Recognizing protein folds by cluster distance geometry
Crippen, Gordon M.
2005-07-01
Citation
Crippen, Gordon M. (2005)."Recognizing protein folds by cluster distance geometry." Proteins: Structure, Function, and Bioinformatics 60(1): 82-89. <http://hdl.handle.net/2027.42/48690>
Abstract
Cluster distance geometry is a recent generalization of distance geometry whereby protein structures can be described at even lower levels of detail than one point per residue. With improvements in the clustering technique, protein conformations can be summarized in terms of alternative contact patterns between clusters, where each cluster contains four sequentially adjacent amino acid residues. A very simple potential function involving 210 adjustable parameters can be determined that favors the native contacts of 31 small, monomeric proteins over their respective sets of nonnative contacts. This potential then favors the native contacts for 174 small, monomeric proteins that have low sequence identity with any of the training set. A broader search finds 698 small protein chains from the Protein Data Bank where the native contacts are preferred over all alternatives, even though they have low sequence identity with the training set. This amounts to a highly predictive method for ab initio protein folding at low spatial resolution. Proteins 2005;. © 2005 Wiley-Liss, Inc.Publisher
Wiley Subscription Services, Inc., A Wiley Company
ISSN
0887-3585 1097-0134
Other DOIs
PMID
15861390
Types
Article
URI
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=15861390&dopt=citationMetadata
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