Multiple model approach--dealing with alignment ambiguities in protein modeling.

K. Pawłowski, L. Jaroszewski, A. Bierzyñski, A. Godzik

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Sequence alignments for distantly homologous proteins are often ambiguous, which creates a weak link in structure prediction by homology. We address this problem by using several plausible alignments in a modeling procedure, obtaining many models of the target. All are subsequently evaluated by a threading algorithm. It is shown that this approach can identify best alignments and produce reasonable models, whose quality is now limited only by the extent of the structural similarity between the known and predicted protein. Using a similar approach structure prediction for the oxidized dimer of S100A1 protein, for which the structure is not known, is presented.

Original languageEnglish (US)
Pages (from-to)328-339
Number of pages12
JournalPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
StatePublished - 1997
Externally publishedYes

ASJC Scopus subject areas

  • Biomedical Engineering
  • Computational Theory and Mathematics

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