Correcting the impact of docking pose generation error on binding affinity prediction.

ABSTRACT:

Background

Pose generation error is usually quantified as the difference between the geometry of the pose generated by the docking software and that of the same molecule co-crystallised with the considered protein. Surprisingly, the impact of this error on binding affinity prediction is yet to be systematically analysed across diverse protein-ligand complexes.

Results

Against commonly-held views, we have found that pose generation error has generally a small impact on the accuracy of binding affinity prediction. This is also true for large pose generation errors and it is not only observed with machine-learning scoring functions, but also with classical scoring functions such as AutoDock Vina. Furthermore, we propose a procedure to correct a substantial part of this error wh

SUBMITTER: Li H 

PROVIDER: S-EPMC5046193 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature