UCSF Laboratory of Andrej Sali QB3

 

SOAP

All of the SOAP potentials listed here can be used in IMP (2.2.0 or later) or Modeller (9.13 or later).

SOAP-PP

soap_pp_atom.hdf5 and soap_pp_pair.hdf5 are distributed with Modeller (in the modlib directory) and can be used with the soap_pp.Assessor class. Equivalently in IMP, soap_score_sas.lib and soap_score.lib store the same data, are distributed with the IMP.score_functor module, and can be used with the IMP.score_functor.SingletonStatistical and IMP.score_functor.Soap classes, respectively.

Sets of training decoys for SOAP-PP: pp_small.tar.gz
Sets of testing decoys for SOAP-PP: pp_small.tar.gz, link to the ZDOCK decoys.
Original script for using SOAP-PP to assess loop structures (requires Modeller and MDT): soap_pp.tar.gz.

SOAP-Loop

SOAP-Loop library file. For use with IMP (2.2.0 or later) or Modeller (9.13 or later).

Sets of training decoys for SOAP-Loop: loop.tar.gz.
Sets of testing decoys for SOAP-Loop: link to PLOP loop decoys.
Original script for using SOAP-Loop to assess loop structures (requires Modeller and MDT): soap_loop.tar.gz.

SOAP-Peptide

SOAP-Peptide library file. For use with IMP (2.2.0 or later) or Modeller (9.13 or later).

SOAP-Protein

SOAP-Protein library file. For use with IMP (2.2.0 or later) or Modeller (9.13 or later).

Source code and documentation

SOAP source code can be found on github. Documentation is also available.

Andrej Sali, PhD, Professor, Department of Bioengineering and Therapeutic Sciences; Department of Pharmaceutical Chemistry; School of Pharmacy, University of California at San Francisco, UCSF MC 2552, Mission Bay, Byers Hall, 1700 4th Street, Suite 503B, San Francisco, CA 94143, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, 4234, , Web https://salilab.org