Difference between revisions of "SCRATCH-1D"

Latest revision as of 20:35, 12 August 2022

Description

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 6.0 (2021) : Protein secondary structure prediction (3-class)
SSpro8 release 6.0 (2021) : Protein secondary structure prediction (8-class)
ACCpro release 6.0 (2021) : Protein relative solvent accessibility prediction (at the 25% threshold)
ACCpro20 release 6.0 (2021) : Protein relative solvent accessibility prediction (thresholds 0% to 95%)
EVALpro release 1.0 (2019) : Evaluation of sequence-based & profile-based predictors
PROFILpro release 2.0 (2021) : Protein evolutionary information / sequence profiles
HOMOLpro release 2.0 (2021) : Homology-based secondary structure & solvent accessibility prediction

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)

@@ Line 1: / Line 1: @@
-[[Category:Software]]
+[[Category:Software]][[Category:biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|scratch1d}}
-|{{#vardefine:url|REPLACE}}
+|{{#vardefine:url|http://download.igb.uci.edu/}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
@@ Line 21: / Line 21: @@
 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)
+*    SSpro release 6.0 (2021) : Protein secondary structure prediction (3-class)
-* ACCpro     Release 5.2  Protein relative solvent accessibility prediction (at the 25% threshold)
+*    SSpro8 release 6.0 (2021) : Protein secondary structure prediction (8-class)
-* ACCpro20   Release 5.2  Protein relative solvent accessibility prediction (thresholds 0% to 95%)
+*    ACCpro release 6.0 (2021) : Protein relative solvent accessibility prediction (at the 25% threshold)
-* PROFILpro  Release 1.1  Protein evolutionary information / sequence profiles for 1D predictors
+*    ACCpro20 release 6.0 (2021) : Protein relative solvent accessibility prediction (thresholds 0% to 95%)
-* HOMOLpro   Release 1.1  Homology-based secondary structure & solvent accessibility prediction
+*    EVALpro release 1.0 (2019) : Evaluation of sequence-based & profile-based predictors
-* 1D-BRNN    Release 3.3  One-dimensional bidirectional recurrent neural networks
+*    PROFILpro release 2.0 (2021) : Protein evolutionary information / sequence profiles
+*    HOMOLpro release 2.0 (2021) : Homology-based secondary structure & solvent accessibility prediction
 <!--Modules-->
@@ Line 33: / Line 35: @@
 Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==