Virtual screening requires three things:

  • a target (X-ray structure if available, a comparative model otherwise)
  • a database of small molecules (we use ZINC)
  • a program to orient and score the molecules in the protein binding site (we use DOCK 3.5.54, a verison of UCSF DOCK).
There are good reasons why this approach might not work (see caveat lector) such as problems in sampling relevant poses, and problems with the scoring function. Despite these problems, there are a growing number of success stories in the literature using this technique. One reason it has been successful is that failure is relatively cheap when using commercially available libraries, such as ZINC. . If the first compound purchased and tested does not work, it is a simple matter to move on and test the next in a series of docking-prioritized compounds, all of which are commercially available.

For more information of this technology in practice, see success stories.

For more information in its possible problems, see caveat lector.

For possible academic collaborations, and vendors of virtual screening software, both outside of Blue Dolphin, see other docking labs and software.