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
This Web site uses US-Align for protein alignment:
Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang. US-align: Universal Structure Alignment of Proteins, Nucleic Acids and Macromolecular Complexes. Nature Methods, 19: 1109-1115 (2022)
https://zhanggroup.org/US-align/
This Web site uses AutoDock Vina for predicting small molecule binding conformations:
Eberhardt, J., et al. J. Chem. Inf. Model. 2021, 61, 8, 3891–3898
https://doi.org/10.1021/acs.jcim.1c00203
Trott, O.; Olson, A. J. Autodock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J. Comput. Chem. 2010, 31, 455−461.
This Web site uses DiffDock for small molecule docking:
Corso, G.; Hannes Stärk; Jing, B.; Barzilay, R.; Jaakkola, T. S. DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. 2022.
https://doi.org/10.48550/arxiv.2210.01776
This Web site uses Boltz-1 for predicting biomolecular folding:
Wohlwend, J.; Corso, G.; Passaro, S.; Mateo Reveiz; Leidal, K.; Swiderski, W.; Tally Portnoi; Chinn, I.; Silterra, J.; Tommi Jaakkola; Barzilay, R. Boltz-1: Democratizing Biomolecular Interaction Modeling. bioRxiv (Cold Spring Harbor Laboratory) 2024.
https://doi.org/10.1101/2024.11.19.624167
This Web site uses Chai-1 for predicting biomolecular folding:
Boitreaud, J.; Dent, J.; McPartlon, M.; Meier, J.; Reis, V.; Rogozhnikov, A.; Wu, K. Chai-1: Decoding the Molecular Interactions of Life. bioRxiv (Cold Spring Harbor Laboratory) 2024.
https://doi.org/10.1101/2024.10.10.615955
This Web site uses the ColabFold server for multiple sequence alignment:
Mirdita, M.; Schütze, K.; Moriwaki, Y.; Heo, L.; Ovchinnikov, S.; Steinegger, M. ColabFold: Making Protein Folding Accessible to All. Nature Methods 2022, 19 (6), 1–4.
https://doi.org/10.1038/s41592-022-01488-1
This Web site uses ProLIF for Ligand Interaction Diagrams:
Bouysset, C.; Fiorucci, S. ProLIF: A Library to Encode Molecular Interactions as Fingerprints. Journal of Cheminformatics 2021, 13 (1).
https://doi.org/10.1186/s13321-021-00548-6
This Web site uses Am1-Bcc:
Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. Am1-Bcc Model: II. Parameterization and Validation. J. Comput. Chem. 2002, 23, 1623−1641.
https://doi.org/10.1002/jcc.10128
This Web site uses AmberTools:
Case, D. A., et al. AmberTools. J. Chem. Inf. Model. 2023, 63, 20, 6183–6191
https://doi.org/10.1021/acs.jcim.3c01153
This Web site uses OpenMM for energy calculations:
Eastman, P., et al. Openmm 7: Rapid Development of High Performance Algorithms for Molecular Dynamics. PLoS Comput. Biol.
2017, 13, No. e1005659.
https://doi.org/10.1371/journal.pcbi.1005659
This Web site uses an algorithm based on DSSP for determining secondary structures of protein:
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577-637. PMID: 6667333.
https://doi.org/10.1002/bip.360221211