Virtual screening protocols

Inosine 5 -Monophosphate Dehydrogenase. A series of 21 known inosine 5 -monophosphate dehydrogenase (IMPDH) inhibitors was used to validate a virtual screening protocol. By application of a molecular weight filter (80 < MW < 400), 3425 compounds were extracted from an in-house reagent inventory system. Docking of these compounds into a substrate-IMPDH complex 3D structure was performed with the program FlexX three... 

Good A. Structure-based virtual screening protocols. Curr Opin Drug Discov Dev 2001 4 301-7. 

Evers, A., Hessler, G., Matter, H. and Klabunde, T. (2005) Virtual screening of biogenic amine-binding G-protein coupled receptors comparative evaluation of protein- and ligand-based virtual screening protocols. 

Smith, R., Hubbard, R.E., Gschwend, D.A., Leach, A.R., and Good, A.C. Analysis and optimization of stmcture-based virtual screening protocols (3). New methods and old problems in scoring function design. 

Chart 8 Chemical structures of the CA4 boronic acid bioisostere (9) and of MDL-27048. The former was proposed by a structure-based molecular modeling study, the latter was used to elaborate a virtual screening protocol for the identification of novel chalcone CSI... 

The shape-based virtual screening protocols performed better than the docking protocols overall. Finally, a consensus rank-byvote selection technique was used and the five best compounds were selected from the hits for synthesis and for determining antiviral activity. Remarkably, two of the five compounds (Fig. 13) showed activity at low micromolar ranges (0.022 pg/mL and 0.058 pg/mL, respectively). 

Figure 3.3 Selection of n molecules from a database containing N entries by a virtual screening protocol.

Good AC, Cheney DL. Analysis and optimization of structure-based virtual screening protocols (1) exploration of ligand conformational sampling techniques. J Mol Graph Model 2003 22(l) 23-30. 

Pvaluation of the performance of 3D virtual screening protocols RMSD comparisons, enrichment assessments, and decoy selection what can we learn from earlier mistakes Journal of Computer-Aided Molecular Design, 22 (3-4), 213-228. 

---