We will be making a regular point of providing you with the latest publications, reports and papers including developments and products from BioSolveIT and its associated owners.
FlexX-Scan: Fast Structure-Based Virtual Screening.
I. Schellhammer and M. Rarey
PROTEINS: Structure, Function, and Genetics 2004, 57, p504-517.
The article describes a new FlexX extension module specially designed for virtual high throughput screening. The novel product is called FlexX-Scan and requires only a few seconds per compound. For sample cases, the authors report and discuss results similar or superior to standard FlexX computations.
Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results
A.E. Klon, M. Glick, and J.W. Davies
J. Med. Chem.; (Letter); 2004; 47(18); 4356-4359
Klon et al. describe a protocol for improving enrichment ratios of docking experiments. The authors use FlexX-generated dockings and a couple of available scoring functions as the basis of their study. The protocol they suggest is as follows: docking -> consensus scoring -> reranking by ML. The rank-by-rank based on the median of ranks was found to be the most consistently successful consensus scoring method. As the Machine Learning method the authors used naive bayes classification based on the assumption that the top 1% of the dataset represents the 'wanted compounds'. The enrichment in the top 1 percentile could be increased by up to a factor of three.
Virtual Screening: finding needles in a haystack on a shoestring
D.E. Clark, N.V. Harris, A.G. Roach, and A.D. Baxter
Drug Discovery World, 2:37-41, 2004
The authors describe the virtual screening infrastructure at Argenta Discovery. On the basis of comparably small resources of a small biotech company the so-called 'rapid reaction terms' paradigm was established, which integrates CADD tightly with biochemistry and medicinal chemistry. The result is an efficient discovery workflow in which FlexX and FlexS among a few other tool are explicitly named as the virtual screening workhorses. A couple of successfully accomplished projects are outlined as a proof of concept.