Software Components Incorporated in BMaps
This Web site builds upon 3DMol for molecular visualization:
Nicholas Rego and David Koes, "3Dmol.js: molecular visualization with WebGL", Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829.
3dmol.csb.pitt.edu
This Web site includes the Ketcher 2D chemistry editor, supported by the Indigo toolkit.
lifescience.opensource.epam.com
This Web site uses LS-align for ligand alignment:
Jun Hu, Zi Liu, Dongjun Yu, Yang Zhang LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. Bioinformatics, in press (2018).
zhanglab.ccmb.med.umich.edu/LS-align
This Web site uses SmilesDrawer for 2D visualization:
Daniel Probst and Jean-Louis Reymond, "SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript", Journal of Chemical Information and Modeling (2018) 58 (1), 1-7 doi:10.1021/acs.jcim.7b00425.
reymond-group/smilesDrawer
This Web site incorporates Open Babel for file format conversion:
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison, "Open Babel: An open chemical toolbox", Journal of Cheminformatics (2011) (3) 33: doi.org/10.1186/1758-2946-3-33
openbabel.org
RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
rdkit.org
The analytic solvent-accessible algorithm adapted from MSL (Molecular Software Libraries)
Daniel W Kulp, Sabareesh Subramaniam, Jason E Donald, Brett T Hannigan, Benjamin K Mueller, Gevorg Grigoryan, Alessandro Senes
“Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).”, J Comput Chem: 2012, 33(20);1645-61
msl-libraries.org
Eigen C++ template library for linear algebra was used for SVD in molecule alignment.
eigen.tuxfamily.org