Software

I contributed to multiple predictors and tools in the renowned SCRATCH suite of predictors of the Institute for Genomics and Bioinformatics. All these predictors can be used online via the SCRATCH interface and most of them are available for download as standalone packages on the SCRATCH download page. All software and related material on these pages can be downloaded and used freely for academic, non-commercial, research purposes only. For any other use, please contact Pierre Baldi. The predictors or tools I contributed to are listed below.


• SSpro releases 5.x Protein secondary structure prediction 3 classes.
• SSpro8 releases 5.x Protein secondary structure prediction 8 classes.
• ACCpro releases 5.x Protein relative solvent accessibility prediction 2 classes.
• ACCpro20 releases 5.x Protein relative solvent accessibility prediction 20 classes.
• 1D-BRNN releases 3.x One-dimensional bidirectional recurrent neural networks.
• PROFILpro releases 1.x Protein evolutionary information / sequence profiles.
• HOMOLpro releases 1.x Homology-based secondary structure & solvent accessibility prediction.
• SCRATCH-1D releases 1.x Suite of 1D predictors including all of the above predictors and tools.
• EVALpro releases 1.x Profile-similarity-based evaluation of profile-based predictors.
• SOLpro releases 1.x Prediction of protein solubility upon overexpression.
• ANTIGENpro releases 1.x Prediction of protein antigenicity.
• VIRALpro releases 1.x Prediction of capsid and tail proteins.

For the latest releases of this software, the corresponding citations, and the full list of predictors included in SCRATCH, please visit directly the SCRATCH homepage, online documentation, and download page.