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Evolution of physics‐based methodology for exploring the conformational energy landscape of proteins
Author(s) -
Scheraga Harold A.,
Pillardy Jaroslaw,
Liwo Adam,
Lee Jooyoung,
Czaplewski Cezary,
Ripoll Daniel R.,
Wedemeyer William J.,
Arnautova Yelena A.
Publication year - 2001
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.1154
Subject(s) - energy landscape , threading (protein sequence) , protein folding , folding (dsp implementation) , protein structure prediction , homology (biology) , coupling (piping) , physics , protein structure , computer science , statistical physics , chemistry , engineering , amino acid , mechanical engineering , biochemistry , nuclear magnetic resonance , thermodynamics
The evolution of our physics‐based computational methods for determining protein conformation without the introduction of secondary‐structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard‐sphere potential captured much of the structural properties of polypeptide chains, and subsequent more refined force fields, together with efficient methods of global optimization provide indications that progress is being made toward an understanding of the interresidue interactions that underlie protein folding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 28–34, 2002