Incorporating intermolecular distance into protein-protein docking

Protein Engineering, Design and Selection

Volumn 17, Issue 12, 2004, Pages 837-845

  Lei, Hongxing ^a   Duan, Yong ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Antibody antigen; Enzyme inhibitor; Intermolecular distance; Protein protein docking

Indexed keywords

ANTIBODIES; ANTIGENS; ENZYME INHIBITION; FILTRATION; SAMPLING;

ANTIBODY-ANTIGEN TARGETS; BINDING MODES; INTERMOLECULAR DISTANCE; PROTEIN-PROTEIN DOCKING;

PROTEINS;

ANTIBODY; ANTIGEN; DOCKING PROTEIN; ENZYME; ENZYME INHIBITOR;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; COMPLEX FORMATION; ENERGY; FILTRATION; GEOMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; SAMPLING; SCORING SYSTEM; STRUCTURE ANALYSIS; TECHNIQUE;

ALGORITHMS; ANIMALS; ANTIGEN-ANTIBODY REACTIONS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENZYME INHIBITORS; ENZYMES; HUMANS; LIGANDS; MODELS, MOLECULAR; MODELS, THEORETICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE; TIME FACTORS;

EID: 15344338993     PISSN: 17410126     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/gzh100     Document Type: Article

References (42)

1. Bahar, I., Atilgan, A.R. and Erman, B. (1997) Fold. Des., 2, 173-181.
2. Ben-Zeev, E., Berchanski, A., Heifetz, A., Shapira, B. and Eisenstein, M. (2003) Proteins, 52, 41-46.
3. Betts, M.J. and Sternberg, M.J. (1999) Protein Eng., 12, 271-283.
4. Bogan, A.A. and Thorn, K.S. (1998) J. Mol. Biol., 280, 1-9.
5. Bradford, J.R. and Westhead, D.R. (2003) Protein Sci., 12, 2099-2103.
6. Camacho, C.J. and Gatchell, D.W. (2003) Proteins, 52, 92-97.
7. Caraacho, C.J. and Vajda, S. (2001) Proc. Natl Acad. Sci. USA, 98, 10636-10641.
8. Camacho, C.J. and Vajda, S. (2002) Curr. Opin. Struct. Biol., 12, 36-40.
9. Chakrabarti, P. and Janin, J. (2002) Proteins, 47, 334-343.
10. Chen, R. and Weng, Z. (2002) Proteins, 47, 281-294.
11. Chen, R., Li, L. and Weng, Z. (2003a) Proteins, 52, 80-87.
12. Chen, R., Mintseris, J., Janin, J. and Weng, Z. (2003b) Proteins, 52, 88-91.
13. Chothia, C. and Lesk, A.M. (1987) J. Mol. Biol., 196, 901-917.
14. Duan, Y. et al. (2003) J. Comput. Chem., 24, 1999-2012.
15. Fernandez-Recio, J., Totrov, M. and Abagyan, R. (2002) Protein Sci., 11, 280-291.
16. Fernandez-Recio, J., Totrov, M. and Abagyan, R. (2003) Proteins, 52, 113-117.
17. Fernandez-Recio, J., Totrov, M. and Abagyan, R. (2004) J. Mol. Biol., 335, 843-865.
18. Gabb, H.A., Jackson, R.M., Sternberg and M.J. (1997) J. Mol. Biol., 272, 106-120.
19. Glaser, F., Steinberg, D.M., Vakser, I.A. and Ben-Tal, N. (2001) Proteins, 43, 89-102.
20. Gray, J.J., Moughon, S., Wang, C., Schueler-Furman, O., Kuhlman, B., Rohl, C.A. and Baker, D. (2003) J. Mol. Biol., 331, 281-299.
21. Halperin, I., Ma, B., Wolfson, H. and Nussinov, R. (2002) Proteins, 47, 409-443.
22. Heifetz, A. and Eisenstein, M. (2003) Protein Eng., 16, 179-185.
23. Jackson, R.M. (1999) Protein Sci., 8, 603-613.
24. Jacobs, D.J., Rader, A.J., Kuhn, L.A. and Thorpe, M.F. (2001) Proteins, 44, 150-165.
25. Jones, S. and Thornton, J.M. (1996) Proc. Natl Acad. Sci. USA, 93, 13-20.
26. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C. and Vakser, J.A. (1992) Proc. Natl Acad. Sci. USA, 89, 2195-2199.
27. Law, D.S., Ten Eyck, L.F., Katzenelson, O., Tsigelny, I., Roberts, V.A., Pique, M.E. and Mitchell, J.C. (2003) Proteins, 52, 33-40.
28. Li, C.H., Ma, X.H., Chen, W.Z. and Wang, C.X. (2003a) Protein Eng., 16, 265-269.
29. L,i C.H., Ma, X.H., Chen, W.Z. and Wang, C.X. (2003b) Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 35, 35-40.
30. Ma, B., Wolfson, H.J. and Nussinov, R. (2001) Curr. Opin. Struct. Biol., 11, 364-369.
31. Ma, B., Elkayam, T., Wolfson, H. and Nussinov, R. (2003) Proc. Natl Acad. Sci. USA, 100, 5772-5777.
32. Mandell, J.G., Roberts, V.A., Pique, M.E., Kotlovyi, V., Mitchell, J.C., Nelson, E., Tsigelny, I. and Ten Eyck, L.F. (2001) Protein Eng., 14, 105-113.
33. Mendez, R., Leplae, R., De Maria, L. and Wodak, S.J. (2003) Proteins, 52, 51-67.
34. Moont, G., Gabb, H.A. and Sternberg, M.J. (1999) Proteins, 35, 364-373.
35. Nooren, I.M. and Thornton, J.M. (2003a) EMBO J., 22, 3486-3492.
36. Nooren, I.M. and Thornton, J.M. (2003b) J. Mol. Biol., 325, 991-1018.
37. Ofran, Y. and Rost, B. (2003) J. Mol. Biol., 325, 377-387.
38. Schneidman-Duhovny, D. et al. (2003) Proteins, 52, 107-112.
39. Smith, G.R. and Sternberg, M.J. (2002) Curr. Opin. Struct. Biol., 12, 28-35.
40. Smith, G.R. and Sternberg, M.J. (2003) Proteins, 52, 74-79.
41. Zacharias, M. (2003) Protein Sci., 12, 1271-1282.
42. Zhang, C., Vasmatzis, G., Cornette, J.L. and DeLisi, C. (1997) J. Mol. Biol., 267, 707-726.