ChemRxiv
These are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information. For more information, please see our FAQs.
Mendenhall_Brown_MeilerBCLConf2_ChemRxiv.pdf (1002.93 kB)
0/0

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

preprint
submitted on 06.04.2020 and posted on 09.04.2020 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

Find out more...

Computational Design of Protein-Ligand Interfaces - a Therapeutic Strategy

National Institute of General Medical Sciences

Find out more...

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

Find out more...

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.

Exports