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Calculation of protein conformation by global optimization of a potential energy function
Author(s) -
Lee Jooyoung,
Liwo Adam,
Ripoll Daniel R.,
Pillardy Jaroslaw,
Scheraga Harold A.
Publication year - 1999
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(1999)37:3+<204::aid-prot26>3.0.co;2-f
Subject(s) - function (biology) , statistical potential , protein structure , chemistry , energy (signal processing) , protein structure prediction , computational chemistry , computational biology , physics , biology , biochemistry , evolutionary biology , quantum mechanics
A novel hierarchical approach to protein folding has been applied to compute the unknown structures of seven target proteins provided by CASP3. The approach is based exclusively on the global optimization of a potential energy function for a united‐residue model by conformational space annealing, followed by energy refinement using an all‐atom potential. Comparison of the submitted models for five globular proteins with the experimental structures shows that the conformations of large fragments (∼60 aa) were predicted with rmsds of 4.2–6.8 Å for the C α atoms. Our lowest‐energy models for targets T0056 and T0061 were particularly successful, producing the correct fold of approximately 52% and 80% of the structures, respectively. These results support the thermodynamic hypothesis that protein structure can be computed solely by global optimization of a potential energy function for a given amino acid sequence. Proteins Suppl 1999;3:204–208. © 1999 Wiley‐Liss, Inc.