3V: Cavity, channel and cleft volume calculator and extractor

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Voss, Neil R ^a   Gerstein, Mark ^b,c  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b YALE UNIVERSITY   (United States)

^c Yale University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOANALYSIS; COMPUTER GRAPHICS; DRUG BINDING SITE; INFORMATION RETRIEVAL; INFORMATION SERVICE; PRIORITY JOURNAL; PROTEIN STRUCTURE; RNA STRUCTURE; STRUCTURE ANALYSIS; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; CONFORMATION; INTERNET; PROTEIN CONFORMATION;

BINDING SITES; INTERNET; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; RNA; SOFTWARE; USER-COMPUTER INTERFACE;

RNA;

EID: 77954262905     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq395     Document Type: Article

References (34)

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
2. Voss, N.R., Gerstein, M., Steitz, T.A. and Moore, P.B. (2006) The geometry of the ribosomal polypeptide exit tunnel. J. Mol. Biol., 360, 893-906.
3. Ban, N., Nissen, P., Hansen, J., Moore, P.B. and Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4A resolution. Science, 289, 905-920.
4. Doyle, D.A., Morais Cabral, J., Pfuetzner, R.A., Kuo, A., Gulbis, J.M., Cohen, S.L., Chait, B.T. and MacKinnon, R. (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science, 280, 69-77.
5. Steinbacher, S., Bass, R., Strop, P. and Rees, D.C. (2007) Structures of the prokaryotic mechanosensitive channels MscL and MscS. Curr. Topics Membranes, 58.
6. Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D.C., Joachimiak, A., Horwich, A.L. and Sigler, P.B. (1994) The crystal structure of the bacterial chaperonin GroEL at 2.8 A. Nature, 371, 578-586.
7. Binkowski, T.A., Naghibzadeh, S. and Liang, J. (2003) CASTp: computed atlas of surface topography of proteins. Nucleic Acids Res., 31, 3352-3355.
8. Ferre, F., Ausiello, G., Zanzoni, A. and Helmer-Citterich, M. (2004) SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res., 32, D240-D244.
9. Hendlich, M., Rippmann, F. and Barnickel, G. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph Model, 15, 359-363, 389.
10. Laskowski, R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph, 13, 323-330, 307-308.
11. Laurie, A.T.R. and Jackson, R.M. (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics, 21, 1908-1916.
12. Tseng, Y.Y., Dupree, C., Chen, Z.J. and Li, W. (2009) SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. Nucleic Acids Res., 37, W384-W389.
13. Venkatachalam, C.M., Jiang, X., Oldfield, T. and Waldman, M. (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph Model, 21, 289-307.
14. Yu, J., Zhou, Y., Tanaka, I. and Yao, M. (2010) Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics, 26, 46-52.
15. Kleywegt, G.J. and Jones, T.A. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D Biol. Crystallogr., 50, 178-185.
16. Kinoshita, K. and Nakamura, H. (2003) Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci., 12, 1589-1595.
17. Levitt, D.G. and Banaszak, L.J. (1992) POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph, 10, 229-234.
18. Hernandez, M., Ghersi, D. and Sanchez, R. (2009) SITEHOUND-web: a server for ligand binding site identification in protein structures. Nucleic Acids Res., 37, W413-W416.
19. Coleman, R.G. and Sharp, K.A. (2009) Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophys. J., 96, 632-645.
20. Smart, O.S., Neduvelil, J.G., Wang, X., Wallace, B.A. and Sansom, M.S. (1996) HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph, 14, 354-360, 376.
21. Pellegrini-Calace, M., Maiwald, T. and Thornton, J.M. (2009) PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput. Biol., 5, e1000440.
22. Petrek, M., Otyepka, M., Banas, P., Kosinova, P., Koca, J. and Damborsky, J. (2006) CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics, 7, 316.
23. Petrek, M., Kosinova, P., Koca, J. and Otyepka, M. (2007) MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure, 15, 1357-1363.
24. Yaffe, E., Fishelovitch, D., Wolfson, H.J., Halperin, D. and Nussinov, R. (2008) MolAxis: a server for identification of channels in macromolecules. Nucleic Acids Res., 36, W210-W215.
25. Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
26. Richards, F.M. (1977) Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng., 6, 151-176.
27. Connolly, M.L. (1983) Analytical molecular surface calculation. J. App. Crystallogr., 16, 548.
28. Sanner, M.F., Olson, A.J. and Spehner, J.C. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38, 305-320.
29. Martick, M. and Scott, W.G. (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell, 126, 309-320.
30. Diamond, R. (1974) Real-space refinement of the structure of hen egg-white lysozyme. J. Mol. Biol., 82, 371-391.
31. Voss, N.R. and Gerstein, M. (2005) Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly. J. Mol. Biol., 346, 477-492.
32. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C. and Ferrin, T.E. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.
33. Klein, D.J., Schmeing, T.M., Moore, P.B. and Steitz, T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J., 20, 4214-4221.
34. Aller, S.G., Yu, J., Ward, A., Weng, Y., Chittaboina, S., Zhuo, R., Harrell, P.M., Trinh, Y.T., Zhang, Q., Urbatsch, I.L. et al. (2009) Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science, 323, 1718-1722.