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AllosMod benchmark

Benchmark of the AllosMod method PubMed logo

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tickVerified to work with the latest stable IMP release (2.20.2). The files are also available at GitHub.
Additional software needed to use these files: IMP allosmod MODELLER install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp modeller

UCSF logo To set up the environment on the UCSF Wynton cluster to run this system, run:

module load Sali
module load imp allosmod modeller
Tags allostery benchmark glycosylation MODELLER

This benchmark tests the AllosMod method, as implemented in the AllosMod library and AllosMod web service.

Benchmark files

To run the benchmark, first install AllosMod and its dependencies. Then, in each directory, run allosmod setup to check the input files; this will generate a file qsub.sh. Run this script to set up the system. In the 3UWPA case, this is in turn will generate input files for MODELLER which should be run with that program.

Information

Author(s): Patrick Weinkam, Ben Webb

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version: build info build info

Testable: Yes.

Parallelizeable: Yes

Publications: