|Small Molecule Databases|
- ADT / AutoDockTools is the graphical user interface that is developed in the MGL (Molecular Graphics Laboratory) to assist in setting up AutoGrid and AutoDock calculations, and in analysing their results.
- BDT (Vaqué et al., 2006) helps with such tasks as: (a) using receptor flexibility during docking; (b) the automatic docking of a large library of ligands onto one or more receptors; and (c) docking a ligand library onto one or more receptors without defining one a priori ligand-binding site on them (the so-called "blind-docking" analysis) and using a short distance between grid points. BDT runs on top of four Fortran programs (i.e. make_grids, combine_grids, make_docks and analyze, one under each BDT window tab), which control the conditions of AutoGrid and AutoDock runs. BDT is available for free, upon request, for non-commercial research.
Small Molecule Databases
- ZINC is a free database of commercially-available compounds for virtual screening, and a great source of input small molecules for AutoDock. ZINC contains over 4.6 million compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). For more details, see: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82.
- Formula for Determining the "Goodness of Hit Lists" in 3D Database Searches
- A measure of the 'Goodness' of hit lists obtained from chemical database searching is proposed (the G-H score). This measure takes into account both the yield (the fraction of active structures hit) and the percentage of actives that are retrieved from the database. By using variable coefficients on these terms and adjusting for the size of the hit list, a flexible but quantitative measure of hit list quality is obtained. We show the application of this measure to several published search results. We also show how the G-H score can be used to measure the quality of clustering results.
- Programs & Scripts by Mihaly Mezei
- Programs and scripts for virtual screening using AutoDock written by Mihaly Mezei, to help with (i) preparing the ligand set, (ii) running the dockings optionally on a cluster, and (iii) extracting, filtering and analyzing the docked conformations.