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Use of residue pairs in protein sequence‐sequence and sequence‐structure alignments
Author(s) -
Jung Jongsun,
Lee Byungkook
Publication year - 2000
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.9.8.1576
Subject(s) - sequence (biology) , structural alignment , sequence alignment , sequence logo , peptide sequence , protein superfamily , protein sequencing , alignment free sequence analysis , sequence analysis , loop modeling , protein structure , multiple sequence alignment , homology modeling , consensus sequence , homology (biology) , computational biology , amino acid , genetics , biology , biochemistry , dna , gene , enzyme
Two new sets of scoring matrices are introduced: H2 for the protein sequence comparison and T 2 for the protein sequence–structure correlation. Each element of H 2 or T 2 measures the frequency with which a pair of amino acid types in one protein, k ‐residues apart in the sequence, is aligned with another pair of residues, of given amino acid types (for H 2 ) or in given structural states (for T 2 ), in other structurally homologous proteins. There are four types, corresponding to the k ‐values of 1 to 4, for both H 2 and T 2 . These matrices were set up using a large number of structurally homologous protein pairs, with little sequence homology between the pair, that were recently generated using the structure comparison program SHEBA. The two scoring matrices were incorporated into the main body of the sequence alignment program SSEARCH in the FASTA package and tested in a fold recognition setting in which a set of 107 test sequences were aligned to each of a panel of 3,539 domains that represent all known protein structures. Six procedures were tested; the straight Smith‐Waterman (SW) and FASTA procedures, which used the Blosum62 single residue type substitution matrix; BLAST and PSI‐BLAST procedures, which also used the Blosum62 matrix; PASH, which used Blosum62 and H 2 matrices; and PASSC, which used Blosum62, H 2 , and T 2 matrices. All procedures gave similar results when the probe and target sequences had greater than 30% sequence identity. However, when the sequence identity was below 30%, a similar structure could be found for more sequences using PASSC than using any other procedure. PASH and PSI‐BLAST gave the next best results.