title: Effective detection of remote homologues by searching in sequence dataset of a protein domain fold.
abstract: Profile matching methods are commonly used in searches in protein sequence databases to detect evolutionary relationships. We describe here a sensitive protocol, which detects remote similarities by searching in a specialized database of sequences belonging to a fold. We have assessed this protocol by exploring the relationships we detect among sequences known to belong to specific folds. We find that searches within sequences adopting a fold are more effective in detecting remote similarities and evolutionary connections than searches in a database of all sequences. We also discuss the implications of using this strategy to link sequence and structure space.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, 560 012 Bangalore, India.
authors.forename: S
authors.initials: S
authors.lastname: Sandhya
authors.forename: S
authors.initials: S
authors.lastname: Kishore
authors.forename: R
authors.initials: R
authors.lastname: Sowdhamini
authors.forename: N
authors.initials: N
authors.lastname: Srinivasan
mesh_terms: D030562:Databases, Protein; D019143:Evolution, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data; D012680:Sensitivity and Specificity
chemical_list: D011506:Proteins