Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: The Collaborative Chemistry Database Tool (CCDBT)

Journal of Molecular Graphics and Modelling

Volumn 34, Issue , 2012, Pages 67-75

  Chen, Mingyang ^a   Stott, Amanda C ^a   Li, Shenggang ^a   Dixon, David A ^a  

^a UNIVERSITY OF ALABAMA   (United States)

Author keywords

Collaborative; Computational chemistry; Data mining; Database; Massive data

Indexed keywords

COLLABORATIVE; COLLABORATIVE DATABASE; COMPUTING SOURCES; DATA SYNCHRONIZATION; DATA TYPE; DATABASE; DATABASE TOOLS; MASSIVE DATA; MYSQL DATABASE;

COMPUTATIONAL CHEMISTRY; DATA MINING;

METADATA;

ARTICLE; COLLABORATIVE CHEMISTRY DATABASE TOOL; COMPUTER PROGRAM; DATA BASE; DATA MINING; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; PRIORITY JOURNAL;

AUTOMATIC DATA PROCESSING; CHEMISTRY; DATA MINING; DATABASES, FACTUAL; MODELS, CHEMICAL; USER-COMPUTER INTERFACE;

EID: 84863150315     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.12.004     Document Type: Article

References (34)

1. S.E. Stein, S.R. Heller, and D. Tchekhovskoi An open standard for chemical structure representation: The IUPAC Chemical Identifier Proceedings of the 2003 International Chemical Information Conference (Nimes), Infonortics 2003 131 143
2. http://www.synapticscience.com/seurat/database/
3. H. Sui, R. Zhang, K. Pan, L. Luo, and S. Chen ChemDataBase - a database management system for facilitating data management in computational chemistry 2008 International Multi-symposiums on Computer and Computational Sciences 2008 190 193
4. L. Li, R. Zhang, J. Chen, Y. Zhang, L. Li, and Z. Zhao ChemDataBase 2: an enhanced chemical database management system for virtual screening 2010 Fifth Annual ChinaGrid Conference (ChinaGrid) 2010 74 79
5. G. Black, K.L. Schuchardt, D.K. Gracio, and B. Palmer The extensible computational chemistry environment: a problem solving environment for high performance theoretical chemistry P.M.A. Sloot, D. Abramson, A.V. Bogdanov, J. Dongarra, Computational Science - ICCS 2003, International Conference Saint Petersburg Russian Federation, Melbourne, Australia, Proceedings 2660, vol. 81 2003 Springer Verlag Berlin, Germany 122 131 G.D.
6. http://ecce.emsl.pnl.gov/index.shtml
7. http://www.primekinetics.org
8. G. van Rossum Python Tutorial, Technical Report CS-R9526 1995, May Centrum voor Wiskunde en Informatica (CWI) Amsterdam
9. G. van Rossum, and F.L. Drake Python Reference Manual 2001 PythonLabs Virginia, USA Python version 2.6 was used in our implementation http://www.python.org
10. MySQL. http://www.mysql.com/.
11. R. Pointer, paramiko: SSH2 protocol for Python. http://www.lag.net/ paramiko/.
12. A. Dustman, mysql-python: MySQL for Python. http://sourceforge.net/ projects/mysql-python/.
13. D.C. Lizenberger, PyCrypto: The Python Cryptography Toolkit. http://www.dlitz.net/software/pycrypto/.
14. J. Galbraith, J. Van Dyke, B. McClure, and J. Bright Secure Shell Public-Key Subsystem 2006 IETF (internet draft) http://tools.ietf.org
15. J. Galbraith, O. Saarenmaa, T. Ylonen, and S. Lehtinen SSH File Transfer Protocol (SFTP) 2005 IETF (internet draft) http://www.ietf.org/internet-drafts/ draft-ietf-secsh-filexfer-07.txt
16. Jmol: an open-source Java viewer for chemical structures in 3D. http://jmol.sourceforge.net/.
17. H.-J. Werner, P.J. Knowles, F.R. Manby, M. Schütz, P. Celani, G. Knizia, T. Korona, R. Lindh, A. Mitrushenkov, G. Rauhut, T.B. Adler, R.D. Amos, A. Bernhardsson, A. Berning, D.L. Cooper, M.J.O. Deegan, A.J. Dobbyn, F. Eckert, E. Goll, C. Hampel, A. Hesselmann, G. Hetzer, T. Hrenar, G. Jansen, C. Köppl, Y. Liu, A.W. Lloyd, R.A. Mata, A.J. May, S.J. McNicholas, W. Meyer, M.E. Mura, A. Nicklass, P. Palmieri, K. Pflüger, R. Pitzer, M. Reiher, T. Shiozaki, H. Stoll, A.J. Stone, R. Tarroni, T. Thorsteinsson, M. Wang, and A. Wolf MOLPRO, Version 2010.1, a Package of Ab initio Programs 2010 http://www.molpro.net
18. CMQCA, R.A. Whiteside, J.S. Binkley, R. Krishnan, D.J. DeFrees, H.B. Schlegel, and J.A. Pople Carnegie Mellon Quantum Chemistry Archive 1981 Carnegie Mellon University Pittsburgh, PA
19. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, N.J. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, and D.J. Fox Gaussian 09, Revision B.1 2009 Gaussian, Inc. Wallingford, CT
20. A.D. Becke Density-functional thermochemistry. III: the role of exact exchange J. Chem. Phys. 98 1993 5648 5652
21. C. Lee, W. Yang, and R.G. Parr Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 37 1988 785 789
22. D.J. Grant, M.H. Matus, J. Switzer, D.A. Dixon, J.S. Francisco, and K.O. Christe Bond dissociation energies in second row compounds J. Phys. Chem. A 112 2008 3145 3156
23. 2, OH, and SH) J. Phys. Chem. A 113 2009 777 787
24. E.J. Bylaska, W.A. de Jong, K. Kowalski, T.P. Straatsma, M. Valiev, D. Wang, E. Aprà, T.L. Windus, S. Hirata, M.T. Hackler, Y. Zhao, P.-D. Fan, R.J. Harrison, M. Dupuis, D.M.A. Smith, J. Nieplocha, V. Tipparaju, M. Krishnan, A.A. Auer, M. Nooijen, E. Brown, G. Cisneros, G.I. Fann, H. Früchtl, J. Garza, K. Hirao, R. Kendall, J.A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. Deegan, K. Dyall, D. Elwood, E. Glendening, M. Gutowski, A. Hess, J. Jaffe, B. Johnson, J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng, T. Nakajima, S. Niu, L. Pollack, M. Rosing, G. Sandrone, M. Stave, H. Taylor, G. Thomas, J. van Lenthe, A. Wong, and Z. Zhang NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.1 2007 Pacific Northwest National Laboratory Richland, Washington 99352-0999, USA
25. M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus, and W.A. de Jong NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations Comput. Phys. Commun. 181 2010 1477 1489
26. L.A. Curtiss, P.C. Redfern, and K. Raghavachari Assessment of Gaussian-3 and density-functional theories on the G3/05 test set of experimental energies J. Chem. Phys. 123 2005 124107 124118
27. J.I. Steinfeld, J.S. Francisco, and W.L. Hase Chemical Kinetics and Dynamics 2nd edition 1999 Prentice Hall New Jersey
28. K.A. Holbrook, M.J. Pilling, and S.H. Robertson Unimolecular Reactions 2nd edition 1996 Wiley Chichester, UK
29. E. Wigner Crossing of potential thresholds in chemical reactions Z. Phys. Chem. B 19 1932 203 207
30. R.T. Skodje, and D.G. Truhlar Parabolic tunneling calculations J. Phys. Chem. 85 1981 624 628
31. http://www.semichem.com/
32. KHIMERA, Version 3.2: A Software Tool for Calculations of Chemical Reactions Thermodynamics and Kinetics from First Principles 2003 Kintech, Kinetic Technologies, Ltd. Moscow http://www.kintechlab.com/products/khimera/
33. http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html; http://www.daylight.com/dayhtml-tutorials/languages/smiles/index.html; http://cactus.nci.nih.gov/translate/.
34. R. Car, and M. Parrinello Unified approach for molecular dynamics and density-functional theory Phys. Rev. Lett. 55 1985 2471 2474