BIROn - Birkbeck Institutional Research Online

    PyFolding: an open-source software package for graphing, simulation and analysis of the biophysical properties of proteins

    Lowe, Alan R. and Perez-Riba, A. and Itzhaki, L.S. and Main, E.R. (2017) PyFolding: an open-source software package for graphing, simulation and analysis of the biophysical properties of proteins. Biophysical Journal 114 (3), pp. 516-521. ISSN 0006-3495.

    [img] Text
    PyFolding_FINAL_BiophsJFormat.pdf - Author's Accepted Manuscript
    Restricted to Repository staff only until 7 February 2019.

    Download (2MB) | Request a copy

    Abstract

    For many years, curve fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large datasets. One field that is relient on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we present PyFolding, a free, open source, and extensible Python framework for graphing, analysis and simulation of the biophysical properties of proteins. To demonstrate the utility of PyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: (i) multi-phase kinetic folding fitted to linked equations, (ii) global fitting of multiple datasets and (iii) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate how Pyfolding is easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show that PyFolding can be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and amongst research teams.

    Metadata

    Item Type: Article
    School: Birkbeck Schools and Departments > School of Science > Biological Sciences
    Depositing User: Alan Lowe
    Date Deposited: 04 Dec 2017 10:48
    Last Modified: 01 Jun 2018 14:50
    URI: http://eprints.bbk.ac.uk/id/eprint/20522

    Statistics

    Downloads
    Activity Overview
    1Download
    48Hits

    Additional statistics are available via IRStats2.

    Archive Staff Only (login required)

    Edit/View Item Edit/View Item