Fast protein fold recognition via sequence to structure alignment and contact capacity potentials.

N. N. Alexandrov*, R. Nussinov, R. M. Zimmer

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

118 Scopus citations

Abstract

We propose new empirical scoring potentials and associated alignment procedures for optimally aligning protein sequences to protein structures. The method has two main applications: first, the recognition of a plausible fold for a protein sequence of unknown structure out of a database of representative protein structures and, second, the improvement of sequence alignments by using structural information in order to find a better starting point for homology based modelling. The empirical scoring function is derived from an analysis of a nonredundant database of known structures by converting relative frequencies into pseudoenergies using a normalization according to the inverse Bolzmann law. These-so called contact capacity-potentials turn out to be discriminative enough to detect structural folds in the absence of significant sequence similarity and at the same time simple enough to allow for a very fast optimization in an alignment procedure.

Original languageEnglish
Pages (from-to)53-72
Number of pages20
JournalPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
StatePublished - 1996
Externally publishedYes

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