</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>4</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>4</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>4</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="doi">10.1002/prot.25007</ArticleId><ArticleId IdType="pubmed">27122118</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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