Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease.

ABSTRACT: HIV-1 protease is a major drug target against AIDS as it permits viral maturation by processing the gag and pol polyproteins of the virus. The cleavage sites in these polyproteins do not have obvious sequence homology or a binding motif and the specificity of the protease is not easily determined. We used various threading approaches, together with the crystal structures of substrate complexes which served as template structures, to study the substrate specificity of HIV-1 protease with the aim of obtaining a better differentiation between binding and nonbinding sequences. The predictions from threading improved when distance-dependent interaction energy functions were used instead of contact matrices. To rank the peptides and properly account for the peptide's conformation in the total en

SUBMITTER: Kurt N 

PROVIDER: S-EPMC1303207 | biostudies-literature | 2003 Aug

REPOSITORIES: biostudies-literature