[1] Shape similarity: WEGA
Yan, X.; Li, J.; Liu, Z.; Zheng, M.; Ge, H.; Xu, J. (2013). Enhancing molecular shape comparison by weighted Gaussian functions. Journal of Chemical Information and Modeling, 53(8):1967-1978.
[2] Molecular pictures obtained with: Pymol
The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
[3] Conversion of molecules: OpenBabel
O'Boyle, N.M.; Banck, M.; James, C.A.; Morley, C.; Vandermeersch, T.; Hutchison, G.R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(33). DOI:10.1186/1758-2946-3-33
[4] Image molecule generated by: MolConvert (Chemaxon)
[5] 3D visualization: Jsmol
http://wiki.jmol.org/index.php/JSmol
[6] Chemical database: ChEMBL
Gaulton, A.; Bellis, L.; Bento, A.P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J.P. (2011). ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Research, 40(D1):D1100-D1107.
[7] Chemical database: DrugBank
Wishart, D. DrugBank: a comprehensive resource for in silico drug discovery and exploration. (2006). Nucleic Acids Research, 34(90001):D668-D672.
[8] Shape similarity: LiSiCA
Lesnik, S.; Stular, T.; Brus, B.; Knez, D.; Gobec, S.; Janezic, D.; Konc, J. LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors. (2015). Journal of Chemical Information and Modeling, 55:1521–1528.
[9] Shape similarity: Screen3D
Kalászi, A.; Szisz D.; Imre G.; Polgár T. Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method. (2014). Journal of Chemical Information and Modeling, 54(4):pp 1036–1049.
[10] Calculation of molecular descriptors: DRAGON
Todeschini, R.; Consonni, V. Molecular Descriptors for Chemoinformatics, 2nd ed. (2009). Wiley-VCH: Weinheim, Germany.
http://www.talete.mi.it/products/dragon_description.htm
[11] Pharmacophore screening: SHAFTS
Liu, X.; Jiang, H.; Li, H. SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening. (2011). Journal of Chemical Information and Modeling, 51:2372-2385.
[12] Chemical database: KEGG
Kanehisa, M.; Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. (2000). Nucleic Acids Research, 28(1):27–30.
[13] Shape similarity: OptiPharm
Puertas-Martín, S.; Redondo, J.L.; Pérez-Sánchez, H.; Ortigosa, P.M. OptiPharm: An evolutionary algorithm to compare shape similarity. (2018). Scientific Reports, 10.1038/s41598-018-37908-6.
[14] Molecule input: JME Molecular Editor
Ertl, P. Molecular structure input on the web. (2010). Journal of Cheminformatics, 2:1, 10.1186/1758-2946-2-1.