A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data

Proteins: Structure, Function and Bioinformatics

Volumn 80, Issue 7, 2012, Pages 1872-1882

  Pérez Cano, Laura ^a   Jiménez García, Brian ^a   Fernández Recio, Juan ^a  

^a BARCELONA SUPERCOMPUTING CENTER   (Spain)

Author keywords

Computational docking; Docking benchmark; Protein and RNA flexibility; Protein RNA interactions; Structural prediction

Indexed keywords

ALGORITHM; ARTICLE; CONFORMATIONAL TRANSITION; EXPERIMENTAL MODEL; MOLECULAR DOCKING; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; QUALITY CONTROL; RNA STRUCTURE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; RNA; RNA-BINDING PROTEINS;

EID: 84862173240     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24075     Document Type: Article

References (33)

1. Pons C, Grosdidier S, Solernou A, Pérez-Cano L, Fernández-Recio J. Present and future challenges and limitations in protein-protein docking. Proteins 2010; 78: 95-108.
2. Andrusier N, Mashiach E, Nussinov R, Wolfson HJ. Principles of flexible protein-protein docking. Proteins 2008; 73: 271-289.
3. Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002; 12: 28-35.
4. Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002; 47: 409-443.
5. Janin J. The targets of CAPRI Rounds 13-19. Proteins 2010; 78: 3067-3072.
6. Lensink MF, Wodak SJ. Docking and scoring protein interactions: CAPRI 2009. Proteins 2010; 78: 3073-3084.
7. Janin J. Protein-protein docking tested in blind predictions: the CAPRI experiment. Mol Biosyst 2010; 6: 2351-2362.
8. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a critical assessment of PRedicted interactions. Proteins 2003; 52: 2-9.
9. Wimberly BT, Brodersen DE, Clemons WMJr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature 2000; 407: 327-339.
10. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 2000; 289: 905-920.
11. Pérez-Cano L, Fernández-Recio J. Dissection and prediction of RNA-binding sites on proteins. BioMol Concept 2010; 1: 345-355.
12. Tuszynska I, Bujnicki JM. DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. BMC Bioinform 2011; 12: 348.
13. Perez-Cano L, Solernou A, Pons C, Fernandez-Recio J. Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials. Pac Symp Biocomput 2010; 2010: 293-301.
14. Zheng S, Robertson TA, Varani G. A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins. FEBS J 2007; 274: 6378-6391.
15. Chen Y, Kortemme T, Robertson T, Baker D, Varani G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res 2004; 32: 5147-5162.
16. Das R, Baker D. Macromolecular modeling with rosetta. Annu Rev Biochem 2008; 77: 363-382.
17. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003; 331: 281-299.
18. Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins 2010; 78: 3212-3218.
19. Huang SY, Zou X. MDockPP: a hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins 2010; 78: 3096-3103.
20. Cheng TM, Blundell TL, Fernández-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 2007; 68: 503-515.
21. Grosdidier S, Pons C, Solernou A, Fernández-Recio J. Prediction and scoring of docking poses with pyDock. Proteins 2007; 69: 852-858.
22. Pons C, Solernou A, Pérez-Cano L, Grosdidier S, Fernández-Recio J. Optimization of pyDock for the new CAPRI challenges: docking of homology-based models, domain-domain assembly and protein-RNA binding. Proteins 2010; 78: 3182-3188.
23. Hyeon C, Dima RI, Thirumalai D. Size, shape, and flexibility of RNA structures. J Chem Phys 2006; 125: 194905.
24. Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2010; 78: 3111-3114.
25. van Dijk M, Bonvin AM. A protein-DNA docking benchmark. Nucleic Acids Res 2008; 36: e88.
26. Klosterman PS, Tamura M, Holbrook SR, Brenner SE. SCOR: a structural classification of RNA database. Nucleic Acids Res 2002; 30: 392-394.
27. Pérez-Cano L, Fernández-Recio J. Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins. Proteins 2010; 78: 25-35.
28. Lewis BA, Walia RR, Terribilini M, Ferguson J, Zheng C, Honavar V, Dobbs D. PRIDB: a protein-RNA interface database. Nucleic Acids Res 2011; 39: D277-D282.
29. Dutta S, Burkhardt K, Young J, Swaminathan GJ, Matsuura T, Henrick K, Nakamura H, Berman HM. Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol 2009; 42: 1-13.
30. Eswar N, Eramian D, Webb B, Shen MY, Sali A. Protein structure modeling with MODELLER. Methods Mol Biol 2008; 426: 145-159.
31. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-3402.
32. Rother M, Rother K, Puton T, Bujnicki JM. ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res 2011; 39: 4007-4022.
33. Tjong H, Zhou HX. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res 2007; 35: 1465-1477.