Optimization of multiple-sequence alignment based on multiple-structure alignment

Maxim Shatsky*, Ruth Nussinov, Haim J. Wolfson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Routinely used multiple-sequence alignment methods use only sequence information. Consequently, they may produce inaccurate alignments. Multiple-structure alignment methods, on the other hand, optimize structural alignment by ignoring sequence information. Here, we present an optimization method that unifies sequence and structure information. The alignment score is based on standard amino acid substitution probabilities combined with newly computed three-dimensional structure alignment probabilities. The advantage of our alignment scheme is in its ability to produce more accurate multiple alignments. We demonstrate the usefulness of the method in three applications: 1) computing more accurate multiple-sequence alignments, 2) analyzing protein conformational changes, and 3) computation of amino acid structure-sequence conservation with application to protein-protein docking prediction.

Original languageEnglish
Pages (from-to)209-217
Number of pages9
JournalProteins: Structure, Function and Genetics
Issue number1
StatePublished - 1 Jan 2006


  • Multiple-sequence alignment
  • Multiple-structure alignment
  • Structure-based sequence alignment
  • Structure-sequence conservation


Dive into the research topics of 'Optimization of multiple-sequence alignment based on multiple-structure alignment'. Together they form a unique fingerprint.

Cite this