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Reducing Docking Score Variations Arising from Input Differences
Miklos Feher and Christopher I. Williams
J. Chem. Inf. Model., 2010, 50 (9), pp 1549–1560

In this interesting work, the authors describe the dependence of docking results from a) the adequacy of conformational search during docking and b) and random chaotic effects, which have moreover a strong effect on reproducibility. They investigated FlexX, Surflex, Gold, and Glide. It turns out that e.g. for FlexX, the dependence on insufficient coverage of conformational sampling (which is the reason for the docking speed of <10 s per compound) is larger than the stochastic/chaotic behavior. In fact, the latter is almost negligible for FlexX. Thus, this finding shows that FlexX is extremely reliable, and results are very well reproducible. Moreover, the conformational sampling can be adjusted in the parameters.
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Three-Dimensional Pharmacophore Modeling of Liver-X Receptor Agonists
Wenxia Zhao, Qiong Gu, Ling Wang, Hu Ge, Jiabo, Li, and Jun Xu
J. Chem. Inf. Model., Article ASAP

Liver X receptors are efficient drug targets for the treatment of hyperlipidemia. The authors show how they used a set of known LXRβ antagonists to build a pharmacophore model; they subsequently used FlexX to verify it - and eventually showed agonist activity of the discovered compounds.
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