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).

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)