Section: New Results

Participation in the D3R Grand Challenge 2 with the Convex-PL scoring function

Participants : Sergei Grudinin, Maria Kadukova.

Figure 13. Structural heterogeneity of the target FXR proteins.

We have participated in the pose prediction stage of the D3R Grand Challenge 2 using Convex-PL to re-score the ligand poses obtained with Autodock Vina. The target protein of this challenge was a farnesoid X receptor (FXR). After the correct co-crystal poses were released, we carefully repeated the experiments and compared them with several other docking protocols. For these protocols we have used a modified version of Autodock Vina with Convex-PL as a built-in scoring function used in sampling. The protocols we have tried include comparison of docking to various co-crystal and mutated co-crystal FXR structures, as well as docking to the correct protein structures to evaluate the influence of receptor flexibility and docking of ligand structures generated with two different algorithms, as well as the co-crystal ones. This study was published in the Journal of Computer-Aided Molecular Design. [9]