pyscreener: A Python Wrapper for Computational Docking Software

Abstract

pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to calculate the docking score of a given molecule in a specified active site. Additionally, pyscreener features first-class support for task distribution, allowing users to seamlessly scale their code from a local, multi-core setup to a large, heterogeneous resource allocation.

Identification of Corosolic and Oleanolic Acids as Molecules Antagonizing the Human RORγT Nuclear Receptor Using the Calculated Fingerprints of the Molecular Similarity

“…For the docking studies, the smina program was used, which is a fork of AutoDock Vina [68] coupled with the pyscreener library [69]. As a receptor, the crystallographic structure retrieved from the PDB database was chosen [70]; in particular, the 3l0j structure with a bound natural ligand-25-hydroxycholesterol-was taken [32].…”

“…All considered stereoisomers were docked into the receptor within the Pyscreener module with the smina docking program in the backend. Pyscreener allows for the automation of the docking procedure and the application of high-throughput virtual screening within the Python ecosystem [69]. The docking calculation was oriented on the orthosteric pocket of the 3l0j receptor.…”