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

Benchmark files

• 3UWPA: basic test of the method
• input_glyc: test of the support for glycosylation

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:

Testable: Yes.

Parallelizeable: Yes

Publications:

• Weinkam P, Pons J, Sali A., Proc Natl Acad Sci USA. (2012) 109, 4875-80.
• Guttman M, Weinkam P, Sali A, Lee KK, Structure (2013) 21, 321-31.