title: A simple method based on multiple alignment and phylogeny to derive a correlation between the protein fold and sequence via motif search.
abstract: Predicting information regarding the structure of the protein from its sequence still remains an uphill task. Though both are intimately linked, it has been found difficult so far to get a direct correlation between the two. In our present approach we use a simple method based on multiple alignment and phylogeny to derive a correlation between the protein structure and sequence via motif search. The protein families which we have considered are SH2 like, Homeodomain, Leucine rich repeat, Alphabeta knot trefoilknot and ferritin like helix bundle. We have been able to successfully predict the protein families with an average prediction of accuracy of 81%, the highest being 89% and the lowest being 73% on our test data set.
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, 781039, India.
authors.forename: Syed Baquer
authors.initials: SB
authors.lastname: Rizvi
authors.forename: Anil Kumar
authors.initials: AK
authors.lastname: Shukla
authors.forename: Vikash Kumar
authors.initials: VK
authors.lastname: Dubey
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D008969:Molecular Sequence Data; D010802:Phylogeny; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins