期刊
NUCLEIC ACIDS RESEARCH
卷 40, 期 W1, 页码 W288-W293出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gks419
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资金
- Institut National de la Sante et de la Recherche Medicale [UMR-S 973]
- Centre National de la Recherche Scientifique
- IA bioinformatics grant [BipBip]
In the context of the renewed interest of peptides as therapeutics, it is important to have an on-line resource for 3D structure prediction of peptides with well-defined structures in aqueous solution. We present an updated version of PEP-FOLD allowing the treatment of both linear and disulphide bonded cyclic peptides with 9-36 amino acids. The server makes possible to define disulphide bonds and any residue-residue proximity under the guidance of the biologists. Using a benchmark of 34 cyclic peptides with one, two and three disulphide bonds, the best PEP-FOLD models deviate by an average RMS of 2.75 A from the full NMR structures. Using a benchmark of 37 linear peptides, PEP-FOLD locates lowest-energy conformations deviating by 3 A RMS from the NMR rigid cores. The evolution of PEP-FOLD comes as a new on-line service to supersede the previous server. The server is available at: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD.
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