LigProf: A simple tool for in silico prediction of ligand-binding sites

Journal of Molecular Modeling

Volumn 13, Issue 3, 2007, Pages 445-455

  Koczyk, Grzegorz ^a,b   Wyrwicz, Lucjan S ^b,c   Rychlewski, Leszek ^b  

^a INSTITUTE OF PLANT GENETICS   (Poland)

^b BIOINFOBANK INSTITUTE   (Poland)

^c INSTITUTE OF ONCOLOGY   (Poland)

Author keywords

Ligand binding sites; Profiles; Structural genomics

Indexed keywords

PROTEIN KINASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; COMPUTER MODEL; COMPUTER PROGRAM; CRYSTALLOGRAPHY; HIGH THROUGHPUT SCREENING; LIGAND BINDING; MATHEMATICAL COMPUTING; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; STRUCTURAL BIOINFORMATICS; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HUMANS; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; VIRAL PROTEINS;

EID: 33947599914     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-006-0165-4     Document Type: Article

References (52)

1. Hegyi H, Gerstein M (2001) Genome Res 11:1632-1640
2. Minshull J, Ness JE, Gustafsson C, Govindarajan S (2005) Curr Opin Chem Biol 9:202-209
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Nucl Acids Res 25:3389-3402
4. Devos D, Valencia A (2001) Trends Genet 17:429-431
5. Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y (2003) Cell Mol Life Sci 60:2637-2650
6. Green ML, Karp PD (2005) Nucl Acids Res 33:4035-4039
7. George RA, Spriggs RV, Thornton JM, Al-Lazikani B, Swindells MB (2004) Bioinformatics 20(Suppl 1):i130-i136
8. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Nucl Acids Res 34:D247-D251
9. Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P (2006) Nucl Acids Res 32:D142-D144
10. Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki C, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2005) Nucl Acids Res 33:D192-196
11. George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, Porter CT, Al-Lazikani B, Thornton JM, Swindells MB (2005) Proc Natl Acad Sci USA 102:12299-12304
12. Gold ND, Jackson RM (2006) J Mol Biol 355:1112-1124
13. Shatsky M, Shulman-Peleg A, Nussinov R, Wolfson HJ (2006) J Comput Biol 13:407-428
14. Stoll V, Stewart KD, Maring CJ, Muchmore S, Giranda V, Gu YG, Wang G, Chen Y, Sun M, Zhao C, Kennedy AL, Madigan DL, Xu Y, Saldivar A, Kati W, Laver G, Sowin T, Sham HL, Greer J, Kempf D (2003) Biochemistry 42:718-727
15. Terasaka T, Kinoshita T, Kuno M, Seki N, Tanaka K, Nakanishi I (2004) J Med Chem 47:3730-3743
16. Schafferhans A, Klebe G (2001) J Mol Biol 307:407-427
17. Carpy AJ, Marchand-Geneste N (2006) SAR QSAR Environ Res 17:1-10
18. Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CW (2006) BMC Bioinformatics 7:152
19. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucl Acids Res 28:235-242
20. Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M (1999) Bioinformatics 15:327-332
21. Eddy SR (1998) Bioinformatics 14:755-763
22. Pils B, Copley RR, Schultz J (2005) BMC Bioinformatics 6:210
23. Sneath PHA, Sokal RR (1973) WH Freeman, San Francisco
24. Gribskov M, McLachlan AD, Eisenberg D (1987) Proc Natl Acad Sci USA 84:4355-4358
25. Tudos E, Cserzo M, Simon I (1990) Int J Pept Protein Res 36:236-239
26. Magliery TJ, Regan L (2005) BMC Bioinformatics 30:240
27. Lichtarge O, Bourne HR, Cohen FE (1996) J Mol Biol 257:342-358
28. Mihalek I, Res I, Lichtarge O (2004) J Mol Biol 336:1265-1282
29. Johnson JM, Church GM (2000) Proc Natl Acad Sci USA 97:3965-3970
30. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M (2003) Nucl Acids Res 31:365-370
31. Henikoff S, Henikoff JG (1992) Proc Natl Acad Sci USA 89:10915-10919
32. Wu TD, Nevill-Manning CG, Brutlag DL (2000) Bioinformatics 16:233-244
33. Sali A, Blundell TL (1993) J Mol Biol 234:779-815
34. Elofsson A (2002) Proteins 46:330-339
35. Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB (2004) Protein Sci 13:443-456
36. Hamelryck T, Manderick B (2003) Bioinformatics 19:2308-2310
37. Yang XL, Otero FJ, Skene RJ, McRee DE, Schimmel P, Pouplana L Ribas de (2003) Proc Natl Acad Sci USA 100:15376-15380
38. Li W, Jaroszewski L, Godzik A (2002) Bioinformatics 18:77-82
39. Qiu X, Janson CA, Smith WW, Green SM, McDevitt P, Johanson K, Carter P, Hibbs M, Lewis C, Chalker A, Fosberry A, Lalonde J, Berge J, Brown P, Houge-Frydrych CS, Jarvest RL (2001) Protein Sci 10:2008-2016
40. Hagglund R, Munger J, Poon AP, Roizman B (2002) J Virol 76:743-754
41. Kato A, Yamamoto M, Ohno T, Tanaka M, Sata T, Nishiyama Y, Kawaguchi Y (2006) J Virol 80:1476-1486
42. Prichard MN, Britt WJ, Daily SL, Hartline CB, Kern ER (2005) J Virol 79:15494-15502
43. Mestres J (2005) Drug Discov Today 10:1629-1637
44. Diwan P, Lacasse JJ, Schang LM (2004) J Virol 78:9352-9365
45. Schang LM, Coccaro E, Lacasse JJ (2005) Nucleosides Nucleotides Nucleic Acids 24:829-837
46. Guo T, Shi Y, Sun Z (2005) Prot Eng Des Sel 18:65-70
47. Shulman-Peleg A, Nussinov R, Wolfson HJ (2004) J Mol Biol 339:607-633
48. Schmitt S, Kuhn D, Klebe G (2002) J Mol Biol 323:387-406
49. Ondrechen MJ, Clifton JG, Ringe D (2001) Proc Natl Acad Sci USA 98:12473-12478
50. Kuhn D, Weskamp N, Schmitt S, Hullermeier E, Klebe G (2006) J Mol Biol 359:1023-1044
51. Ko J, Murga LF, Wei Y, Ondrechen MJ (2005) Bioinformatics 21:i258-i265
52. Kinoshita K, Nakamura H (2005) Protein Sci 14:711-718