Efficient unbound docking of rigid molecules

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2452, Issue , 2002, Pages 185-200

  Duhovny, Dina ^a   Nussinov, Ruth ^a,b   Wolfson, Haim J ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL EFFICIENCY; CURVE FITTING; MATHEMATICAL TRANSFORMATIONS; MOLECULES; PROTEINS; SURFACE FITTING;

ACCURATE COMPUTATIONS; BIOLOGICAL INFORMATION; DISTANCE TRANSFORMS; GEOMETRIC HASHING; MOLECULAR SURFACES; SHAPE COMPLEMENTARITY; SHAPE REPRESENTATION; SURFACE VARIABILITY;

CLUSTERING ALGORITHMS;

EID: 84956979675     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45784-4_14     Document Type: Conference Paper

References (34)

1. C. Branden and J. Tooze. Introduction to Protein Structure. Garland Publishing, Inc., New York and London, 1991.
2. J.C. Camacho, D.W. Gatchell, S.R. Kimura, and S. Vajda. Scoring docked conformations generated by rigid body protein-protein docking. PROTEINS: Structure, Function and Genetics, 40:525-537, 2000.
3. R. Chen and Z Weng. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. PROTEINS: Structure, Function and Genetics, 47:281-294, 2002.
4. M.L. Connolly. Analytical molecular surface calculation. J. Appl. Cryst., 16:548-558, 1983.
5. M.L. Connolly. Solvent-accessible surfaces of proteins and nucleic acids. Science, 221:709-713, 1983.
6. M.L. Connolly. Shape complementarity at the hemoglobin α1β1 subunit interface. Biopolymers, 25:1229-1247, 1986.
7. T. H. Cormen, C. E. Leiserson, and R. L. Rivest. Introduction to Algorithms, chapter 26. The MIT Press, 1990.
8. M. de Berg, M. van Kreveld, M. Overmars, and O. Schwarzkopf. Computational Geometry: Algorithms and Applications. Springer-Verlag, 2000.
9. T.J.A. Ewing, Makino S., Skillman A.G., and I.D. Kuntz. Dock 4.0: Search strategies for automated molecular docking of flexible molecule databases. J. Computer-Aided Molecular Design, 15:411-428, 2001.
10. D. Fischer, S. L. Lin, H.J. Wolfson, and R. Nussinov. A geometry-based suite of molecular docking processes. J. Mol. Biol., 248:459-477, 1995.
11. H.A. Gabb, R.M. Jackson, and J.E. Sternberg. Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J. Mol. Biol., 272:106-120, 1997.
12. E.J. Gardiner, P. Willett, and P.J. Artymiuk. Protein docking using a genetic algorithm. PROTEINS: Structure, Function and Genetics, 44:44-56, 2001.
13. B.B. Goldman and W.T. Wipke. Molecular docking using quadratic shape descriptors (qsdock). PROTEINS: Structure, Function and Genetics, 38:79-94, 2000.
14. I. Halperin, B. Ma, H. Wolfson, and R. Nussinov. Principles of docking: An overview of search algorithms and a guide to scoring functions. PROTEINS: Structure, Function and Genetics, 47:409-443, 2002.
15. Z. Hu, B. Ma, H.J Wolfson, and R. Nussinov. Conservation of polar residues as hot spots at protein-protein interfaces. PROTEINS: Structure, Function and Genetics, 39:331-342, 2000.
16. R.M. Jackson. Comparison of protein-protein interactions in serine proteaseinhibitor and antibody-antigen complexes: Implications for the protein docking problem. Protein Science, 8:603-613, 1999.
17. F. Jiang and S.H. Kim. Soft docking : Matching of molecular surface cubes. J. Mol. Biol., 219:79-102, 1991.
18. G. Jones, P. Willet, R. Glen, and Leach A.R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267:727-748, 1997.
19. E. Katchalski-Katzir, I. Shariv, M. Eisenstein, A.A. Friesem, C. Aflalo, and I.A. Vakser. Molecular Surface Recognition: Determination of Geometric Fit between Protein and their Ligands by Correlation Techniques. Proc. Natl. Acad. Sci. USA, 89:2195-2199, 1992.
20. I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge, and T.E. Ferrin. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol., 161:269-288, 1982.
21. H.P. Lenhof. Parallel protein puzzle: A new suite of protein docking tools. In Proc. of the First Annual International Conference on Computational Molecular Biology RECOMB 97, pages 182-191, 1997.
22. S. L. Lin, R. Nussinov, D. Fischer, and H.J. Wolfson. Molecular surface representation by sparse critical points. PROTEINS: Structure, Function and Genetics, 18:94-101, 1994.
23. R. Norel, S. L. Lin, H.J. Wolfson, and R. Nussinov. Shape complementarity at protein-protein interfaces. Biopolymers, 34:933-940, 1994.
24. R. Norel, S. L. Lin, H.J. Wolfson, and R. Nussinov. Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse points in docking. J. Mol. Biol., 252:263-273, 1995.
25. R. Norel, D. Petrey, H.J. Wolfson, and R. Nussinov. Examination of shape complementarity in docking of unbound proteins. PROTEINS: Structure, Function and Genetics, 35:403-419, 1999.
26. P.N. Palma, L. Krippahl, J.E. Wampler, and J.G Moura. Bigger: A new (soft)docking algorithm for predicting protein interactions. PROTEINS: Structure, Function and Genetics, 39:372-384, 2000.
27. M. Rarey, B. Kramer, and Lengauer T. Time-efficient docking of flexible ligands into active sites of proteins. In 3’rd Int. Conf. on Intelligent Systems for Molecular Biology (ISMB’95), pages 300-308, Cambridge, UK, 1995. AAAI Press.
28. B. Sandak, H.J. Wolfson, and R. Nussinov. Flexible docking allowing induced fit in proteins. PROTEINS: Structure, Function and Genetics, 32:159-174, 1998.
29. G. Stockman. Object recognition and localization via pose clustering. J. of Computer Vision, Graphics, and Image Processing, 40(3):361-387, 1987.
30. I.A. Vakser. Protein docking for low resolution structures. Protein Engineering, 8:371-377, 1995.
31. I.A. Vakser. Main chain complementarity in protein recognition. Protein Engineering, 9:741-744, 1996.
32. I.A. Vakser, O.G. Matar, and C.F. Lam. A systematic study of low resolution recognition in protein-protein complexes. Proc. Natl. Acad. Sci. USA, 96:8477-8482, 1999.
33. P.H. Walls and J.E. Sternberg. New algorithms to model protein-protein recognition based on surface complementarity; applications to antibody-antigen docking. J. Mol. Biol., 228:227-297, 1992.
34. H.J. Wolfson and I. Rigoutsos. Geometric hashing: An overview. IEEE Computational Science and Eng., 11:263-278, 1997.