BCL::Conf – Improved Open-Source Knowledge-Based Conformation Sampling using the Crystallographic Open Database

Jeffrey Mendenhall; Benjamin Brown; Sandeepkumar Kothiwale; Jens Meiler

doi:10.26434/chemrxiv.12085521.v1

Theoretical and Computational Chemistry

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BCL::Conf – Improved Open-Source Knowledge-Based Conformation Sampling using the Crystallographic Open Database

09 April 2020, Version 1

Working Paper

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This content is an early or alternative research output and has not been peer-reviewed by Cambridge University Press at the time of posting.

Abstract

This paper describes recent improvements made to the BCL::Conf rotamer generation algorithm and comparison of its performance against other freely available and commercial conformer generation software. We demonstrate that BCL::Conf, with the use of rotamers derived from the COD, more effectively recovers crystallographic ligand-binding conformations seen in the PDB than other commercial and freely available software. BCL::Conf is now distributed with the COD-derived rotamer library, free for academic use. The BCL can be downloaded at http://meilerlab.org/ bclcommons for Windows, Linux, or Apple operating systems.

Keywords

Conformer Sampling

Computer-Aided Drug Design

open-source tool

knowlege-based

Small Molecule Drug Discovery Drug discovery

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