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      The FoldX web server: an online force field

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          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.

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          Most cited references20

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          The interpretation of protein structures: estimation of static accessibility.

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            Molecular basis for amyloid fibril formation and stability.

            The molecular structure of the amyloid fibril has remained elusive because of the difficulty of growing well diffracting crystals. By using a sequence-designed polypeptide, we have produced crystals of an amyloid fiber. These crystals diffract to high resolution (1 A) by electron and x-ray diffraction, enabling us to determine a detailed structure for amyloid. The structure reveals that the polypeptides form fibrous crystals composed of antiparallel beta-sheets in a cross-beta arrangement, characteristic of all amyloid fibers, and allows us to determine the side-chain packing within an amyloid fiber. The antiparallel beta-sheets are zipped together by means of pi-bonding between adjacent phenylalanine rings and salt-bridges between charge pairs (glutamic acid-lysine), thus controlling and stabilizing the structure. These interactions are likely to be important in the formation and stability of other amyloid fibrils.
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              Effective energy functions for protein structure prediction.

              Protein structure prediction, fold recognition, homology modeling and design rely mainly on statistical effective energy functions. Although the theoretical foundation of such functions is not clear, their usefulness has been demonstrated in many applications. Molecular mechanics force fields, particularly when augmented by implicit solvation models, provide physical effective energy functions that are beginning to play a role in this area.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Research
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                01 July 2005
                01 July 2005
                27 June 2005
                : 33
                : Web Server issue
                : W382-W388
                Affiliations
                Switch Laboratory, Flanders Interuniversity Institute for Biotechnology (VIB), Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussel, Belgium
                1European Molecular Biology Laboratory, Meyerhofstrasse 1 62117 Heidelberg, Germany
                2Niels Bohr Institute, Blegdamsvej 17 DK2100 Copenhagen, Denmark
                Author notes
                *To whom correspondence should be addressed. Tel: +32 2 629 1425; Fax: +32 2 629 2963; Email: joost.schymkowitz@ 123456skynet.be
                Article
                10.1093/nar/gki387
                1160148
                15980494
                37d8af51-19ec-42db-ad87-57af1f2f7b9b
                © 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. For commercial re-use, please contact journals.permissions@ 123456oupjournals.org

                History
                : 14 February 2005
                : 10 March 2005
                Categories
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                Genetics
                Genetics

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