BINANA: A novel algorithm for ligand-binding characterization

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 6, 2011, Pages 888-893

  Durrant, Jacob D ^a   McCammon, J Andrew ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b San Diego   (United States)

Author keywords

BINANA; Computer algorithm; Computer aided drug design; Ligand binding analysis; Structural biology; Virtual screening

Indexed keywords

BINANA; COMPUTER ALGORITHM; COMPUTER-AIDED DRUG DESIGN; LIGAND-BINDING ANALYSIS; STRUCTURAL BIOLOGY; VIRTUAL SCREENING;

ALGORITHMS; COMPLEXATION; COMPUTER AIDED ANALYSIS; HYDROPHOBICITY; VAN DER WAALS FORCES;

LIGANDS;

LIGAND; RECEPTOR;

ALGORITHM; ANALYZER; ARTICLE; BINDING ANALYZER; HYDROGEN BOND; HYDROPHOBICITY; LIGAND BINDING; PRIORITY JOURNAL; SCREENING TEST; STATIC ELECTRICITY;

ALGORITHMS; BINDING SITES; COMPUTER-AIDED DESIGN; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; SOFTWARE;

EID: 79953277006     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.01.004     Document Type: Article

References (27)

1. M.F. Sanner Python: a programming language for software integration and development J. Mol. Graph. Model. 17 1999 57 61 (Pubitemid 30029318)
2. G.B. McGaughey, M. Gagne, and A.K. Rappe Pi-stacking interactions. Alive and well in proteins J. Biol. Chem. 273 1998 15458 15463 (Pubitemid 28298153)
3. J.D. Durrant, and J.A. McCammon NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes J. Chem. Inf. Model. 50 2010 1865 1871
4. R. Wang, X. Fang, Y. Lu, and S. Wang The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures J. Med. Chem. 47 2004 2977 2980 (Pubitemid 38702694)
5. R. Wang, X. Fang, Y. Lu, C.Y. Yang, and S. Wang The PDBbind database: methodologies and updates J. Med. Chem. 48 2005 4111 4119 (Pubitemid 40800619)
6. L. Hu, M.L. Benson, R.D. Smith, M.G. Lerner, and H.A. Carlson Binding MOAD (Mother Of All Databases) Proteins 60 2005 333 340 (Pubitemid 41061630)
7. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The protein data bank Nucl. Acids Res. 28 2000 235 242 (Pubitemid 30047768)
8. J. Deng, A. Schnaufer, R. Salavati, K.D. Stuart, and W.G. Hol High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1 J. Mol. Biol. 343 2004 601 613 (Pubitemid 39311608)
9. T.J. Dolinsky, P. Czodrowski, H. Li, J.E. Nielsen, J.H. Jensen, and G. Klebe PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Res. 35 2007 W522 W525
10. T.J. Dolinsky, J.E. Nielsen, J.A. McCammon, and N.A. Baker PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res. 32 2004 W665 W667
11. M.F. Sanner A component-based software environment for visualizing large macromolecular assemblies Structure 13 2005 447 462 (Pubitemid 40342884)
12. J. Gasteiger, and M. Marsili Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
13. R.E. Amaro, A. Schnaufer, H. Interthal, W. Hol, K.D. Stuart, and J.A. McCammon Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei Proc. Natl. Acad. Sci. U.S.A. 105 2008 17278 17283
14. J.D. Durrant, L. Hall, R.V. Swift, M. Landon, A. Schnaufer, and R.E. Amaro Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1 PLoS Negl. Trop. Dis. 4 2010 e803
15. O. Trott, and A.J. Olson AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J. Comput. Chem. 31 2009 455 461
16. P.J. Lupardus, A. Shen, M. Bogyo, and K.C. Garcia Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain Science 322 2008 265 268
17. N.A. Baker, D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl. Acad. Sci. U.S.A. 98 2001 10037 10041 (Pubitemid 32802969)
18. A. Varshney, F.P. Brooks, and W.V. Wright Linearly scalable computation of smooth molecular surfaces IEEE Comp. Graph. Appl. 14 1994 19 25
19. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 (Pubitemid 26152973)
20. A.M. Davis, and S.J. Teague Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis Angew. Chem. Int. Ed. 38 1999 736 749 (Pubitemid 29146588)
21. T. Young, R. Abel, B. Kim, B.J. Berne, and R.A. Friesner Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding Proc. Natl. Acad. Sci. U.S.A. 104 2007 808 813 (Pubitemid 46154692)
22. L.C. James, P. Roversi, and D.S. Tawfik Antibody multispecificity mediated by conformational diversity Science 299 2003 1362 1367 (Pubitemid 36254643)
23. E.A. Meyer, R.K. Castellano, and F. Diederich Interactions with aromatic rings in chemical and biological recognition Angew. Chem. Int. Ed. Engl. 42 2003 1210 1250 (Pubitemid 36410287)
24. C. Oswald, S.H. Smits, M. Hoing, L. Sohn-Bosser, L. Dupont, and D. Le Rudulier Crystal structures of the choline/acetylcholine substrate-binding protein ChoX from Sinorhizobium meliloti in the liganded and unliganded-closed states J. Biol. Chem. 283 2008 32848 32859
25. J.C. Ma, and D.A. Dougherty The cation-pi interaction Chem. Rev. 97 1997 1303 1324
26. R.E. Hibbs, G. Sulzenbacher, J. Shi, T.T. Talley, S. Conrod, and W.R. Kem Structural determinants for interaction of partial agonists with acetylcholine binding protein and neuronal alpha7 nicotinic acetylcholine receptor EMBO J. 28 2009 3040 3051
27. D.A. Dougherty Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp Science 271 1996 163 168 (Pubitemid 26033294)