Difference between revisions of "SCRATCH-1D"

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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
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{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Revision as of 21:24, 6 December 2019

Description

scratch1d website  

SCRATCH-1D is a suite of one-dimensional predictors included in the long-established and widely used SCRATCH suite of predictors developed by the Institute for Genomics and Bioinformatics (IGB) of the University of California, Irvine (UCI).

SCRATCH-1D currently includes the following predictors and tools:

  • SSpro Release 5.2 Protein secondary structure prediction (3-class)
  • SSpro8 Release 5.2 Protein secondary structure prediction (8-class)
  • ACCpro Release 5.2 Protein relative solvent accessibility prediction (at the 25% threshold)
  • ACCpro20 Release 5.2 Protein relative solvent accessibility prediction (thresholds 0% to 95%)
  • PROFILpro Release 1.1 Protein evolutionary information / sequence profiles for 1D predictors
  • HOMOLpro Release 1.1 Homology-based secondary structure & solvent accessibility prediction
  • 1D-BRNN Release 3.3 One-dimensional bidirectional recurrent neural networks

Environment Modules

Run module spider scratch1d to find out what environment modules are available for this application.

System Variables

  • HPC_SCRATCH1D_DIR - installation directory




Citation

If you publish research that uses scratch1d you have to cite it as follows:

  • C.N. Magnan & P. Baldi (2014). SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity.

Bioinformatics, vol 30 (18), 2592-2597

  • J. Cheng, A. Randall, M. Sweredoski, & P. Baldi. SCRATCH: a Protein Structure and Structural Feature Prediction Server.

Nucleic Acids Research, vol. 33 (web server issue), w72-76, (2005)