Distributed chemical computing using ChemStar: An open source java remote method invocation architecture applied to large scale molecular data from PubChem

Journal of Chemical Information and Modeling

Volumn 48, Issue 4, 2008, Pages 691-703

  Karthikeyan, M ^a   Krishnan, S ^a   Pandey, Anil Kumar ^b   Bender, Andreas ^c   Tropsha, Alexander ^d  

^a NATIONAL CHEMICAL LABORATORY   (India)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

^c LEIDEN UNIVERSITY   (Netherlands)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMMING INTERFACES (API); DISTRIBUTED COMPUTER SYSTEMS; JAVA PROGRAMMING LANGUAGE; MOLECULAR STRUCTURE;

DISTRIBUTED CHEMICAL COMPUTING; MOLECULAR DATA; REMOTE METHOD INVOCATION (RMI);

CHEMICAL ANALYSIS;

EID: 44449151644     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700334f     Document Type: Article

References (48)

1. Richards, W. G. Virtual screening using grid computing: the screen-saver project. Nat. Rev. Drug. Discou. 2002, I, 551-5.
2. Davies, E. K.; Glick, M.; Harrison, K. N.; Richards, W. G. Pattern recognition and massively distributed computing. J. Comput. Chem. 2002, 23, 1544-50.
3. BBC World News, Saturday, 18 September, 2004. http://newswww.bbc.net.uk/ 2/hi/health/3597738.stm (accessed January 31, 2008).
4. Glick, M.; Grant, G. H.; Richards, W. G. Pinpointing anthrax-toxin inhibitors. Nat. Biotechnol. 2002, 20, 118-9.
5. Top500. http://www.top500.org/list/1999/11/ (accessed January 31, 2008).
6. Berkeley Open Infrastructure for Network Computing. http://boinc. berkeley.edu/ (accessed January 31, 2008).
7. http://boinc.berkeley.edu/projects.php (accessed January 31, 2008).
8. Mullender, S. J.; van Rossum, G.; Tanenbaum, A. S.; van Renesse, R.; van Staveren, H. Amoeba - A Distributed Operating System for the 1990s. IEEE Comput. 1990, 23, 44-53.
9. Foster, I. The grid: A new infrastructure for 21st century science. Phys. Today 2002, 55, 42-41.
10. Foster, I.; Kesselman, C. Computational Grids. In The Grid: Blueprint for a Future Computing Infrastructure; Foster, I., Kesselman, C., Eds.; Morgan Kaufman Publishers: San Francisco, CA, 1998.
11. Thain, D.; Tannenbaum, T.; Livny, M. Distributed computing in practice: the Condor experience. Concurrency Comput: Pract. Experience 2005, 17, 323-356.
12. Sunderam, V. S.; Geist, G. A.; Dongarra, J.; Manchek, R. The PVM Concurrent Computing System-Evolution, Experiences, and Trends. Parallel Comput. 1994, 20, 531-545.
13. Fich, F.; Ruppert, E. Hundreds of impossibility results for distributed computing. Distrib. Comput. 2003, 16, 121-163.
14. Karthikeyan, M.; Krishnan, S.; Pandey, A. K.; Bender, A. Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme. J. Chem. Inf. Model. 2006, 46, 452-461.
15. Google, Inc., Mountain View, CA, USA. http://www.google.com (accessed January 31, 2008).
16. Csizmadia, F. JChem: Java applets and modules supporting chemical database handling from web browsers. J. Chem. inf. Comput. Sci. 2000, 40, 323-4.
17. ChemAxon. http://www.chemaxon.com (accessed January 31, 2008).
18. JOELib - a java based computational chemistry package, http:// joelib.sourceforge.net/ (accessed January 31, 2008).
19. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 1997, 23, 3-25.
20. Ertl, P.; Rohde, B.; Selzer, P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 2000, 43, 3714-7.
21. Steinbeck, C.; Han, Y.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci. 2003, 43, 493-500.
22. Fechner, U.; Guha, R. Descriptor Validation on the CDK Project. 1. XlogP. CDK News 2006, 3, 33-37.
23. http://moltable.ncl.res.in/chemstar/ (accessed January 31, 2008).
