The protein folding problem: finding a few minimums in a near infinite space.
Folding a protein from only a knowledge of its amino acid sequence is a formidable many-body problem. Since it is computationally impossible to test all possible atomic conformations to determine the global minimum representing the compact state, methods need to be developed to sample only a small part of the configurational space and yet delineate the free energy optimum (or nearly so). This article largely reviews such techniques as applied by the authors and their colleagues.
Argos
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European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Abagyan
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R
D000465:Algorithms; D000595:Amino Acid Sequence; D003201:Computers; D004744:Enkephalin, Methionine / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010970:Plastocyanin / Q000737:chemistry / Q000235:genetics; D011487:Protein Conformation; D017510:Protein Folding; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics
D004744:Enkephalin, Methionine; D010970:Plastocyanin