title: Alternative approach to protein structure prediction based on sequential similarity of physical properties.
abstract: The relationship between protein sequence and structure arises entirely from amino acid physical properties. An alternative method is therefore proposed to identify homologs in which residue equivalence is based exclusively on the pairwise physical property similarities of sequences. This approach, the property factor method (PFM), is entirely different from those in current use. A comparison is made between our method and PSI BLAST. We demonstrate that traditionally defined sequence similarity can be very low for pairs of sequences (which therefore cannot be identified using PSI BLAST), but similarity of physical property distributions results in almost identical 3D structures. The performance of PFM is shown to be better than that of PSI BLAST when sequence matching is comparable, based on a comparison using targets from CASP10 (89 targets) and CASP11 (51 targets). It is also shown that PFM outperforms PSI BLAST in informatically challenging targets.
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and.
authors.forename: Yi
authors.initials: Y
authors.lastname: He
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and Department of Pharmacology and Systems Therapeutics, The Icahn School of Medicine at Mount Sinai, New York, NY 10029.
authors.forename: S
authors.initials: S
authors.lastname: Rackovsky
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Yin
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and has5@cornell.edu.
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D055585:Physical Phenomena; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins
keywords: amino acid physical properties; homology modeling; protein structure prediction
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