In Structure-Based Drug Discovery, we have a number of resources, including both hardware and software, and several small-molecule libraries.
We use high-end workstations and servers for molecular modeling and graphics. Data is stored and backed up on arrays of disks totaling 20 TB (Tera bytes). Additionally, we use the Icahn School of Medicine at Mount Sinai’s new Minerva high performance computing system. On this system, virtual screening computations of millions of compounds can be completed in a matter of days.
We use an array of state-of-the-art software for Structural Bioinformatics, Cheminformatics, and Molecular Modeling. These include: AutoDock, eHiTs, DOCK, Gold, and AutoDock VINA for docking and virtual screening; DockRes for analyzing virtual screening results; MODELLER for protein structure modeling and protein structure analysis; SiteHound and fPocket for binding site identification and analysis; and many others for various tasks.
Several small-molecule libraries are available for virtual screening.
- The National Cancer Institute (NCI) Open Database library contains about 265,000 compounds from the Developmental Therapeutics Program at NCI/NIH. Compounds identified as hits through virtual screening can be obtained from the NCI.
- The ZINC library and libraries from various commercial vendors contain more than 20 million purchasable compounds. While these compounds are not available in-house, the larger library provides a chemical space that is two orders of magnitude larger than the in-house libraries, thus increasing the chance of identifying high quality hits. Individual compounds identified as hits through virtual screening can be purchased from various vendors. (We provide vendor IDs for each compound to facilitate purchasing).
Frequently Asked Questions
Below are some Frequently Asked Questions about our Structure-Based Drug Discovery services.