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Inverse Monte Carlo procedure for conformation determination of macromolecules
Author(s) -
Bathe Mark,
Rutledge Gregory C.
Publication year - 2003
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.10246
Subject(s) - macromolecule , monte carlo method , random coil , inverse , chemistry , statistical physics , thermodynamics , physics , crystallography , mathematics , circular dichroism , biochemistry , statistics , geometry
A novel numerical method for determining the conformational structure of macromolecules is applied to idealized biomacromolecules in solution. The method computes effective inter‐residue interaction potentials solely from the corresponding radial distribution functions, such as would be obtained from experimental data. The interaction potentials generate conformational ensembles that reproduce thermodynamic properties of the macromolecule (mean energy and heat capacity) in addition to the target radial distribution functions. As an evaluation of its utility in structure determination, we apply the method to a homopolymer and a heteropolymer model of a three‐helix bundle protein [Zhou, Y.; Karplus, M. Proc Natl Acad Sci USA 1997, 94, 14429; Zhou, Y. et al. J Chem Phys 1997, 107, 10691] at various thermodynamic state points, including the ordered globule, disordered globule, and random coil states. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 876–890, 2003