Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.

A M Mathiowetz; W A Goddard

doi:10.1002/pro.5560040619

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Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.

A M Mathiowetz·W A Goddard

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Abstract

Dihedral probability grid Monte Carlo (DPG-MC) is a general-purpose method of conformational sampling that can be applied to many problems in peptide and protein modeling. Here we present the DPG-MC method and apply it to predicting complete protein structures from C alpha coordinates. This is useful in such endeavors as homology modeling, protein structure prediction from lattice simulations, or fitting protein structures to X-ray crystallographic data. It also serves as an example of how DPG-MC can be applied to systems with geometric constraints. The conformational propensities for individual residues are used to guide conformational searches as the protein is built from the amino-terminus to the carboxyl-terminus. Results for a number of proteins show that both the backbone and side chain can be accurately modeled using DPG-MC. Backbone atoms are generally predicted with RMS errors of about 0.5 A (compared to X-ray crystal structure coordinates) and all atoms are predicted to an RMS error of 1.7 A or better.

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Amino Acids Computer Simulation Crystallography, X-Ray Databases, Factual Mathematical Computing Models, Molecular Monte Carlo Method Plant Proteins Probability Protein Conformation Protein Structure, Secondary Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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A M Mathiowetz, W A Goddard. 1995. Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.. https://doi.org/10.1002/pro.5560040619

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