A generalized threading model using integer programming that allows for secondary structure element deletion.
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.
Ellrott
Kyle
K
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30622, USA. kellrott@csbl.bmb.uga.edu
Guo
Jun-tao
JT
Olman
Victor
V
Xu
Ying
Y
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
D011506:Proteins