AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules
Identifieur interne : 000110 ( Main/Exploration ); précédent : 000109; suivant : 000111AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules
Auteurs : Crina-Maria Ionescu [République tchèque] ; David Sehnal [République tchèque] ; Francesco L. Falginella [République tchèque] ; Purbaj Pant [République tchèque] ; Lukáš Pravda [République tchèque] ; Tomáš Bouchal [République tchèque] ; Radka Svobodová Va Eková [République tchèque] ; Stanislav Geidl [République tchèque] ; Jaroslav Ko A [République tchèque]Source :
- Journal of Cheminformatics [ 1758-2946 ] ; 2015.
Abstract
Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.
This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form.
Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at
The online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13321-015-0099-x
PubMed: 26500704
PubMed Central: 4613891
Affiliations:
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Falginella</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno</wicri:regionArea><wicri:noRegion>625 00 Brno</wicri:noRegion></affiliation></author><author><name sortKey="Pant, Purbaj" sort="Pant, Purbaj" uniqKey="Pant P" first="Purbaj" last="Pant">Purbaj Pant</name><affiliation wicri:level="1"><nlm:aff id="Aff2">National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno</wicri:regionArea><wicri:noRegion>611 37 Brno</wicri:noRegion></affiliation></author><author><name sortKey="Pravda, Lukas" sort="Pravda, Lukas" uniqKey="Pravda L" first="Lukáš" last="Pravda">Lukáš Pravda</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno</wicri:regionArea><wicri:noRegion>625 00 Brno</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno</wicri:regionArea><wicri:noRegion>611 37 Brno</wicri:noRegion></affiliation></author><author><name sortKey="Bouchal, Tomas" sort="Bouchal, Tomas" uniqKey="Bouchal T" first="Tomáš" last="Bouchal">Tomáš Bouchal</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno</wicri:regionArea><wicri:noRegion>625 00 Brno</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno</wicri:regionArea><wicri:noRegion>611 37 Brno</wicri:noRegion></affiliation></author><author><name sortKey="Svobodova Va Ekova, Radka" sort="Svobodova Va Ekova, Radka" uniqKey="Svobodova Va Ekova R" first="Radka" last="Svobodová Va Eková">Radka Svobodová Va Eková</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno</wicri:regionArea><wicri:noRegion>625 00 Brno</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno</wicri:regionArea><wicri:noRegion>611 37 Brno</wicri:noRegion></affiliation></author><author><name sortKey="Geidl, Stanislav" sort="Geidl, Stanislav" uniqKey="Geidl S" first="Stanislav" last="Geidl">Stanislav Geidl</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno</wicri:regionArea><wicri:noRegion>625 00 Brno</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno</wicri:regionArea><wicri:noRegion>611 37 Brno</wicri:noRegion></affiliation></author><author><name sortKey="Ko A, Jaroslav" sort="Ko A, Jaroslav" uniqKey="Ko A J" first="Jaroslav" last="Ko A">Jaroslav Ko A</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno</wicri:regionArea><wicri:noRegion>625 00 Brno</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno</wicri:regionArea><wicri:noRegion>611 37 Brno</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of Cheminformatics</title><idno type="eISSN">1758-2946</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.</p></sec><sec><title>Results</title><p> This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical
method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form.</p></sec><sec><title>Conclusions</title><p>Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at <ext-link ext-link-type="uri" xlink:href="http://ncbr.muni.cz/ACC">http://ncbr.muni.cz/ACC</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Grodick, Ma" uniqKey="Grodick M">MA Grodick</name></author><author><name sortKey="Muren, Nb" uniqKey="Muren N">NB Muren</name></author><author><name sortKey="Barton, Jk" uniqKey="Barton J">JK Barton</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Zheng, G" uniqKey="Zheng G">G Zheng</name></author><author><name sortKey="Xiao, M" uniqKey="Xiao M">M Xiao</name></author><author><name sortKey="Lu, Xh" uniqKey="Lu X">XH 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Fc" uniqKey="Cheng F">FC Cheng</name></author><author><name sortKey="Loury, Dj" uniqKey="Loury D">DJ Loury</name></author><author><name sortKey="Fiddes, Jc" uniqKey="Fiddes J">JC Fiddes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dong, N" uniqKey="Dong N">N Dong</name></author><author><name sortKey="Zhu, X" uniqKey="Zhu X">X Zhu</name></author><author><name sortKey="Chou, S" uniqKey="Chou S">S Chou</name></author><author><name sortKey="Shan, A" uniqKey="Shan A">A Shan</name></author><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author><author><name sortKey="Jiang, J" uniqKey="Jiang J">J Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mohanram, H" uniqKey="Mohanram H">H Mohanram</name></author><author><name sortKey="Bhattacharjya, S" uniqKey="Bhattacharjya S">S Bhattacharjya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ostberg, N" uniqKey="Ostberg N">N 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last="Bouchal">Tomáš Bouchal</name><name sortKey="Falginella, Francesco L" sort="Falginella, Francesco L" uniqKey="Falginella F" first="Francesco L." last="Falginella">Francesco L. Falginella</name><name sortKey="Geidl, Stanislav" sort="Geidl, Stanislav" uniqKey="Geidl S" first="Stanislav" last="Geidl">Stanislav Geidl</name><name sortKey="Geidl, Stanislav" sort="Geidl, Stanislav" uniqKey="Geidl S" first="Stanislav" last="Geidl">Stanislav Geidl</name><name sortKey="Ko A, Jaroslav" sort="Ko A, Jaroslav" uniqKey="Ko A J" first="Jaroslav" last="Ko A">Jaroslav Ko A</name><name sortKey="Ko A, Jaroslav" sort="Ko A, Jaroslav" uniqKey="Ko A J" first="Jaroslav" last="Ko A">Jaroslav Ko A</name><name sortKey="Pant, Purbaj" sort="Pant, Purbaj" uniqKey="Pant P" first="Purbaj" last="Pant">Purbaj Pant</name><name sortKey="Pravda, Lukas" sort="Pravda, Lukas" uniqKey="Pravda L" first="Lukáš" last="Pravda">Lukáš Pravda</name><name sortKey="Pravda, Lukas" sort="Pravda, Lukas" uniqKey="Pravda L" first="Lukáš" last="Pravda">Lukáš Pravda</name><name sortKey="Sehnal, David" sort="Sehnal, David" uniqKey="Sehnal D" first="David" last="Sehnal">David Sehnal</name><name sortKey="Sehnal, David" sort="Sehnal, David" uniqKey="Sehnal D" first="David" last="Sehnal">David Sehnal</name><name sortKey="Sehnal, David" sort="Sehnal, David" uniqKey="Sehnal D" first="David" last="Sehnal">David Sehnal</name><name sortKey="Svobodova Va Ekova, Radka" sort="Svobodova Va Ekova, Radka" uniqKey="Svobodova Va Ekova R" first="Radka" last="Svobodová Va Eková">Radka Svobodová Va Eková</name><name sortKey="Svobodova Va Ekova, Radka" sort="Svobodova Va Ekova, Radka" uniqKey="Svobodova Va Ekova R" first="Radka" last="Svobodová Va Eková">Radka Svobodová Va Eková</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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