title: NdPASA: a pairwise sequence alignment server for distantly related proteins.
abstract: 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.
authors.affiliation: Department of Chemistry, Temple University Philadelphia, PA 19122, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
authors.forename: Jin-An
authors.initials: JA
authors.lastname: Feng
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D020407:Internet; D008969:Molecular Sequence Data; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins