ConfBuster: Open-Source Tools for Macrocycle Conformational Search and Analysis. Issue 1 (8th January 2018)

• Record Type: Journal Article
• Authors: Barbeau, Xavier; Vincent, Antony T.; Lagüe, Patrick
• Is Part Of: Journal of open research software. Volume 6:Issue 1(2018)
• Publication Date: 2018-01-08
• Subjects: Macrocycles -- conformational search -- conformational sampling -- molecular modelling -- open-source tools -- click chemistry tools -- cheminformatics -- rational drug design -- drug development; Computer software -- Reusability -- Periodicals; Open source software -- Periodicals; 005
• DOI: 10.5334/jors.189
• Languages: English
• ISSNs: 2049-9647

Abstract

Macrocycles are cyclic macromolecules that have gained an increased interest in drug development. To our knowledge, the current bioinformatics tools that are available to investigate and predict macrocycles 3D conformations are limited in their availability. In this paper, we introduce ConfBuster, a suite of tools written in Python with the goal of sampling the lower energy conformations of macrocycles. The suite also includes tools for the analysis and visualisation of the conformational search results. Coordinate sets of single molecules in MOL2 or PDB format are required as input, and a set of lower energy conformation coordinates is returned as output, as well as PyMOL script and graphics for results analysis. In addition to Python and the optional R programming languages with freely available packages, the tools require Open Babel and PyMOL to work properly. For several examples, ConfBuster found macrocycle conformations that are within few tenths of Å of the experimental structures in minutes. To our knowledge, this is the only open-source tools for macrocycle conformational search available to the scientific community.