Profasp

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Contents

INTRO

ASP predicts conformational switches, i.e. it looks for switches that involve transitions between secondary structure types. The program was developed by MM Young, K Kirshenbaum, KA Dill and S Highsmith. ASP was designed to identify the location of conformational switches in proteins with known switches. It is NOT designed to predict whether a given sequence does or does not contain a switch. For best results, ASP should be used on sequences of length >150 amino acids with >10 sequence homologues in the SWISS-PROT data bank. ASP has been validated against a set of globular proteins and may not be generally applicable. Please see Young et al., Protein Science 8(9):1752-64. 1999. for details and for how best to interpret this output. We consider ASP to be experimental at this time, and would appreciate any feedback from our users.

Availability/Web server

This program can be accessed via the PredictProtein service.

Recommended Packages

In order to properly run ASP(called profasp) you will need to install the following packages. These will be used to create the required ASP input files.

  • PROFphd - Secondary structure and solvent accessibility predictor.

Generating Input Files for ASP

ASP takes 3 input files:

  • rdbProf_file - Secondary structure and solvent accessibility prediction by PROFphd in rdb format.

Generating an rdbProf File

Generating an rdbProf file requires generating an HSSP input file. The HSSP input file is used as input to the prof program.

 prof <filtered_hssp_file> both numresMin=17 nresPerLineAli=60 riSubSec=4 riSubAcc=3 fileRdb=<rdbProf_file>

Running ASP

Please see the profasp man page:

 man profasp

Questions

Please see the FAQ section or contact the maintainer

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