title: A generalized threading model using integer programming that allows for secondary structure element deletion.
abstract: Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30622, USA. kellrott@csbl.bmb.uga.edu
authors.forename: Kyle
authors.initials: K
authors.lastname: Ellrott
authors.forename: Jun-tao
authors.initials: JT
authors.lastname: Guo
authors.forename: Victor
authors.initials: V
authors.lastname: Olman
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011382:Programming, Linear; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein; D012984:Software; D013698:Templates, Genetic
chemical_list: D011506:Proteins