The FoldX web server: an online force field
Identifieur interne : 000569 ( Istex/Corpus ); précédent : 000568; suivant : 000570The FoldX web server: an online force field
Auteurs : Joost Schymkowitz ; Jesper Borg ; Francois Stricher ; Robby Nys ; Frederic Rousseau ; Luis SerranoSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2005-07-01.
Abstract
FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at http://foldx.embl.de/. The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed.
Url:
DOI: 10.1093/nar/gki387
Links to Exploration step
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Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oupjournals.org</p></availability><date>2005</date></publicationStmt><notesStmt><note>*To whom correspondence should be addressed. 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Acids Res.</abbrev-journal-title><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="other">gki387</article-id><article-id pub-id-type="doi">10.1093/nar/gki387</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>The FoldX web server: an online force field</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Schymkowitz</surname><given-names>Joost</given-names></name><xref rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Borg</surname><given-names>Jesper</given-names></name><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Stricher</surname><given-names>Francois</given-names></name><xref rid="AU1">1</xref></contrib><contrib contrib-type="author"><name><surname>Nys</surname><given-names>Robby</given-names></name><xref rid="AU1">1</xref></contrib><contrib contrib-type="author"><name><surname>Rousseau</surname><given-names>Frederic</given-names></name></contrib><contrib contrib-type="author"><name><surname>Serrano</surname><given-names>Luis</given-names></name><xref rid="AU1">1</xref></contrib><aff>Switch Laboratory, Flanders Interuniversity Institute for Biotechnology (VIB), Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussel, Belgium</aff><aff id="AU1"><sup>1</sup>European Molecular Biology Laboratory, Meyerhofstrasse 1 62117 Heidelberg, Germany</aff><aff id="AU2"><sup>2</sup>Niels Bohr Institute, Blegdamsvej 17 DK2100 Copenhagen, Denmark</aff></contrib-group><author-notes><corresp id="COR1"><sup>*</sup>To whom correspondence should be addressed. Tel: +32 2 629 1425; Fax: +32 2 629 2963; Email: <ext-link xlink:href="joost.schymkowitz@skynet.be" ext-link-type="email">joost.schymkowitz@skynet.be</ext-link></corresp></author-notes><pub-date pub-type="ppub"><day>1</day><month>7</month><year>2005</year></pub-date><volume>33</volume><issue>suppl_2</issue><fpage>W382</fpage><lpage>W388</lpage><history><date date-type="accepted"><day>10</day><month>3</month><year>2005</year></date><date date-type="received"><day>14</day><month>2</month><year>2005</year></date></history><permissions><copyright-statement>© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. 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The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. 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