Determinants of side chain conformational preferences in protein structures |
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Authors: | Samudrala R; Moult J |
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Affiliation: | Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA. |
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Abstract: | A discriminatory function based on a statistical analysis of atomic
contacts in protein structures is used for selecting side chain rotamers
given a peptide main chain. The function allows us to rank different
possible side chain conformations on the basis of contacts between side
chain atoms and atoms in the environment. We compare the differences in
constructing side chain conformations using contacts with only the local
main chain, using the entire main chain, and by building pairs of side
chains simultaneously with local main chain information. Using only the
local main chain allows us to construct side chains with approximately 75%
of the chi1 angles within 30 degrees of the experimental value, and an
average side chain atom r.m.s.d. of 1.72 A in a set of 10 proteins. The
results of constructing side chains for the 10 proteins are compared with
the results of other side chain building methods previously published. The
comparison shows similar accuracies. An advantage of the present method is
that it can be used to select a small number of likely side chain
conformations for each residue, thus permitting limited combinatorial
searches for building multiple protein side chains simultaneously.
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