NPDock: A web server for protein-nucleic acid docking

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W425-W430

  Tuszynska, Irina ^a,b   Magnus, Marcin ^a   Jonak, Katarzyna ^a   Dawson, Wayne ^a   Bujnicki, Janusz M ^a,c  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^b UNIVERSITY OF WARSAW   (Poland)

^c ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; MOLECULAR DOCKING; NUCLEIC ACID PROTEIN DOCKING; NUCLEIC ACID STRUCTURE; PREDICTION; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RNA STRUCTURE; SOFTWARE; THREE DIMENSIONAL IMAGING; WEB BROWSER; WORKFLOW; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; INTERNET; METABOLISM; PROCEDURES; PROTEIN CONFORMATION;

DNA; DNA BINDING PROTEIN; RNA; RNA BINDING PROTEIN;

DNA; DNA-BINDING PROTEINS; INTERNET; MOLECULAR DOCKING SIMULATION; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; RNA; RNA-BINDING PROTEINS; SOFTWARE;

EID: 84979858763     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv493     Document Type: Article

References (31)

1. Lukong, K.E., Chang, K.W., Khandjian, E.W. and Richard, S. (2008) RNA-binding proteins in human genetic disease. Trends Genet., 24, 416-425.
2. Cooper, T.A., Wan, L. and Dreyfuss, G. (2009) RNA and disease. Cell, 136, 777-793.
3. Doudna, J.A. (2000) Structural genomics of RNA. Nat. Struct. Biol., 7, 954-956.
4. Rodrigues, J.P. and Bonvin, A.M. (2014) Integrative computational modeling of protein interactions. FEBS J., 281, 1988-2003.
5. Wichadakul, D., McDermott, J. and Samudrala, R. (2009) Prediction and integration of regulatory and protein-protein interactions. Methods Mol. Biol., 541, 101-143.
6. Moreira, I.S., Fernandes, P.A. and Ramos, M.J. (2010) Protein-protein docking dealing with the unknown. J. Comp. Chem., 31, 317-342.
7. Janin, J. (2010) Protein-protein docking tested in blind predictions: the CAPRI experiment. Mol. Biosyst., 6, 2351-2362.
8. Laing, C. and Schlick, T. (2010) Computational approaches to 3D modeling of RNA. J. Phys. Condens Matter, 22, 283101.
9. Rother, K., Rother, M., Boniecki, M., Puton, T. and Bujnicki, J.M. (2011) RNA and protein 3D structure modeling: similarities and differences. J. Mol. Model., 17, 2325-2336.
10. Dominguez, C., Boelens, R. and Bonvin, A.M. (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737.
11. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C. and Vakser, I.A. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. U.S.A., 89, 2195-2199.
12. Ritchie, D.W. and Kemp, G.J. (2000) Protein docking using spherical polar Fourier correlations. Proteins, 39, 178-194.
13. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. and Wolfson, H.J. (2005) Patch Dock and Symm Dock: servers for rigid and symmetric docking. Nucleic Acids Res., 33, W363-W367.
14. Gabb, H.A., Jackson, R.M. and Sternberg, M.J. (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol., 272, 106-120.
15. Tuszynska, I. and Bujnicki, J.M. (2011) DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. BMC Bioinformatics, 12, 348.
16. Zheng, S., Robertson, T.A. and Varani, G. (2007) A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins. FEBS J., 274, 6378-6391.
17. Perez-Cano, L., Solernou, A., Pons, C. and Fernandez-Recio, J. (2010) Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials. Pac. Symp. Biocomput., 15, 269-280.
18. Huang, S.Y. and Zou, X. (2014) A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Res., 42, e55.
19. Vakser, I.A. and Aflalo, C. (1994) Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins, 20, 320-329.
20. Zhang, C., Liu, S., Zhu, Q. and Zhou, Y. (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem., 48, 2325-2335.
21. Robertson, T.A. and Varani, G. (2007) An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins, 66, 359-374.
22. Shortle, D., Simons, K.T. and Baker, D. (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. U.S.A., 95, 11158-11162.
23. Kirkpatrick, S., Gelatt, C.D. Jr and Vecchi, M.P. (1983) Optimization by simulated annealing. Science, 220, 671-680.
24. O'Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T. and Hutchison, G.R. (2011) Open Babel: an open chemical toolbox. J. Cheminform., 3, 33.
25. Humphrey, W., Dalke, A. and Schulten, K. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 33-38.
26. Huang, S.Y. and Zou, X. (2013) A nonredundant structure dataset for benchmarking protein-RNA computational docking. J. Comput. Chem., 34, 311-318.
27. van Dijk, M. and Bonvin, A.M. (2008) A protein-DNA docking benchmark. Nucleic. Acids. Res., 36, e88.
28. Fislage, M., Roovers, M., Tuszynska, I., Bujnicki, J.M., Droogmans, L. and Versees, W. (2012) Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life. Nucleic Acids Res., 40, 5149-5161.
29. Sulej, A.A., Tuszynska, I., Skowronek, K.J., Nowotny, M. and Bujnicki, J.M. (2012) Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger. Nucleic Acids Res., 40, 11563-11570.
30. Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A. (2003) Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des., 17, 725-738.
31. Rother, K., Rother, M., Boniecki, M., Puton, T., Tomala, K., Lukasz, P. and Bujnicki, J.M. (2012) Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling. In: Leontis, NB and Westhof, E (eds). RNA 3D Structure Analysis and Prediction. Springer-Verlag, Berlin, 67-90.