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Exploring the conformational space of protein loops using a mean field technique with MOLS sampling
Author(s) -
Kanagasabai V.,
Arunachalam J.,
Arun Prasad P.,
Gautham N.
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21333
Subject(s) - protein data bank (rcsb pdb) , loop (graph theory) , loop modeling , sequence (biology) , sequence space , protein structure , force field (fiction) , space (punctuation) , sampling (signal processing) , crystallography , physics , computational biology , protein structure prediction , chemistry , computer science , mathematics , combinatorics , stereochemistry , biology , biochemistry , discrete mathematics , artificial intelligence , optics , detector , banach space , operating system
We have recently developed a computational technique that uses mutually orthogonal Latin square sampling to explore the conformational space of oligopeptides in an exhaustive manner. In this article, we report its use to analyze the conformational spaces of 120 protein loop sequences in proteins, culled from the PDB, having the length ranging from 5 to 10 residues. The force field used did not have any information regarding the sequences or structures that flanked the loop. The results of the analyses show that the native structure of the loop, as found in the PDB falls at one of the low energy points in the conformational landscape of the sequences. Thus, a large portion of the structural determinants of the loop may be considered intrinsic to the sequence, regardless of either adjacent sequences or structures, or the interactions that the atoms of the loop make with other residues in the protein or in neighboring proteins. Proteins 2007. © 2007 Wiley‐Liss, Inc.