Linear programming based approach to the derivation of a contact potential for protein threading.
This paper proposes a novel method of deriving a contact potential (a pair score function) for protein threading. In this method, the constraint that the score of the native threading is minimum over all possible threadings is expressed in a form of linear inequalities, and then parameters defining the contact potential are determined by applying a program package of linear programming. The most important advantage of this method over the previous methods is that this method can learn a score function from a small number of training data. The proposed method was evaluated using Lathrop and Smith's algorithm for finding optimal threadings and was shown to be effective for computing nearly correct threadings.
Akutsu
T
T
Human Genome Center, University of Tokyo, Japan. takutsu@ims.u-tokyo.ac.jp
Tashimo
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H
D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D008838:Microcomputers; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011381:Programming Languages; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012984:Software
D011506:Proteins