Efficient computational algorithms for docking and for generating and matching a library of functional epitopes I. Rigid and flexible hinge-bending docking algorithms

Combinatorial Chemistry and High Throughput Screening

Volumn 2, Issue 5, 1999, Pages 249-259

  Nussinov, Ruth ^a,b,c   Wolfson, Haim J ^b  

^a SAIC FREDERICK INC   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DOCKING PROTEIN; EPITOPE;

ALGORITHM; BINDING KINETICS; COMPUTER ANALYSIS; COMPUTER INTERFACE; LIBRARY; PRIORITY JOURNAL; REVIEW; ROBOTICS;

ALGORITHMS; BINDING SITES; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPUTER SIMULATION; EPITOPES; LIGANDS; MOLECULAR CONFORMATION; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; ROBOTICS;

EID: 0032706309     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (48)

1. Nussinov, R.; Wolfson, H.; Combin. Chem. High Throughput Screen., 1999, 2, 289-297.
2. Apostolakis, J.; Caflisch, A.; Combin. Chem. High Throughput Screen., 1999, 2, 91-104.
3. Goodsell, D.; Olson, A.; Prof. Struct. Funct. Genet., 1990, 8, 195-202.
4. Bacon, D.; Moult, J.; J. Mol. Biol., 1992, 225, 849-858.
5. Kuntz, I.; Blaney, J.; Oatley, S.; Langridge, R.; Ferrin, T.; J. Mol. Biol., 1982, 161, 269-288.
6. Connolly, M.; Biopolymers. 1986, 25, 1229-1247.
7. Cherfils, J.; Duquerroy, S.; Janin, J.; Prof. Struct. Funct. Genet., 1991, 11, 271-280.
8. Katchalski-Katzir, E.; Shariv, I.; Eisenstein, M.; Friesem, A.; Aflalo, C.; Vakser, I.; Proc. Natl. Acad. Sci. USA, 1992, 89, 2195-2199.
9. Jiang, F.; Kim, S.; J. Mol. Biol., 1991, 219, 79-102.
10. Shoichet, B.; Kuntz, I.; J. Mol. Biol., 1991, 221, 327-346.
11. Wang, H.; J. Comp. Chem., 1991, 12, 746-750.
12. Cherfils, J.; Janin, J.; Curr. Opin. Struct. Biol., 1993 , 3, 265-269.
13. Norel, R.; Fischer, D.; Wolfson, H.; Nussinov, R.; Protein Eng., 1994, 7, 39-46.
14. Norel, R.; Lin, S.L.; Wolfson, H.; Nussinov, R.; Biopolymers, 1994, 34, 933-940.
15. Helmer-Citterich, M.; Tramonato, A.; J. Mol. Biol., 1994, 235, 1021-1031.
16. Fischer, D.; Lin, S.L.; Wolfson, H.; Nussinov, R.; J. Mol. Biol., 1995, 243, 459-477.
17. Norel, R.; Lin, S.L.; Wolfson, H.; Nussinov, R.; J. Mol. Biol., 1995, 252, 263-273.
18. Lengauer, T.; Rarey, M.; Curr. Opin. Struct. Biol., 1996, 6, 402-406.
19. Wallqvist, A.; Covell, D.; Prot. Struct. Funct. Genet. 1996, 25, 403-419.
20. Rarey, M.; Wefing, S.; Lengauer, T.; J. Comp.-Aided Mol. Design, 1996, 10, 41-54.
21. Jones, G.; Willet, P.; Glen, R.; Leach, A.; Taylor, R.; J. Mol. Biol., 1997, 267, 727-748.
22. Kasinos, N.; Lilley, G.; Subbarao, N.; Haneef, I.; Protein Eng., 1992, 5, 69-75.
23. Gabb, H.A.; Jackson, R.M.; Sternberg, M. J.E.; J. Mol. Biol., 1997, 272, 106-120.
24. Peters, K.P.; Fauck, J.; Frommel, C.; J. Mol. Biol., 1996, 256, 201-213.
25. Laskowski, R.A.; Luscombe, N.M.; Swindells, M.B.; Thornton, J.M.; Prot. Sci., 1996, 5, 2438-2452.
26. Norel, R.; Lin, S.-L.; Xu, D.; Wolfson, H.; Nussinov, R.; Structure, Motion, Interaction and Expression of Biological Macromolecules, Ed. Sarma, R.H. and Sarma, M.H., Eds. Adenine Press, Albany, N.Y., 1998, 33-51.
27. Norel, R.; Petrey, D.; Wolfson, H.; Nussinov, R Prot. Struct. Funct. Genet 1999, 36, 307-317.
28. Norel, R.; Wolfson, H.; Nussinov, R.; Combin. Chem. High Throughput Screen., 1999, 2, 223-237.
29. Sandak, B.; Wolfson, H. J.; Nussinov, R.; J. Biomol. Struct. Dynamics, Proceedings of the Ninth Conversation, Eds., R.H. Sarma and M.H. Sarma, Adenine Press (New York), 1996, 1, 233-252.
30. Sandak, B.; Nussinov, R.; Wolfson, H. J.; Comp. Appl. BioSci., 1995, 11, 87-99.
31. Sandak, B.; Nussinov, R.; Wolfson, H. J.; Seventh Symposium on Combinatorial Pattern Matching, Laguna Beach, California, USA. Lecture Notes in Computer Science, Springer Verlag. 1996, 1075, 271-287.
32. Sandak, B.; Wolfson, H. J.; Nussinov, R.; Prot. Struct. Funct. Genet., 1998, 32, 159-174.
33. Sandak, B.; Nussinov, R.; Wolfson, H. J.; J. Comput. Biol, 1999, 5, 631-654.
34. Connolly, M.; J. Appl. Cryst., 1983, 16, 548-558.
35. Connolly, M.; Science, 1983, 221, 709-713.
36. Lin, S.L.; Nussinov, R.; Fischer, D.; Wolfson, H.J.; Prot. Struct. Funct. Genet. 1994, 18, 94-101.
37. Lin, S.L; Nussinov, R.; J. Mol. Graphics. 1996, 14, 78-90.
38. Schwartz, J.T.; Sharir, M.; Int. J. Robotics Res. 1987, 6, 29-44.
39. Gerstein, M.; Lesk, A. M.; Chothia, C.; Biochemistry, 1994, 6739-6749.
40. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M.; J. Mol. Biol., 1977, 112, 535-542.
41. Wolfson, H. J.; Pattern Recog. Lett., 1991, 12, 565-573.
42. Mangoni, M.; Roccatano, D.; Di Nola, A. D.; Prot. Struct. Funct. Genet 1999, 35, 153-162.
43. Wang, J.; Kollman, P. A.; Kuntz, I. D.; Prot. Struct. Funct. Genet. 1999, 36, 1-19.
44. Leach, A.R.; Kuntz, I.D.; J. Comp. Chem., 1992, 13, 730-748.
45. Leach, A.R.; J. Mol. Biol., 1994, 235, 345-356.
46. Verbitsky, G.; Nussinov, R.; Wolfson, H.; Prot. Struct. Funct. Genet. 1999, 34, 232-254.
47. Lamdan, Y.; Wolfson, H.J; Proc. 2nd Int. Conf. on Computer Vision , 1988, IEEE Comp. Soc. Press, 238-249.
48. Lamdan, Y.; Schwartz, J.T.; Wolfson, H.J; Trans. Robotics Autom., 1999, 6, 578-589.