One of the projects underway at the NMPDR is generating in silico docking results for proteins that are believed to be good drug targets. For each selected protein, its PDB is selected from the Protein Data Bank and compared against a database of over 3 million ligands taken from the ZINC database. For each PDB put through this process, the NMPDR selects from 55 to 60 significant results. The results are displayed on the Drug Target Search Form. Simply select a PDB in the dropdown box, and the docking energies computed for the ligands will be displayed. The energies displayed are in kcal/mol. The total energy is divided into two components: Van der Waals energy is computed from the shapes of the interlocking surfaces; Electrostatic energy is computed from the electrical attraction between the molecules.
Topic revision: r2 - 22 Jan 2008 - 03:52:31 - BruceParrello
NMPDR is a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.