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Supported Applications

Proteus

  • Description

    a general purpose program for protein design, to redesign entire proteins or functional sites such as ligand-binding pockets. It uses a physics-based energy function and a stochastic method to search sequence and conformation space and allows users to directly select mutations that increase ligand binding free energy or ligand specificity. It can perform constant-pH Monte Carlo, which yields acid/base constants or pKa’s.

  • Usage

    To list all executables provided by Proteus, run: $ sbgrid-list proteus Copy to clipboard

  • Usage Notes

    The command proteus copy /path/to/working_directory can be used to copy the required files that are described in the user manual.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install proteus Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    T. Simonson, T. Gaillard, D. Mignon, M. Schmidt_am_Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart, and G. Archontis. 2013. Computational protein design: the Proteus software and selected applications. Journal of Computational Chemistry. 34(28): 2472-84.


    • *Full citation information available through

  • Citation Note

    Additional citation information can be found at https://proteus.polytechnique.fr/#Credits.

  • Webinars

    Proteus

    Topic: Proteus software for physics-based protein design
    Presenter: Prof. Thomas Simonson, BIOS Research Group, BIOcomputing and Structure, Ecole Polytechnique and the Centre National de la Recherche Scientifique

    Host: Pete Meyer
    Recorded on Dec 13, 2022

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