Projects start with a consultation with our director to determine the feasibility of a computational approach. Once it is determined which services are needed, a user agreement describing the services and the cost is then drafted and sent to the user for approval or modification. Once the agreement is approved, the services start. A project usually includes additional meetings between the user and our staff to clarify approaches and to discuss results.

Virtual screening for small-molecule ligands requires a 3D structure of the target protein (target-based virtual screening) or at least one active compound (ligand-based virtual screening). Additionally, an assay should be available to test the compounds selected using the virtual screen.

No. Usually 20 to 200 compounds are selected from a virtual screen for experimental testing. A low-throughput assay is generally sufficient for this.

In many cases, the structure of the target protein can be modeled based on a homolog of known structure. We provide protein structure modeling services. Alternatively, if at least one active compound is known, ligand-based virtual screening can be used, which does not require a target structure.

Yes. We can fine-tune target-based virtual screening approaches to increase the chances of identifying additional active compounds. The active compounds can be used to initiate ligand-based virtual screening. Also, we can identify purchasable compounds similar to the existing hits to facilitate initial structure-activity relationship studies.

The commercial libraries contain two orders of magnitude more compounds than the Mount Sinai and National Cancer Institute (NCI) libraries. They provide a much larger chemical search space, which increases the chances of finding high-quality (active) hits. Commercial compounds are not available in-house, and hits obtained from a screen of these libraries must be purchased from vendors. Our library compounds are maintained in-house and are usually available for experimental validation in a day or two for a nominal fee. NCI compounds can be obtained free-of-charge from the NCI; only shipping costs need to be covered.

Yes. If a structure of the target protein is available (or can be modeled), molecular docking can be used to model the interaction of the known (active) compounds with the protein.