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Protein folding simulation with genetic algorithm and supersecondary structure constraints
Author(s) -
Cui Yan,
Chen Run Sheng,
Wong Wing Hung
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(19980515)31:3<247::aid-prot2>3.0.co;2-g
Subject(s) - computation , algorithm , protein folding , accessible surface area , set (abstract data type) , folding (dsp implementation) , surface protein , solvent , surface (topology) , protein structure , crystallography , computer science , biological system , chemistry , mathematics , biology , geometry , engineering , computational chemistry , biochemistry , virology , electrical engineering , programming language
We describe an algorithm to compute native structures of proteins from their primary sequences. The novel aspects of this method are: 1) The hydrophobic potential was set to be proportional to the nonpolar solvent accessible surface. To make computation feasible, we developed a new algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and used as restraints during the conformation searching processes. This algorithm was applied to five proteins. The overall fold of these proteins can be computed from their sequences, with deviations from crystal structures of 1.48–4.48 Å for C α atoms. Proteins 31:247–257, 1998. © 1998 Wiley‐Liss, Inc.