Development of an affinity evaluation and prediction system by using the shape complementary characteristic between proteins

Journal of Bioinformatics and Computational Biology

Volumn 6, Issue 6, 2008, Pages 1133-1156

  Tsukamoto, Koki ^a   Yoshikawa, Tatsuya ^a,b   Hourai, Yuichiro ^a   Fukui, Kazuhiko ^a   Akiyama, Yutaka ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

Affinity analysis; FFT; Massive parallel computing; Prediction system; Protein protein docking; Protein protein interaction

Indexed keywords

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 58149467654     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720008003904     Document Type: Article

References (44)

1. Jones S, Thornton JM, Principles of protein-protein interactions, Proc Natl Acad Sci USA 93(1):13-20, 1996.
2. Teichmann SA, Principles of protein-protein interactions, Bioinformatics 18:S249, 2002.
3. Ayub MJ, Smulski CR, Nyambega B, Bercovich N, Masiga D, Vazquez MP, Aguilar CF, Levin MJ, Protein-protein interaction map of the Trypanosoma cruzi ribosomal P protein complex, Gene 357 2):129-136, 2005.
4. Rual JF et al., Towards a proteome-scale map of the human protein-protein interaction network, Nature 437 7062):1173-1178, 2005.
5. Collins SR et al., Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map, Nature 446(7137):806-810, 2007.
6. Parrish JR, Yu JK, Liu GZ, Hines JA, Chan JE, Mangiola BA, Zhang HM, Pacifico S, Fotouhi F, DiRita VJ, Ideker T, Andrews P, Finley RL, A proteome-wide protein interaction map for Campylobacter jejuni, Genome Biol 8(7):R130, 2007.
7. Wong J, Nakajima Y, Westermann S, Shang C, Kang JS, Goodner C, Houshmand P, Fields S, Chan CSM, Drubin D, Barnes G, Hazbun T, A protein interaction map of the mitotic spindle, Mol Biol Cell 18 10):3800-3809, 2007.
8. Giot L et al., A protein interaction map of Drosophila melanogaster, Science 302(5651):1727-1736, 2003.
9. Stanyon CA, Liu GZ, Mangiola BA, Patel N, Giot L, Kuang B, Zhang HM, Zhong JH, Finley RL, A Drosophila protein-interaction map centered on cell-cycle regulators, Genome Biol 5(12):R96, 2004.
10. Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, Chemama Y, Labigne A, Legrain P, The protein-protein interaction map of Helicobacter pylori, Nature 409(6817):211-215, 2001.
11. Wojcik J, Schachter V, Protein-protein interaction map inference using interacting domain profile pairs, Bioinformatics 17(Suppl 1):S296-S305, 2001.
12. Ofran Y, Rost B, Predicted protein-protein interaction sites from local sequence information, FEBS Lett 544(1-3):236-239, 2003.
13. Smith GR, Sternberg MJ, Prediction of protein-protein interactions by docking methods, Curr Opin Struct Biol 12(1):28-35, 2002.
14. Park DU, Lee SM, Bolser D, Schroeder M, Lappe M, Oh DH, Bhak J, Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map), Bioinformatics 21(15):3234-3240, 2005.
15. Gong S et al., PSIbase: A database of Protein Structural Interactome map (PSIMAP), Bioinformatics 21(10):2541-2543, 2005.
16. Nukada A, Hourai Y, Nishida A, High performance 3D convolution for protein docking on IBM Blue Gene, in Proc ISPA2007, Lecture Notes in Computer Science, Vol. 4742, pp. 958-969, 2007.
17. Chen R, Li L, Weng ZP, ZDOCK: An initial-stage protein-docking algorithm, Proteins 52(1):80-87, 2003.
18. Chen R, Tong WW, Mintseris J, Li L, Weng ZP, ZDOCK predictions for the CAPRI Challenge, Proteins 52(1):68-73, 2003.
19. i symmetric multimer docking, Bioinformatics 21(8):1472-1478, 2005.
20. Zhang C, Liu S, Zhou YQ, Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function, Proteins 60(2):314-318, 2005.
21. Kiselyov O, Taha W, Relating FFTW, split-radix, Embed Softw Syst 3605:488-493, 2005.
22. Vuduc R, Demmel JW, Code generators for automatic tuning of numerical kernels: Experiences with FFTW - Position paper, in Proceedings of the International Workshop on Semantics, Applications and Implementation of Program Generation, Lecture Notes on Computer Science, Vol. 1924, pp. 190-211, 2000.
23. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng ZP, Protein-Protein Docking Benchmark 2.0: An update, Proteins 60 2):214-216, 2005.
24. Chen R, Mintseris J, Janin J, Weng ZP, A protein-protein docking benchmark, Proteins 52(1):88-91, 2003.
25. Kobe B, Deisenhofer J, A structural basis of the interactions between leucine-rich repeats and protein ligands, Nature 374 6518):183-186, 1995.
26. Ng KKS, Petersen JFW, Cherney MM, Garen C, Zalatoris JJ, Rao-Naik C, Dunn BM, Martzen MR, Peanasky RJ, James MNG, Structural basis for the inhibition of porcine pepsin by Ascaris pepsin inhibitor-3, Nat Struct Biol 7(8):653-657, 2000.
27. Mittl PRE, DiMarco S, Fendrich G, Pohlig G, Heim J, Sommerhoff C, Fritz H, Priestle JP, Grutter MG, A new structural class of serine protease inhibitors revealed by the structure of the hirustasin-kallikrein complex, Structure 5(2):253-264, 1997.
28. Gao GF, Tormo J, Gerth UC, Wyer JR, McMichael AJ, Stuart DI, Bell JI, Jones EY, Jakobsen BK, Crystal structure of the complex between human CD8 alpha alpha and HLA-A2, Nature 387(6633):630-634, 1997.
29. Zapf J, Sen U, Madhusudan, Hoch JA, Varughese KI, A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction, Structure 8 8):851-862, 2000.
30. Renault L, Kuhlmann J, Henkel A, Wittinghofer A, Structural basis for guanine nucleotide exchange on Ran by the regulator of chromosome condensation (RCC1), Cell 105(2):245-255, 2001.
31. Syed RS et al., Efficiency of signalling through cytokine receptors depends critically on receptor orientation, Nature 395(6701):511-516, 1998.
32. Bode W, Greyling HJ, Huber R, Otlewski J, Wilusz T, The refined 2.0 Å X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds ( Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes, FEBS Lett 242(2):285-292, 1989.
33. Strobl S, Maskos K, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R, A novel strategy for inhibition of alpha-amylases: Yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 Å resolution, Structure 6(7):911-921, 1998.
34. Savva R, Pearl LH, Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex, Nat Struct Biol 2(9):752-757, 1995.
35. Scheffzek K, Ahmadian MR, Kabsch W, Wiesmuller L, Lautwein A, Schmitz F, Wittinghofer A, The Ras-RasGAP complex: Structural basis for GTPase activation and its loss in oncogenic Ras mutants, Science 277 5324):333-338, 1997.
36. Gillmor SA, Takeuchi T, Yang SQ, Craik CS, Fletterick RJ, Compromise and accommodation in ecotin, a dimeric macromolecular inhibitor of serine proteases, J Mol Biol 299(4):993-1003, 2000.
37. Chen LY, Durley RCE, Mathews FS, Davidson VL, Structure of an electron transfer complex: Methylamine dehydrogenase, amicyanin, cytochrome c551i, Science 264(5155):86-90, 1994.
38. Nishida M, Nagata K, Hachimori Y, Horiuchi M, Ogura K, Mandiyan V, Schlessinger J, Inagaki F, Novel recognition mode between Vav and Grb2 SH3 domains, EMBO J 20(12):2995-3007, 2001.
39. Bewley MC, Springer K, Zhang YB, Freimuth P, Flanagan JM, Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR, Science 286(5444):1579-1583, 1999.
40. Choe H, Burtnick LD, Mejillano M, Yin HL, Robinson RC, Choe S, The calcium activation of gelsolin: Insights from the 3A structure of the G4-G6/actin complex, J Mol Biol 324(4):691-702, 2002.
41. Fieulaine S, Morera S, Poncet S, Mijakovic I, Galinier A, Janin J, Deutscher J, Nessler S, X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr, Proc Natl Acad Sci USA 99(21):13437-13441, 2002.
42. Obsil T, Ghirlando R, Klein DC, Ganguly S, Dyda F, Crystal structure of the 14-3-35 zeta : Serotonin N-acetyltransferase complex: A role for scaffolding in enzyme regulation, Cell 105(2):257-267, 2001.
43. Desmyter A, Spinelli S, Payan F, Lauwereys M, Wyns L, Muyldermans S, Cambillau C, Three camelid VHH domains in complex with porcine pancreatic alpha-amylase - Inhibition and versatility of binding topology, J Biol Chem 277(26):23645-23650, 2002.
44. Vetter IR, Arndt A, Kutay U, Gorlich D, Wittinghofer A, Structural view of the Ran-importin beta interaction at 2.3 Å resolution, Cell 97(5):635-646, 1999.