Modern drug discovery for inflammatory bowel disease: The role of computational methods

Table 3 Molecular docking programs most frequently employed in drug discovery

Program	Description	Website
AutoDock[152]	A docking toolkit. It is meant to foretell the binding mode of small molecules to a receptor with a known 3D structure, such as a substrate or a drug candidate. There have been multiple engines developed, and it has undergone constant evolution and refinement over the years to incorporate new features	https://autodock.scripps.edu/
AutoDock Vina[153]	One of the AutoDock Suite’s docking engines. It is a free and open-source molecular docking software. Dr. Oleg Trott of The Scripps Research Institute’s Molecular Graphics Lab (now CCSB) created and initially implemented the system. The most recent version of AutoDock Vina is v.1.2.0	https://vina.scripps.edu/
Hex[154]	Invented by Dave Ritchie and is a program for molecular superposition and protein docking. Hex can read protein and DNA structures in the Protein Data Bank format as well as small-molecule SDF files. It has been downloaded over 40000 times as of December 2015	http://hex.loria.fr/
MOE[155]	Integrated computer-aided molecular design platform for small molecule and biological therapeutics. Common platform for chemists, biologists and crystallographers. Small Molecules - Peptides – Biologics	https://www.chemcomp.com/
Glide Schrodinger[156]	Provides a full range of speed vs accuracy options, ranging from the high-throughput virtual screening mode that efficiently enriches million compound libraries to the standard precision) mode that reliably docks tens to hundreds of thousands of ligands with high accuracy to the extra precision mode that eliminates false positives by sampling more extensively and using more advanced scoring, resulting in even higher enrichment	https://www.schrodinger.com/

CCSB: Center for Computational Structural Biology; SDF: Structure data files; DNA: Deoxyribonucleic Acid; MOE: Molecular operating environment.