Small molecule recognition: Solid angles surface representation and molecular shape complementarity

Combinatorial Chemistry and High Throughput Screening

Volumn 2, Issue 4, 1999, Pages 223-236

  Norel, R ^a,c   Wolfson, H J ^a   Nussinov, R ^a,b  

^a TEL AVIV UNIVERSITY   (Israel)

^b NATIONAL CANCER INSTITUTE   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DRUG RECEPTOR BINDING; MATHEMATICAL ANALYSIS; MOLECULAR RECOGNITION; MOLECULAR SIZE; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION; RECEPTOR AFFINITY;

RUMEX;

EID: 0032885291     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (31)

1. 1subunit interface. Biopolymers, 1986, 25, 1229-1247.
2. Connolly, M. Analytical molecular surface calculation. J. Appl. Cryst., 1983, 16, 548-558.
3. Connolly, M. Solvent-accessible surfaces of proteins and nucleic acids. Science, 1983, 221, 709-713.
4. Norel, R.; Lin, S.L.; Wolfson, H.; Nussinov, R. Shape complementarity at protein-protein interfaces. Biopolymers, 1994, 34, 933-940.
5. Norel, R.; Lin, S.L.; Wolfson, H.; Nussinov, R. Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse points in docking. J. Mol. Biol., 1995, 252, 263-273.
6. Norel, R.; Petrey, D.; Wolfson, H.; Nussinov, R. Examination of Shape Complementarity in Docking of Unbound Proteins. PROTEINS: Structure, Function and Genetics, 1999, 36, 307-317.
7. Norel R.; Lin S.L.; Xu D.; Wolfson H.; Nussinov R. Molecular Surface Variability and Induced Conformational Changes upon Protein-Protein Association. Structure, Motion, Interaction and Expression of Biological Macromolecules, Ed. Sarma, R.H. & Sarma, M.H., Eds. Adenine Press, Albany, N.Y., 1998, 33-51.
8. Kuntz, I.; Blaney, J.; Oatley, S.; Langridge, R.; Ferrin, T. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol., 1982, 161, 269-288.
9. Jones, G.; Willet, P.; Glen, R.; Leach, A.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 1997, 267, 727-748.
10. Hendrix, D.K.; Klein, T.E.; Kuntz, I.D. Macromolecular docking of a three-body system: The recognition of human growth hormone by its receptor. Prof. Sci., 1999, 8, 1010-1022.
11. Rarey, M.; Wefing, S.; Lengauer, T. Placement of medium-sized molecular fragments into active sites of proteins. J. Comp.-Aided Mol. Design, 1996, 10, 41-54.
12. Xu, D.; Lin, S.; Nussinov, R. Protein binding versus protein folding: The role of hydrophilic bridges in protein associations. J. Mol. Biol., 1997, 265, 68-84.
13. Besl, P.J.; McKay, N.D. A method for registration of 3-D shapes. IEEE Trans. on Pattern Analysis and Machine Intelligence, 1992, 14(2), 239-256.
14. Bernstein, F.; Koetzle, T.; Williams, G.; Meyer, E.; Brice, M.; Rodgers, J., Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol., 1977, 112, 535-542.
15. Goodsell, D.; Olson, A. Automated docking of substrates to proteins by simulated annealing. PROTEINS: Structure, Function and Genetics, 1995, 8, 195-202.
16. Cherfils, J.; Duquerroy, S.; Janin, J. Protein-protein recognition analyzed by docking simulations. PROTEINS: Structure, Function and Genetics, 1991, 11, 271-280.
17. Jiang, F.; Kim, S. Soft docking : Matching of molecular surface cubes. J. Mol. Biol., 1995, 219, 79-102.
18. Shoichet, B.; Kuntz, I. Protein docking and complementarity. J. Mol. Biol., 1991, 221, 327-346.
19. Wang, H. Grid-search molecular accessible algorithm for solving the protein docking problem. J. Comp. Chem., 1991, 12, 746-750.
20. Katchalski-Katzir, E.; Shariv, I.; Eisenstein, M.; Friesem, A.; Aflalo, C.; Vakser, I. Molecular surface recognition: determination of geometric fit between protein and their ligands by correlation techniques}. Proc. Natl. Acad. Sci. USA, 1992, 89, 2195-2199.
21. Bacon, D.; Moult, J. Docking by least-square fitting of molecular surface patterns. J. Mol. Biol., 1992, 225, 849-858.
22. Kasinos, N.; Lilley, G.; Subbarao, N.; Haneef, I. A Robust and efficient automated docking algorithm for molecular recognition. Protein Engineering, 1992, 5(1), 69-75.
23. Cherfils, J.; Janin, J. Protein docking algorithms: simulating molecular recognition. Curr. Opin. Struct. Biol., 1993, 3, 265-269.
24. Helmer-Citterich, M.; Tramonato, A. Puzzle: a new method for automated protein docking based on surface shape complementarity. J. Mol. Biol., 1994, 35, 1021-1031.
25. Fischer, D.; Lin, S.-L.; Wolfson, H.; Nussinov, R. A geometry-based suite of molecular docking processes. J. Mol. Biol., 1995, 248, 459-477.
26. Lengauer, T.; Rarey, M. Computational methods for biomolecular docking. Curr. Opin. Struct. Biol., 1996, 6, 402-406.
27. Walqvist, A.; Covell, D. Docking enzyme-inhibitor complexes using a preference-based free-energy surface. PROTEINS: Structure, Function and Genetics, 1996, 25, 403-419.
28. Peters, K.P.; Fauck, J.; Frommel, C. The automatic search for ligand binding sites in proteins in proteins of known three-dimensional structure using only geometric criteria. J. Mol. Biol., 1996, 256, 201-213.
29. Laskowski, R.A.; Luscombe, N.M.; Swindells, M.B.; Thornton, J.M. Protein clefts in molecular recognition and function. Prot. Sci., 1996, 5, 2438-2452.
30. Gabb, H.A.; Jackson, R.M.; and Sternberg; M. J.E. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol., 1997, 272, 106-120.
31. Jackson, R.; Gabb, H.; Sternberg, M. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol., 1998, 276, 265-285.