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A molecular dynamics approach for the generation of complete protein structures from limited coordinate data
Author(s) -
van Gelder Celia W. G.,
Leusen Frank J. J.,
Leunissen Jack A. M.,
Noordik Jan H.
Publication year - 1994
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/prot.340180209
Subject(s) - molecular dynamics , biological system , protein structure , side chain , computer science , minification , protein structure prediction , homology modeling , algorithm , chemistry , computational chemistry , biology , biochemistry , enzyme , organic chemistry , polymer , programming language
Generation of full protein coordinates from limited information, e.g., the Cα coordinates, is an important step in protein homology modeling and structure determination, and molecular dynamics (MD) simulations may prove to be important in this task. We describe a new method, in which the protein backbone is built quickly in a rather crude way and then refined by minimization techniques. Subsequently, the side chains are positioned using extensive MD calculations. The method is tested on two proteins, and results compared to proteins constructed using two other MD‐based methods. In the first method, we supplemented an existing backbone building method with a new procedure to add side chains. The second one largely consists of available methodology. The constructed proteins are compared to the corresponding X‐ray structures, which became available during this study, and they are in good agreement (backbone RMS values of 0.5–0.7 Å, and all‐atom RMS values of 1.5–1.9 Å). This comparative study indicates that extensive MD simulations are able, to some extent, to generate details of the native protein structure, and may contribute to the development of a standardized methodology to predict reliably (parts of) protein structures when only partial coordinate data are available. © 1994 John Wiley & Sons, Inc.