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Large loop conformation sampling using the activation relaxation technique, ART‐nouveau method
Author(s) -
StPierre JeanFrançois,
Mousseau Normand
Publication year - 2012
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.24085
Subject(s) - loop (graph theory) , sampling (signal processing) , scaling , folding (dsp implementation) , relaxation (psychology) , computation , sequence (biology) , exponential function , scale (ratio) , space (punctuation) , energy (signal processing) , algorithm , mathematics , computer science , physics , chemistry , statistics , combinatorics , geometry , biology , mathematical analysis , biochemistry , filter (signal processing) , quantum mechanics , neuroscience , electrical engineering , computer vision , engineering , operating system
We present an adaptation of the ART‐nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled conformations needed by ART nouveau to find the global energy minimum for a loop was found to scale linearly with the sequence length of the loop for loops between 8 and about 20 amino acids. Considering the linear scaling dependence of the computation cost on the loop sequence length for sampling new conformations, we estimate the total computational cost of sampling larger loops to scale quadratically compared to the exponential scaling of exhaustive search methods. Proteins 2012; © 2012 Wiley Periodicals, Inc.