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Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships
Author(s) -
Chakrabarti Saikat,
Sowdhamini R.
Publication year - 2004
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2004.05.028
Subject(s) - template , structural alignment , loop modeling , homology modeling , computational biology , structural motif , structural classification of proteins database , protein secondary structure , structural similarity , protein structure , structural bioinformatics , biology , homology (biology) , sequence (biology) , biological system , sequence alignment , peptide sequence , protein structure prediction , computer science , amino acid , biochemistry , enzyme , programming language , gene
Structurally conserved regions or structural templates have been identified and examined for features such as amino acid content, solvent accessibility, secondary structures, non‐polar interaction, residue packing and extent of structural deviations in 179 aligned members of superfamilies involving 1208 pairs of protein domains. An analysis of these structural features shows that the retention of secondary structural conservation and similar hydrogen bonding pattern within the templates is 2.5 and 1.8 times higher, respectively, than full‐length alignments suggesting that they form the minimum structural requirement of a superfamily. The identification and availability of structural templates find value in different areas of protein structure prediction and modelling such as in sensitive sequence searches, accurate sequence alignment and three‐dimensional modelling on the basis of distant relationships.