PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.

ABSTRACT: Often in pharmaceutical research the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket-based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct

SUBMITTER: Roy A 

PROVIDER: S-EPMC4593500 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature