Modeling, informatics, and the quest for reproducibility

Journal of Chemical Information and Modeling

Volumn 53, Issue 7, 2013, Pages 1529-1530

  Walters, W Patrick ^a  

^a VERTEX PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MODELING;

CHEMICAL INFORMATION; CHEMINFORMATICS; REPRODUCIBILITIES; REPRODUCIBLE RESEARCH; SCIENTIFIC INFORMATION;

INFORMATICS;

CHEMICAL STRUCTURE; COMPUTER; COMPUTER PROGRAM; INFORMATION SCIENCE; REPRODUCIBILITY; LETTER;

COMPUTERS; INFORMATICS; MODELS, MOLECULAR; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84880519482     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400197w     Document Type: Article

References (12)

1. Morin, A.; Urban, J.; Adams, P.; Foster, I.; Sali, A.; Baker, D.; Sliz, P. Shining light into black boxes Science 2012, 336, 159-160
2. Open Babel: The Open Source Chemistry Toolbox. http://openbabel.org/wiki/ Main-Page (accessed May 27, 2013).
3. The Chemistry Development Kit. http://sourceforge.net/projects/cdk/ (accessed May 27, 2013).
4. RDKit: Cheminformatics and Machine Learning Software. http://www.rdkit.org/ (accessed May 27, 2013).
5. Depth First. http://depth-first.com/articles/2006/08/23/readily- available-without-infringements-or-restrictions (accessed May 27, 2013).
6. Figueras, J. Letter to the editor. Comment on editorial on software distribution in science J. Chem. Inf. Comput. Sci. 1984, 24, 276-276
7. Landrum, G. A.; Stiefl, N. Is that a scientific publication or an advertisement? Reproducibility, source code and data in the computational chemistry literature Future Med. Chem. 2012, 4, 1885-1887
8. Ince, D. C.; Hatton, L.; Graham-Cumming, J. The case for open computer programs Nature 2012, 482, 485-488
9. Neylon, C.; Aerts, J.; Brown, C. T.; Coles, S. J.; Hatton, L.; Lemire, D.; Millman, K. J.; Murray-Rust, P.; Perez, F.; Saunders, N. Changing computational research. The challenges ahead Source Code Biol. Med. 2012, 7, 1-2
10. Jorgensen, W. L. QSAR/QSPR and proprietary data J. Chem. Inf. Model. 2006, 46, 937-937
11. Stahl, M.; Bajorath, J. Computational medicinal chemistry J. Med. Chem. 2011, 54, 1
12. 2012 Workshop on Free Energy Methods in Drug Design. http://www. alchemistry.org/wiki/index.php?title=2012-Workshop-on-Free-Energy-Methods-in- Drug-Design (accessed May 27, 2013).