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Tertiary structure prediction of mixed α/β proteins via energy minimization
Author(s) -
Standley Daron M.,
Gunn John R.,
Friesner Richard A.,
McDermott Ann E.
Publication year - 1998
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/(sici)1097-0134(19981101)33:2<240::aid-prot8>3.0.co;2-m
Subject(s) - simulated annealing , monte carlo method , energy minimization , protein folding , minification , algorithm , cluster (spacecraft) , protein tertiary structure , protein structure , computer science , chemistry , biological system , statistical physics , crystallography , mathematics , physics , computational chemistry , mathematical optimization , statistics , biology , biochemistry , programming language
We describe an improved algorithm for protein structure prediction, assuming that the location of secondary structural elements is known, with particular focus on prediction for proteins containing β‐strands. Hydrogen bonding terms are incorporated into the potential function, supplementing our previously developed residue‐residue potential which is based on a combination of database statistics and an excluded volume term. Two small mixed α/β proteins, 1‐CTF and BPTI, are studied. In order to obtain native‐like structures, it is necessary to allow the β‐strands in BPTI to distort substantially from an ideal geometry, and an automated algorithm to carry this out efficiently is presented. Simulated annealing Monte Carlo methods, which contain a genetic algorithm component as well, are used to produce an ensemble of low‐energy structures. For both proteins, a cluster of structures with low RMS deviation from the native structure is generated and the energetic ranking of this cluster is in the top 2 or 3 clusters obtained from simulations. These results are encouraging with regard to the possibility of constructing a robust procedure for tertiary folding which is applicable to β‐strand containing proteins. Proteins 33:240–252, 1998. © 1998 Wiley‐Liss, Inc.