AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets

Bioinformatics

Volumn 22, Issue 14, 2006, Pages

  Bottegoni, Giovanni ^a   Rocchia, Walter ^b   Recanatini, Maurizio ^a   Cavalli, Andrea ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMSACRINE; ASTEMIZOLE; BEPRIDIL; CITALOPRAM; DOFETILIDE; FENTANYL; FEXOFENADINE; MIZOLASTINE; PIMOZIDE; PRAZOSIN;

ALGORITHM; BIOINFORMATICS; CLUSTER ANALYSIS; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFERENCE PAPER; CONTROLLED STUDY; CRYSTALLOGRAPHY; DRUG CONFORMATION; DRUG STRUCTURE; INFORMATION PROCESSING; MONTE CARLO METHOD; PRIORITY JOURNAL;

EID: 33747882592     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl212     Document Type: Conference Paper

References (18)

1. Bottegoni,G., Cavalli,A. and Recanatini,M. (2006) A comparative study on the application of hierarchical-agglomerative clustering approaches to organize outputs of reiterated docking runs. J. Chem. Inf. Mod., 46, 852-862.
2. Bourne,Y., Taylor,P., Radic,Z. and Marchot,P. (2003) Structural insights into ligand interactions at the acetylcholinesterase peripheral anionic site. Embo J., 22, 1-12.
3. Cavalli,A., Bottegoni,G., Raco,C., De Vivo,M. and Recanatini,M. (2004) A computational study of the binding of propidium to the peripheral anionic site of human acetylcholinesterase. J. Med. Chem., 47, 3991-3999.
4. Chang,G., Guida,W.C. and Still,W.C. (1989) An internal coordinate Monte Carlo method for searching conformational space. J. Am. Chem. Soc., 111, 4379-4386.
5. Chema,D., Eren,D., Yayon,A., Goldblum,A. and Zaliani,A. (2004) Identifying the binding mode of a molecular scaffold. J. Comput. Aided Mol. Des., 18, 23-40.
6. Everitt,B.S., Landau,S. and Leese,M. (2001) Cluster Analysis. Arnold, a member of the Hodder Headline Group,London.
7. Ewing,T.J., Makino,S., Skillman,A.G. and Kuntz,I.D. (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des., 15, 411-428.
8. Hopkins,B. (1954) A new method for determining the type of distribution of plant individuals. Ann. Bot.-London, 18, 213-227.
9. Hubert,L.J. and Arabie,P. (1985) Comparing partitions. J. Classif., 2, 193-218.
10. Jones,G., Willett,P., Glen,R.C., Leach,A.R. and Taylor,R. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267, 727-748.
11. Kelley,L.A., Gardner,S.P. and Sutcliffe,M.J. (1997) An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng., 10, 737-741.
12. Metropolis,N., Rosenbluth,A.W., Rosenbluth,M.N., Teller,A.H. and Teller,E. (1953) Equation of state calculations by fast computing machines. J. Chem. Phys., 21, 1087-1092.
13. Mohamadi,F., Richards,N.G.J., Guida,W.C., Liskamp,R.M.J., Lipton,M.A., Caulfield,C.E., Chang,G., Hendrickson,T.F. and Still,W.C. (1990) MacroModel - an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J. Comput. Chem., 1, 440-467.
14. Morris,G.M., Goodsell,D.S., Halliday,R.S., Huey,R., Hart,W.E., Belew,R.K. and Olson,A.J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem., 19, 1639-1662.
15. Rarey,M., Kramer,B., Lengauer,T. and Klebe,G. (1996) A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol., 261, 470-489.
16. Shenkin,P.S. and McDonald,D.Q. (1994) Cluster analysis of molecular conformations. J. Comput. Chem., 15, 899-916.
17. Taylor,R.D., Jewsbury,P.J. and Essex,J.W. (2002) A review of protein-small molecule docking methods. J. Comput. Aided Mol. Des., 16, 151-166.
18. Ward,J.H.J. and Hook,M.E. (1963) Application of a hierarchical grouping procedure to problem of grouping profiles. Educ. Psychol. Meas., 23, 69-92.