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.

Virtual Screening in Drug Discovery
Edited by Juan Alvarez and Brian Shoichet, Taylor and Francis, Florida (2005)

This book, edited by Juan Alvarez and Brian Shoichet, compiles 16 chapters in 5 parts that target different strategies of virtual screening and docking. One of the 16 chapters is dedicated to the Flex* approach to virtual screening. It lists advanced concepts for VS tools, such as FlexX^C for docking combinatorial libraries or FlexX-Pharm for docking under pharmacophore constraints, respectively. The handling of large amounts of VS data is facilitated with the docking database (DDB), an ORACLE® -based application for uploading and organizing docking data to make it a routine task. With the help of the Seeker^TM, its graphical front end, applying sophisticated filter functions becomes easy and also scriptable.

Design of Small-Sized Libraries by Combinatorial Assembly of Linkers and Functional Groups to a given Scaffold: Application to the Structure-Based Optimization of a Phosphodiesterase 4 Inhibitor
Mireille Krier, João X. de Araújo-Júnior, Martine Schmitt, Jérôme Duranton, Hélène Justiano-Basaran, Claire Lugnier, Jean-Jacques Bourguignon, and Didiér Rognan
J. Med. Chem. 48(11), 3816-3822 (2005)

The authors describe the scaffold-linker-functional group approach (SLFa) in order to minimize the size of a virtual library while maximizing the diversity, for combinatorial enumeration of a PDE4-focused library. For their docking experiments, they chose FlexX over Gold and Surflex, because only FlexX docked the original ligand, zardaverine, with reliable accuracy (below 2.0 Å with respect to the X-ray structure) into the binding site of the protein (1Q9M, 1MKD).

Virtual docking approaches to Protein kinase B inhibition
Martino Forino, Dawoon Jung, John B. Easton, Peter J. Houghton, and Maurizio Pellecchia
J. Med. Chem. 48 (7), 2278-2281 (2005)

In this paper several virtual screening strategies were followed for finding low micro molar Protein Kinase B (Akt) inhibitors. A successful strategy turned out to be the usage of FlexX with consensus scoring, coupled with visual analysis of the produced docking poses. Taking the knowledge of observed H-bonding interactions into account, 3 out of 30 selected compounds were found to be active.