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Mendenhall_Brown_MeilerBCLConf2_ChemRxiv.pdf (1002.93 kB)

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

preprint
submitted on 06.04.2020, 05:30 and posted on 09.04.2020, 05:50 by Jeffrey Mendenhall, Benjamin Brown, Sandeepkumar Kothiwale, Jens Meiler
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.

Funding

Structural Determinants of Allosteric Modulation of Brain GPCRs

National Institute on Drug Abuse

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Computational Design of Protein-Ligand Interfaces - a Therapeutic Strategy

National Institute of General Medical Sciences

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Targeting receptor tyrosine kinases with novel methods in computer-aided drug discovery for the treatment of fibrotic renal disease

National Institute of Diabetes and Digestive and Kidney Diseases

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History

Email Address of Submitting Author

benjamin.p.brown17@gmail.com

Institution

Vanderbilt University

Country

United States

ORCID For Submitting Author

0000-0001-5296-087X

Declaration of Conflict of Interest

The authors report no conflicts of interest.

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