RAPTOR swMATH ID: 9002 Software Authors: Xu, J.; Li, M.; Lin, G.; Kim, D.; Xu, Y. Description: RAPTOR: optimal protein threading by linear programming. This paper presents a novel linear programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based on the contact map graph of the protein 3D structure template, the protein threading problem is formulated as a large scale integer programming (IP) problem. The IP formulation is then relaxed to a linear programming (LP) problem, and then solved by the canonical branch-and-bound method. The final solution is globally optimal with respect to energy functions. In particular, our energy function includes pairwise interaction preferences and allowing variable gaps which are two key factors in making the protein threading problem NP-hard. A surprising result is that, most of the time, the relaxed linear programs generate integral solutions directly. Our algorithm has been implemented as a software package RAPTOR–RApid Protein Threading by Operation Research technique. Large scale benchmark test for fold recognition shows that RAPTOR ignificantly outperforms other programs at the fold similarity level. The CAFASP3 evaluation, a blind and public test by the protein structure prediction community, ranks RAPTOR as top 1, among individual prediction servers, in terms of the recognition capability and alignment accuracy for Fold Recognition (FR) family targets. RAPTOR also performs very well in recognizing the hard Homology Modeling (HM) targets. RAPTOR was implemented at the University of Waterloo. Homepage: http://www.ncbi.nlm.nih.gov/pubmed/15290783 Related Software: GenThreader; CPLEX; BLAST; PSI-BLAST; FUGUE; GreedyBB; Algorithm 457; SHOT; Bonmin; SNDlib; MIPLIB; Concorde; CHARMM; Pfam; Cluster-C; X-PLOR; DYANA; NPSOL; PICKY; T-coffee Cited in: 15 Publications all top 5 Cited by 33 Authors 4 Xu, Jinbo 3 Andonov, Rumen A. 3 Xu, Ying 3 Yanev, Nicola 2 Balev, Stefan 2 Li, Ming 1 Althaus, Ernst 1 Berger, Bonnie 1 Błażewicz, Jacek 1 Floudas, Christodoulos Achilleus 1 Gibrat, J. F. 1 Guo, Juntao 1 Kim, Dongsup 1 Klau, Gunnar W. 1 Kohlbacher, Oliver 1 Lancia, Giuseppe G. 1 Lenhof, Hans-Peter 1 Li, Guojun 1 Lin, Guohin 1 Liu, Zhijie 1 Łukasiak, Piotr 1 Ma, Bin 1 McAllister, Scott R. 1 Miłostan, Maciej 1 Reinert, Knut 1 Santos, Haroldo Gambini 1 Singh, Rohit R. 1 Souza Brito, Samuel 1 Steyaert, Jean-Marc 1 Veber, Philippe 1 Waldispühl, Jérôme 1 Wu, Lieyu 1 Zhang, Kaizhong all top 5 Cited in 10 Serials 1 Computers & Mathematics with Applications 1 Discrete Applied Mathematics 1 Theoretical Computer Science 1 Algorithmica 1 Computers & Operations Research 1 Annals of Operations Research 1 Computational Optimization and Applications 1 INFORMS Journal on Computing 1 Journal of Combinatorial Optimization 1 Algorithms Cited in 4 Fields 11 Biology and other natural sciences (92-XX) 10 Operations research, mathematical programming (90-XX) 3 Computer science (68-XX) 2 Combinatorics (05-XX) Citations by Year