Prediction of protein side-chain conformations from local three-dimensional homology relationships.
J Mol Biol
; 235(3): 1088-97, 1994 Jan 21.
Article
em En
| MEDLINE
| ID: mdl-7507173
ABSTRACT
A method for predicting the conformations of protein side-chains, starting from main-chain co-ordinates alone, is described. The method involves the comparison of the local environment of each residue whose side-chain conformation is to be predicted with a database of local environments for the same residue type constructed from an analysis of high-resolution protein structures. Local environments are described in terms of the residue type and location in space of residues that interact with the side-chain of interest. The best (most three-dimensionally homologous) few matches to each residue are then input to a Monte-Carlo procedure to give a final predicted structure. The method has been tested on a selection of eight proteins, ranging in size from 46 to 323 amino acid residues. The average side-chain atom root-mean-square deviation between the actual and predicted structures is 1.71 A taken over all residues, and 1.00 A if restricted to buried residues. Over all residues, an average of 59.8% of all side-chain dihedral angles are predicted within +/- 30 degrees of the crystal structure values. Considering buried residues only, this rises to 79.6%.
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Base de dados:
MEDLINE
Assunto principal:
Alinhamento de Sequência
/
Homologia de Sequência de Aminoácidos
/
Estrutura Terciária de Proteína
Idioma:
En
Ano de publicação:
1994
Tipo de documento:
Article