Posts tegged as 'virtual screening'

Computational methods applied to the discovery of stem cell factor ligands

A computational study of the stem cell factor (SCF) and potential ligands was carried out starting with a crystallographic model deposited in the protein data bank. The inhibition of the SCF dimerization equilibrium was considered as the rationale for the lead identi?cation of spe- ci?c ligands. A preliminary molecular dynamics characteri- zation of the SCF dimer allowed to verify the most ?exible loop involved in the dimeric area. Then a virtual screening, coupled with energy minimization in GB/SA water, scored the compounds implemented in the NCI diversity molecu- lar database. Ten top ranked ligands were analyzed conside- ring both the SCF loop perturbation in the dimerization area and the network of intermolecular hydrogen bonds. Among these ten compounds two natural agents were identi?ed. The computational work revealed useful new insights for rational design of novel SCF dimerization inhibitors.

Visit publication

Practical virtual screening using the Instant JChem platform

Apr 19, 2013Daniel Butler

Silicon and Iron have been “co-operating” for a very, very long time.

Silicon and Iron have been “co-operating” under pressure for a very, very long time…

The problem

Virtual screening (VS) is not a definitive answer to finding the needle in the haystack but it can provide a sensible set of starting points relative to “random”. The available screening techniques are many and varied in design and approach and use different molecular representations, alignments (or not), scoring functions and if available, use information obtained from the target protein. The merits of 2D vs 3D screening are much debated within the literature coming down marginally favourably on the side of 2D (interestingly of course, since 2D does not inherently consider chirality) methods being more effective at isolating true positives 1.

Read the more »