Citing Ligand Expo:
Please reference our prior publication describing Ligand Depot:
Ligand Depot: a data warehouse for ligands bound to macromolecules.
Bioinformatics. 2004 Sep 1;20(13):2153-5.
Feng Z, Chen L, Maddula H, Akcan O, Oughtred R, Berman HM, Westbrook J.
PubMed: 15059838
Acknowledgements:
Ligand Expo is being developed at Rutgers University as part of the RCSB PDB project.
The RCSB PDB is managed by two members of the RCSB:
Rutgers, The
State University of New Jersey and the
San Diego
Supercomputer Center and
Skaggs School
of Pharmacy and Pharmaceutical Sciences at the
University of
California, San Diego. It is supported by funds from the
National Science
Foundation (NSF), the
National
Institute of General Medical Sciences (NIGMS), the
Office of
Science, Department of Energy (DOE), the
National Library
of Medicine (NLM), the
National Cancer
Institute (NCI), the
National Center
for Research Resources (NCRR), the
National
Institute of Biomedical Imaging and Bioengineering (NIBIB),
National
Institute of Neurological Disorders and Stroke (NINDS), and the
National
Institute of Diabetes and Digestive and Kidney Diseases (NIDDK).
The wwPDB Chemical Component Dictionary is a primary source of information for
Ligand Expo. This dictionary is maintained by the Worldwide Protein Data Bank
(wwPDB).
H.M. Berman, K. Henrick, H. Nakamura (2003):
Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980
We also gratefully acknowledge the following resources and software packages that have been
used in developing this site.
- OpenEye Scientific Software (http://www.eyesopen.com/)
OECHEM Toolkit, LexiChem, Omega
- OpenBabel (http://openbabel.sourceforge.net)
The Open Babel Package, version 2.0.1
Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, Henry Rzepa,
Christoph Steinbeck, Joerg Kurt Wegner, Egon Willighagen.
"The Blue Obelisk -- Interoperability in Chemical Informatics."
J. Chem. Inf. Model. (2006) 46(3) 991-998. DOI:10.1021/ci050400b
- CACTVS
(http://www2.chemie.uni-erlangen.de/software/cactvs/index.html)
CACTVS: A Chemistry Algorithm Development Environment
W. D. Ihlenfeldt, Y. Takahasi, H. Abe, S. Sasaki,
in: Daijuukagakutouronkai Dainijuukai Kouzoukasseisoukan Shinpojiumu Kouenyoushishuu,
Machida, K., Nishioka, T. (Eds),
Kyoto University Press (1992), 102-105
- CORINA (http://www2.chemie.uni-erlangen.de/software/corina/index.html)
Gasteiger, J.; Rudolph, C.; Sadowski, J.
Automatic Generation of 3D-Atomic Coordinates for Organic Molecules.
Tetrahedron Comp. Method. 1990, 3, 537-547.
- AstexViewer@MSD-EBI (
http://www.ebi.ac.uk/msd-srv/apps/Viewer/index.html)
An extended version of AstexViewer
developed by Tom Oldfield at MSD EBI.
Michael J. Hartshorn (2003) "AstexViewer: A visualisation aid for structure-based drug
design", Journal of Computer Aided Molecular Design 16 (12), 871-881 (2002).
-
Jmol (http://www.jmol.org/ An open-source Java viewer for chemical structures in 3D.
- ACDLABS (http://www.acdlabs.com/)
Name Batch - IUPAC naming application
- InChi (http://www.iupac.org/inchi/)
The IUPAC International Chemical Identifier (InChI)
Stephen E. Stein, Stephen R. Heller, and Dmitrii Tchekhovskoi, An Open Standard for Chemical Structure Representation: The IUPAC Chemical Identifier, in Proceedings of the 2003 International Chemical Information Conference (Nimes),
Infonortics, pp. 131-143.