PSICO: Solving protein structures with constraint programming and optimization

Constraints

Volumn 7, Issue 3-4, 2002, Pages 317-331

  Krippahl, Ludwig ^a   Barahona, Pedro ^a  

^a UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

Bioinformatics; Constraint programming; Optimisation; Protein structure

Indexed keywords

ALGORITHMS; DATA ACQUISITION; NUCLEAR MAGNETIC RESONANCE; PROTEINS; SIMULATED ANNEALING; X RAY ANALYSIS;

BIOINFORMATICS;

LINEAR PROGRAMMING;

EID: 0036662961     PISSN: 13837133     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1020577603762     Document Type: Conference Paper

References (23)

1. Abe, H., Braun, W., Noguti, T., & Go, N. (1984). Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins. general recurrent equations. Computers Chemistry, 5(4): 239.
2. Archer, M., Huber, R., Tavares, P., Moura, I., Moura, J.J., Carrondo, M.A., Sieker, L.C., LeGall, J., & Romão, M.J. (1995). Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8, A resolution: a novel non-berne iron protein structure. Journal of Molecular Biology, 251 (5): 690.
3. Backofen, R. (1998). Constraint Techniques for Solving the Protein Structure Prediction Problem, CP98, Lecture Notes in Computer Science, Vol. 1520, page 72. Springer-Verlag.
4. Backofen, R. (2001). The protein structure prediction problem: a constraint optimisation approach using a new lower bound. Constraints, 6: 223.
5. Beldiceanu, N., & Contejean, E. (1994). Introducing Global Constraints in CHIP. Mathl. Comp. Modelling, 20(12): 97.
6. Buckle, A.M., Schreiber, G., & Fersht, A.R. (1994). Protein-protein recognition: crystal structural analysis of a Barnase-Barstar complex at 2.0-A resolution. Biochemistry, 33: 8878.
7. Bushnell, G.W., Louie, G.V., & Brayer, G.D. (1990). High-resolution three-dimensional structure of horse heart cytochrome c., Journal of Molecular Biology, 214: 585.
8. Cheng, B., Choi, K., Lee, J., & Wu, J. (1999). Increasing constraint propagation by redundant modeling: an experience report. Constraints, 4: 167.
9. Gaspin, C. (2001). RNA secondary structure determination and representation based on constraints satisfaction. Constraints, 6: 201.
10. Gilbert, D., Backofen, R., & Yap, R. (2001). Special issue on bioinformatics. Constraints, 6: 139.
11. Goodfellow, B., Rusnak, F., Moura, I., Domke, T., & Moura, J.J.G. (1998). NMR determination of the global structure of the 113Cd derivative of Desulforedoxin: Investigation of the hydrogen bonding pattern at the metal center. Protein Science, 7: 928.
12. Güntert, P., Mumenthaler, C., & Wüthrich, K. (1997). Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273: 283.
13. Hecht, H.J., Szardenings, M., Collins, J., & Shomburg, D. (1991). Three-dimensional structure of the complexes between bovine chymotrypsinogen *A and two recombinant variants of human pancreatic secretory trypsin inhibitor (*Kazal-Type). J. Mol. Biol., 220: 711.
14. Jia, Z., Quail, J.W., Waygood, E.B., & Delbaere, L.T.J. (1993). The 2.0 angstroms resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPR: a redetermination, J. Biol. Chem., 268: 22490.
15. Krippahl, L., & Barahona, P. (1999). Applying Constraint Programming to Protein Structure Determination, CP99, Lecture Notes in Computer Science, Vol. 1713, page 289. Springer-Verlag.
16. Krippahl, L., Trosset, M., & Barahona, P. (2001). Combining constraint programming and multidimensional scaling to solve distance geometry problems. In Proceedings of CP-AI-OR'2001, Imperial College, Kent UK, 67-80.
17. Leishman, S., Gray, P.M.D., & Fothergill, I.E. (1994). ASSASSIN: a constraint based assignment system for protein 2D nuclear magnetic resonance. In Milne, R., & Montgomery A., eds. Applications and Innovations in Expert Systems II, (Proceedings of Expert Systems 94, Cambridge), page 263.
18. Marquart, W., Deisenhofer, Bode J., & Huber, R. (1983). The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors, Acta Crystallography, Section B, 39: 480.
19. McCoy, M., Stavridi, E.S., Waterman, J.L., Wieczorek, A.M., Opella, S.J., & Halazonetis, T.D. (1997). Hydrophobic side-chain size is a determinant of the throe-dimensional structure of the P53 oligomerization domain. EMBO Journal, 16: 6230.
20. Revesz, P. (1997). Refining restriction enzyme genome maps. Constraints, 2: 361.
21. Rodošek, R. (2001). A constraint-based approach for deriving 3-D structures of cyclic polypeptides. Constraints, 6(2&3): 257.
22. Sam-Haroud, D., & Faltings, B. (1996). Consistency techniques for continuous constraints. Constraints, 1.
23. Zimmerman, D.E., Kulikowski, C.A., & Montelione, G.T. (1993). A constraint reasoning system for automating sequence-specific resonance assignments from multidimensional protein NMR spectra. Ismb 1: 447.