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Folding in lipid membranes (FILM): A novel method for the prediction of small membrane protein 3D structures
Author(s) -
PellegriniCalace M.,
Carotti A.,
Jones D. T.
Publication year - 2003
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.10304
Subject(s) - globular protein , membrane protein , membrane , protein structure prediction , transmembrane protein , folding (dsp implementation) , crystallography , ab initio , solvation , statistical potential , topology (electrical circuits) , protein folding , pairwise comparison , chemistry , protein structure , materials science , biological system , computer science , molecule , biology , mathematics , artificial intelligence , biochemistry , engineering , receptor , organic chemistry , combinatorics , electrical engineering
We present the results of applying a novel knowledge‐based method (FILM) to the prediction of small membrane protein structures. The basis of the method is the addition of a membrane potential to the energy terms (pairwise, solvation, steric, and hydrogen bonding) of a previously developed ab initio technique for the prediction of tertiary structure of globular proteins (FRAGFOLD). The method is based on the assembly of supersecondary structural fragments taken from a library of highly resolved protein structures using a standard simulated annealing algorithm. The membrane potential has been derived by the statistical analysis of a data set made of 640 transmembrane helices with experimentally defined topology and belonging to 133 proteins extracted from the SWISS‐PROT database. Results obtained by applying the method to small membrane proteins of known 3D structure show that the method is able to predict, at a reasonable accuracy level, both the helix topology and the conformations of these proteins. Proteins 2003;50:537–545. © 2003 Wiley‐Liss, Inc.