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.

FlexNovo: structure-based searching in large fragment spaces.
J. Degen and M. Rarey
Chem. Med. Chem., 1(8), 854-68 (2006)

The authors report on a novel De Novo design software called FlexNovo, which searches large fragment spaces, following a sequential growth strategy. It is based on the FlexX molecular docking software, using its chemical models as well as its underlying incremental construction algorithm. It has been validated by designing potential inhibitors for pharmaceutically relevant targets such as COX-2, CDK2 or ER. Reproduced structural motifs often resemble those seen in known actives.
Link to article: http://www3.interscience.wiley.com/cgi-bin/abstract/112735265/ABSTRACT

Prediction of Multiple Binding Modes of the CDK2 Inhibitors, Anilinopyrazoles, Using the Automated Docking Programs GOLD, FlexX, and LigandFit: An Evaluation of Performance.
H. Sato, L. M. Shewchuk, and J. Tang
J. Chem. Inf. Model., ASAP article

The authors describe the evaluation of FlexX, Gold, and LigandFit on CDK2 inhibitors using 63 anilinpyrazole inhibitor analogues as ligands. These are particularly interesting because they can adopt multiple binding modes. It is shown that for this target class, FlexX provides equally good results with both flexxscore and drugscore.
Link to article: http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/asap/abs/ci600186b.html

Virtual Screening for beta-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228.
T. Polgár and G. M. Keserü
J. Med. Chem., 48, 3749-3755 (2005)

The authors describe how they significantly improved their screening results with FlexX for beta-secretase (BACE1) inhibitors by applying calculated protonation states to catalytic Asp32 and Asp228 amino acid residues. Using these important protonation states, enrichment at 1% of the database could be improved up to 36, using FlexX-Pharm even further improves enrichment to 41. This publication shows the importance of careful preparation of the investigated system.
Link to article: http://pubs.acs.org/cgi-bin/abstract.cgi/jmcmar/2005/48/i11/abs/jm049133b.html