Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces

Journal of Molecular Modeling

Volumn 13, Issue 11, 2007, Pages 1157-1167

  Negi, Surendra S ^a   Braun, Werner ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Hot spots; Molecular recognition; Physical chemical properties of interface residues; Protein protein interface

Indexed keywords

ADENOSINE TRIPHOSPHATASE; CAPSID PROTEIN; ARCHAEAL PROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BINDING SITE; HEPATITIS B VIRUS; METHANOCOCCUS THERMOLITHOTROPHICUS; NONHUMAN; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DIMERIZATION; ENZYMOLOGY; METABOLISM; METHANOCOCCUS; PROTEIN DATABASE;

HEPATITIS B VIRUS; METHANOCALDOCOCCUS JANNASCHII; MIRIDAE;

ADENOSINE TRIPHOSPHATASES; ALGORITHMS; ARCHAEAL PROTEINS; AUTOMATION; DATABASES, PROTEIN; DIMERIZATION; METHANOCOCCUS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEINS;

EID: 34848854803     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-007-0237-0     Document Type: Article

References (64)

1. Kinoshita K, Nakamura H (2003) Curr Opin Struct Biol 13:396-400
2. Archakov AI, Govorun VM, Dubanov AV, Ivanov YD, Veselovsky AV, Lewi P, Janssen P (2003) Proteomics 3:380-391
3. Lo Conte L, Chothia C, Janin J (1998) J Mol Biol 285:2177-2198
4. Janin J, Chothia C (1990) J Bio Chem 265:16027-16030
5. Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1997) Protein Sci 6:53-64
6. Hu ZJ, Ma BY, Wolfson H, Nussinov R (2000) Proteins-Structure Function Genetics 39:331-342
7. Jones S, Thornton JM (1996) Proc Natl Acad Sci USA 93:13-20
8. McCoy AJ, Epa VC, Colman PM (1997) J Mol Biol 268:570-584
9. Thorn KS, Bogan AA (2001) Bioinformatics 17:284-285
10. Bader GD, Betel D, Hogue CWV (2003) Nucleic Acids Res 31:248-250
11. Xenarios I, Salwinski L, Duan XQJ, Higney P, Kim SM, Eisenberg D (2002) Nucleic Acids Res 30:303-305
12. Xenarios L, Eisenberg D (2001) Curr Opin Biotechnol 12:334-339
13. DeLano WL (2002) Curr Opin Struct Biol 12:14-20
14. DeLano WL, Ultsch MH, de Vos AM, Wells JA (2000) Science 287:1279-1283
15. Kortemme T, Baker D (2002) Proc Natl Acad Sci USA 99:14116-14121
16. Bogan AA, Thorn KS (1998) J Mol Biol 280:1-9
17. Clackson T, Wells JA (1995) Science 267:383-386
18. Jones S, Thornton JM (1997) J Mol Biol 272:133-143
19. Jones S, Thornton JM (1997) J Mol Biol 272:121-132
20. Jones S, Thornton JM (1995) Prog Biophys Mol Biol 63:31-35
21. Jones S, Marin A, Thornton JM (2000) Protein Eng 13:77-82
22. Bordner AJ, Abagyan R (2005) Proteins: Structure, Function, Bioinformatics 60:353-366
23. Murakami Y, Jones S (2006) Bioinformatics 22:1794-1795
24. Brinda KV, Kannan N, Vishveshwara S (2002) Protein Eng 15:265-277
25. Landgraf R, Xenarios I, Eisenberg D (2001) J Mol Biol 307:1487-1502
26. Morrison KL, Weiss GA (2001) Curr Opin Chem Biol 5:302-307
27. Kortemme T, Kim DE, Baker D (2004) Sci STKE 219:12
28. Massova I, Kollman PA (1999) J Am Chem Soc 121:8133-8143
29. Zhou HX, Shan Y (2001) Proteins 44:336-343
30. Fariselli P, Pazos F, Valencia A, Casadio R (2002) Eur J Biochem 269:1356-1361
31. Koike A, Takagi T (2004) Protein Engineering Design & Selection 17:165-173
32. Bradford JR, Westhead DR (2004) Bioinformatics 21:1487-1494
33. Gallet X, Charloteaux B, Thomas A, Brasseur R (2000) J Mol Biol 302:917-926
34. Bock JR, Gough DA (2001) Bioinformatics 17:455-460
35. Gao Y, Wang RX, Lai LH (2004) J Mol Model 10:44-54
36. Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L, Lichtarge O (2003) J Mol Biol 326:255-261
37. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N (2003) Bioinformatics 19:163-164
38. Chakrabarti P, Janin J (2002) Proteins 47:334-343
39. Bahadur RP, Chakrabarti P, Rodier F, Janin J (2004) J Mol Biol 336:943-955
40. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N (2001) Proteins-Structure Function Genetics 43:89-102
41. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N (2005) Nucleic Acids Res 33:W299-W302
42. Neuvirth H, Raz R, Schreiber G (2004) J Mol Biol 338:181-199
43. Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A (2005) Nucleic Acids Res 33:W331-W336
44. Mihalek I, Res I, Lichtarge O (2006) Bioinformatics 22:1656-1657
45. Venkatarajan MS, Braun W (2001) J Mol Model 7:445-453
46. Negi SS, Kolokoltsov AA, Schein CH, Davey RA, Braun W (2006) J Mol Model 12:921-929
47. Altschul S, Madden T, Schaffer A, Zhang JH, Zhang Z, Miller W, Lipman D (1998) Faseb J 12:A1326-A1326
48. Thompson JD, Higgins DG, Gibson TJ (1994) Nucleic Acids Res 22:4673-4680
49. Fraczkiewicz R, Braun W (1998) J Comp Chem 19:319
50. Liang S, Liu Z, Li W, Ni L, Lai L (2000) Biopolymers 54:515-523
51. Singh RK, Tropsha A, Vaisman II (1996) J Comp Biol 3:213-221
52. Linde Y, Buzo A, Gray RM (1980) IEEE Trans Commun 28:84-95
53. Sayood K (2000) Introduction to data compression, 2nd edn. Morgan Kaufmann Publishers Inc
54. Patane G, Russo M (2001) Neural Netw 14:1219-1237
55. Equitz HW (1989) IEEE Trans Acoustics Speech Signal Process 37:1568-1575
56. Cosman PC, Oehler KL, Riskin EA, Gray RM (1993) Proc I E E E 81:1326-1341
57. Lin CL, Tai SC (1998) IEEE Trans Circuits Syst, II Analog Digit Signal Process 45:432-435
58. Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H (2000) Bioinformatics 16:412-424
59. Ma B, Elkayam T, Wolfson H, Nussinov R (2003) Proc Natl Acad Sci USA 100:5772-5777
60. Nagano N, Ota M, Nishikawa K (1999) FEBS Lett 458:69-71
61. Karlin S, Zhu ZY, Baud F (1999) Proc Natl Acad Sci USA 96:12500-12505
62. Mathura VS, Schein CH, Braun W (2003) Bioinformatics 19:1381-1390
63. Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH (1998) Proc Natl Acad Sci USA 95:15189-15193
64. Wynne SA, Crowther RA, Leslie AGW (1999) Mol Cell 3:771-780