SCRATCH-1D¶

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) : http://scratch.proteomics.ics.uci.edu.

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

SSpro Release 5.1 Protein secondary structure prediction (3-class) - SSpro8 Release 5.1 Protein secondary structure prediction (8-class) - ACCpro Release 5.1 Protein relative solvent accessibility prediction (at the 25% threshold) - ACCpro20 Release 5.1 Protein relative solvent accessibility prediction (thresholds 0% to 95%)
PROFILpro Release 1.0 Protein evolutionary information / sequence profiles for 1D predictors - HOMOLpro Release 1.0 Homology-based secondary structure & solvent accessibility prediction - 1D-BRNN Release 3.2 One-dimensional bidirectional recurrent neural networks

Environment Modules¶

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

Environment Variables¶

HPC_SCRATCH1D_DIR - installation directory

Citation¶

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

Magnan, C. N., & Baldi, P. (2014). SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. Bioinformatics, 30(18), 2592-2597. https://doi.org/10.1093/bioinformatics/btu352

Cheng, J., Randall, A., Sweredoski, M., & Baldi, P. (2005). SCRATCH: a Protein Structure and Structural Feature Prediction Server. Nucleic Acids Research, 33(Web Server issue), W72-W76. https://doi.org/10.1093/nar/gki396

Categories¶

biology, ngs