NdPASA: A pairwise sequence alignment server for distantly related proteins

Wei Li, Junwen Wang, Jin An Feng

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Summary: NdPASA is a web server specifically designed to optimize sequence alignment between distantly related proteins. The program integrates structure information of the template sequence into a global alignment algorithm by employing neighbor-dependent propensities of amino acids as a unique parameter for alignment. NdPASA optimizes alignment by evaluating the likelihood of a residue pair in the query sequence matching against a corresponding residue pair adopting a particular secondary structure in the template sequence. NdPASA is most effective in aligning homologous proteins sharing low percentage of sequence identity. The server is designed to aid homologous protein structure modeling. A PSI-BLAST search engine was implemented to help users identify template candidates that are most appropriate for modeling the query sequences.

Original languageEnglish (US)
Pages (from-to)3803-3805
Number of pages3
JournalBioinformatics
Volume21
Issue number19
DOIs
StatePublished - Oct 2005

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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