The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
Identifieur interne : 002272 ( PubMed/Corpus ); précédent : 002271; suivant : 002273The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
Auteurs : G C P. Van Zundert ; J P G L M. Rodrigues ; M. Trellet ; C. Schmitz ; P L Kastritis ; E. Karaca ; A S J. Melquiond ; M. Van Dijk ; S J De Vries ; A M J J. BonvinSource :
- Journal of molecular biology [ 1089-8638 ] ; 2016.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Macromolecular Substances.
- methods : Computational Biology, Molecular Biology.
- Internet.
Abstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
DOI: 10.1016/j.jmb.2015.09.014
PubMed: 26410586
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pubmed:26410586Le document en format XML
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Rodrigues</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Trellet, M" sort="Trellet, M" uniqKey="Trellet M" first="M" last="Trellet">M. Trellet</name><affiliation><nlm:affiliation>Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France.</nlm:affiliation></affiliation></author><author><name sortKey="Schmitz, C" sort="Schmitz, C" uniqKey="Schmitz C" first="C" last="Schmitz">C. 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Van Zundert</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Rodrigues, J P G L M" sort="Rodrigues, J P G L M" uniqKey="Rodrigues J" first="J P G L M" last="Rodrigues">J P G L M. Rodrigues</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Trellet, M" sort="Trellet, M" uniqKey="Trellet M" first="M" last="Trellet">M. Trellet</name><affiliation><nlm:affiliation>Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France.</nlm:affiliation></affiliation></author><author><name sortKey="Schmitz, C" sort="Schmitz, C" uniqKey="Schmitz C" first="C" last="Schmitz">C. Schmitz</name><affiliation><nlm:affiliation>Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Kastritis, P L" sort="Kastritis, P L" uniqKey="Kastritis P" first="P L" last="Kastritis">P L Kastritis</name><affiliation><nlm:affiliation>European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Karaca, E" sort="Karaca, E" uniqKey="Karaca E" first="E" last="Karaca">E. Karaca</name><affiliation><nlm:affiliation>European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Melquiond, A S J" sort="Melquiond, A S J" uniqKey="Melquiond A" first="A S J" last="Melquiond">A S J. Melquiond</name><affiliation><nlm:affiliation>Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Van Dijk, M" sort="Van Dijk, M" uniqKey="Van Dijk M" first="M" last="Van Dijk">M. Van Dijk</name><affiliation><nlm:affiliation>Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="De Vries, S J" sort="De Vries, S J" uniqKey="De Vries S" first="S J" last="De Vries">S J De Vries</name><affiliation><nlm:affiliation>Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Bonvin, A M J J" sort="Bonvin, A M J J" uniqKey="Bonvin A" first="A M J J" last="Bonvin">A M J J. Bonvin</name><affiliation><nlm:affiliation>Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="eISSN">1089-8638</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Internet</term><term>Macromolecular Substances (chemistry)</term><term>Molecular Biology (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Macromolecular Substances</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Molecular Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Internet</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26410586</PMID><DateCreated><Year>2016</Year><Month>03</Month><Day>07</Day></DateCreated><DateCompleted><Year>2016</Year><Month>07</Month><Day>22</Day></DateCompleted><DateRevised><Year>2017</Year><Month>07</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8638</ISSN><JournalIssue CitedMedium="Internet"><Volume>428</Volume><Issue>4</Issue><PubDate><Year>2016</Year><Month>Feb</Month><Day>22</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.</ArticleTitle><Pagination><MedlinePgn>720-725</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0022-2836(15)00537-9</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jmb.2015.09.014</ELocationID><Abstract><AbstractText>The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.</AbstractText><CopyrightInformation>Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>van Zundert</LastName><ForeName>G C P</ForeName><Initials>GCP</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rodrigues</LastName><ForeName>J P G L M</ForeName><Initials>JPGLM</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Trellet</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmitz</LastName><ForeName>C</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kastritis</LastName><ForeName>P L</ForeName><Initials>PL</Initials><AffiliationInfo><Affiliation>European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Karaca</LastName><ForeName>E</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Melquiond</LastName><ForeName>A S J</ForeName><Initials>ASJ</Initials><AffiliationInfo><Affiliation>Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van Dijk</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>de Vries</LastName><ForeName>S J</ForeName><Initials>SJ</Initials><AffiliationInfo><Affiliation>Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bonvin</LastName><ForeName>A M J J</ForeName><Initials>AMJJ</Initials><AffiliationInfo><Affiliation>Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType 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