NAOMI: On the almost trivial task of reading molecules from different file formats

Journal of Chemical Information and Modeling

Volumn 51, Issue 12, 2011, Pages 3199-3207

  Urbaczek, Sascha ^a   Kolodzik, Adrian ^a   Fischer, J Robert ^a   Lippert, Tobias ^a   Heuser, Stefan ^b   Groth, Inken ^b   Schulz Gasch, Tanja ^c   Rarey, Matthias ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

^b BEIERSDORF AG   (Germany)

^c F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

ALMOST TRIVIAL; CHEMICAL INFORMATION; CHEMICAL MODEL; CHEMINFORMATICS; DATA-SOURCES; DRUG DISCOVERY; FILE FORMATS; STANDARD TESTS;

MOLECULES;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; COMPUTER PROGRAM; DRUG DEVELOPMENT; FACTUAL DATABASE; INFORMATION SCIENCE; METHODOLOGY;

DATABASES, FACTUAL; DRUG DISCOVERY; INFORMATICS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; SOFTWARE;

EID: 84555177559     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200324e     Document Type: Article

References (25)

1. Symyx CTfile Formats; http://www.symyx.com/downloads/public/ctfile/ ctfile.jsp, (accessed January 27, 2011).
2. TRIPOS Mol2 File Format; http://tripos.com/data/support/mol2.pdf, (accessed January 27, 2011).
3. Weininger, D. SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules J. Chem. Inf. Comput. Sci. 1988, 28, 31-36
4. The Open Babel Package, version 2.3.0; http://openbabel.org, (accessed January 18, 2011)
5. Neudert, G.; Klebe, G. fconv: format conversion, manipulation and feature computation of molecular data Bioinformatics 2011, 27, 1021-1022
6. Mol2Mol; http://www.gunda.hu/mol2mol/index.html, (accessed January 27, 2011).
7. MN.Convert; Molecular Networks GmbH-Computerchemie: Erlangen, Germany; http://www.molecular-networks.com/products/convert, (accessed January 27, 2011)
8. Babel; OpenEye Scientific Software, Inc.: Santa Fe, NM; http://www.eyesopen.com/docs/babel/current/pdf/BABEL.pdf, (accessed January 27, 2011).
9. Guha, R.; Howard, M.; Hutchison, G.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J.; Willighagen, E. The Blue Obelisk-Interoperability in Chemical Informatics J. Chem. Inf. Model. 2006, 46, 991-998
10. 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
11. Ihlenfeldt, W.; Takahashi, Y.; Abe, H.; Sasaki, S. Computation and Management of Chemical Properties in CACTVS: An Extensible Networked Approach toward Modularity and Compatibility J. Chem. Inf. Comput. Sci. 1994, 34, 109-116
12. JOELib/JOELib2; http://sourceforge.net/projects/joelib/, (accessed January 27, 2011).
13. PerlMol; http://www.perlmol.org/, (accessed January 27, 2011).
14. OEChem; OpenEye Scientific Software, Inc.: Santa Fe, NM; http://www.eyesopen.com/oechem-tk, (accessed January 27, 2011).
15. RDKit; http://rdkit.org/, (accessed Jan 27, 2011).
16. Sadowski, J.; Gasteiger, J.; Klebe, G. Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008
17. LigPrep; Schrödinger, LLC: Cambridge, MA; http://www.schrodinger. com/products/14/10/, (accessed January 27, 2011).
18. Concord; Tripos: St. Louis, MO; http://tripos.com/data/SYBYL/Concord- 072505.pdf, (accessed January 27, 2011).
19. Lewis, G. N. The Atom and the Molecule J. Am. Chem. Soc. 1916, 38, 762-785
20. Daylight theory manual, Daylight version 4.9; Daylight Chemical Information Systems, Inc.: Aliso Viejo, CA; http://www.daylight.com/dayhtml/doc/ theory/index.pdf, (accessed March 8, 2011).
21. Vismara, P. Union of all the minimum cycle bases of a graph Electron. J. Comb. 1997, 4, 1-15
22. Weininger, D.; Weininger, A.; Weininger, J. SMILES. 2. Algorithm for Generation of Unique SMILES Notation J. Chem. Inf. Comput. Sci. 1989, 29, 97-101
23. Huang, N.; Shoichet, B.; Irwin, J. Benchmarking Sets for Molecular Docking J. Med. Chem. 2006, 49, 6789-6801 Data sets (SDF and Mol2) downloaded April 12, 2011
24. CORINA-Fast Generation of High-Quality 3D Molecular Models, version 3.48; Molecular Networks GmbH-Computerchemie: Erlangen, Germany; http://www. molecular-networks.com/products/corina, (accessed January 18, 2011).
25. MOE, version 2010.10; Chemical Computing Group: Montreal, Quebec, Canada; http://www.chemcomp.com/software.htm, (accessed January 18, 2011).