24. PubChem Database, http://pubchem.ncbi.nlm.nih.gov/ (accessed January 31, 2008).
25. ChemBank. http://chembank.broad.harvard.edu/ (accessed January 31, 2008).
26. Chemical Entities of Biological Interest (ChEBI). http://www.ebi.ac.uk/ chebi/ (accessed January 31, 2008).
27. Lind, P.; Aim, M. A database-centric virtual chemistry system. J. Chem. Inf. Model. 2006, 46, 1034-9.
28. Sild, S.; Maran, U.; Romberg, M.; Schuller, B.; Benfenati, E. OpenMolGRID: Using automated workflows in GRID computing environment. In Advances in Grid Computing-Egc 2005; Springer-Verlag Berlin: Berlin, 2005; Vol. 3470, pp 464-473.
29. Sild, S.; Maran, U.; Lomaka, A.; Karelson, M. Open computing grid for molecular science and engineering. J. Chem. Inf. Model. 2006, 46, 9539.
30. Mazzatorta, P.; Smiesko, M.; Lo Piparo, E.; Benfenati, E. QSAR Model for Predicting Pesticide Aquatic Toxicity. J. Chem. Inf. Model. 2005, 45, 1767-1774.
31. Romberg, M. The UNICORE Grid Infrastructure. Sci. Comp. 2002, 10, 149-157.
32. Java, http://java.sun.com/ (accessed January 31, 2008).
33. Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 2000, 43, 4759-67.
34. Blaney, J. M.; Martin, E. J. Computational approaches for combinatorial library design and molecular diversity analysis. Curr. Opin. Chem. Biol. 1997, 1, 54-9.
35. Tetko, I. V.; Tanchuk, V. Y.; Kasheva, T. N.; Villa, A. E. P. Internet Software for the Calculation of the Lipophilicity and Aqueous Solubility of Chemical Compounds. J. Chem. Inf. Comput. Sci. 2001, 41, 246-252.
36. Tetko, I. V.; Gasteiger, J.; Todeschini, R.; Mauri, A.; Livingstone, D.; Ertl, P.; Palyulin, V. A.; Radchenko, E. V.; Zefirov, N. S.; Makarenko, A. S.; Tanchuk, V. Y.; Prokopenko, V. V. Virtual computational chemistry laboratory - design and description. J. Comput.-Aided Mol. Des. 2005, 19, 453-63.
37. http://www.vcclab.org/servers/ (accessed January 31, 2008).
38. http://www.sun.com/2006-1113/feature/index.jsp(accessed January 31, 2008).
39. Kaffee, http://www.kaffe.org/ (accessed January 31, 2008).
40. GNU Classpath. http://www.gnu.org/software/classpath/ (accessed January 31, 2008).
41. MOE (Molecular Operating Environment); Chemical Computing Group Inc.: Montreal, Quebec, Canada.
42. Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K. Atomic Physicochemical Parameters for Three Dimensional Structure Directed Quantitative Structure-Activity Relationships. 4. Additional Parameters for Hydrophobic and Dispersive Interactions and Their Application for an Automated Superposition of Certain Naturally Occurring Nucleoside Antibiotics. J. Chem. Inf. Comput. Sci. 1989, 29, 162-172.
43. Wildman, S. A.; Crippen, G. M. Prediction of physicochemical parameters by atomic contributions. J. Chem. Inf. Comput. Sci. 1999, 39, 868-873.
44. http://www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins. html#logp (accessed January 31, 2008).
45. http://www.chemaxon.com/marvin/chemaxon/marvin/help/logPlogD. html (accessed January 31, 2008).
46. Winiwarter, S.; Bonham, N. M.; Ax, F.; Hallberg, A.; Lennernas, H.; Karlen, A. Correlation of human jejunal permeability (in vivo) of drugs with experimentally and theoretically derived parameters. A multivariate data analysis approach. J. Med. Chem. 1998, 41, 4939-49.
47. Proschak, E.; Wegner, J. K.; Schuller, A.; Schneider, G.; Fechner, U. Molecular query language (MQL) - a context-free grammar for substructure matching. J. Chem. Inf. Model. 2007, 47, 295-301.
48. Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J.; Willighagen, E. L. The Blue Obelisk-interoperability in chemical informatics. J. Chem. Inf. Model. 2006, 46, 991-8.