SCRATCH-1D

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) : 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:

• 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)

Categories

biology, ngs