Welcome to the SCRATCH download page.



Thank you for your interest. All software and related material contained herein can be downloaded freely for academic, non-commercial, research use on ly.

For any other use, please contact pfbaldi@ics.uci.edu.


Copyright 2006. Institute for Genomics and Bioinformatics. University of California, Irvine. USA.

1. SSpro/ACCpro 4.03: Protein Secondary Structure (3-class) and Solvent Accessibility(20-class) Prediction

Download SSpro and ACCpro 4.03 package (Linux version (1.6GB), Solaris version (3.1GB) ) | Access SSpro 4.0 Web Server | Installation instructions.
SSpro/ACCpro 4 is the first hybrid approach of combining neural network (ab initio) and homology analysis to improve the prediction of secondary structure and solvent accessibility.

Reference:
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.[PDF] [PDF at NAR website]

2. MUpro 1.1: Prediction of Stability Changes (delta delta G) of Single Site Mutations from Protein Sequences

Download MUpro 1.1 source code and executable (200K, Linux version) | Installation instructions | Access MUpro server | MUpro dataset (1615 mutations) | MUpro dataset (388 mutations)

Reference:
J. Cheng A. Randall, P. Baldi. Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines. Proteins, vol. 62, no. 4, pp. 1125-1132, 2006. [PDF][PDF at Proteins website]

3. DOMpro 1.0: Protein Domain Prediction

Download DOMpro 1.0 (Linux version, about 1M) | Access DOMpro web server | Multi-domain dataset | Single domain dataset

Reference:
J. Cheng, M. Sweredoski, P. Baldi. DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. Knowledge Discovery and Data Mining, vol. 13, no. 1, pp. 1-20, 2006. [PDF]

4. DIpro 2.0: Protein Disulfide Bond Prediction

Download DIpro 2.0 here (Linux version) | Access DIpro Web Server |Download Dataset

Reference:
[1] J. Cheng, H. Saigo, P. Baldi, Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching, Proteins, vol. 62, no. 3, pp. 617-629, 2006. [PDF] [PDF at Proteins website]
[2] P. Baldi, J. Cheng, A. Vullo, Large-Scale Prediction of Disulphide Bond Connectivity , Advances in Neural Information Processing Systems 17 (NIPS 2004), L. Saul,Y. Weiss, and L. Bottou editors, MIT press, pp.97-104, Cambridge, MA, 2005. [PDF] [PDF at NIPS website]

5. BETApro 1.0: Prediction of beta-residue pairs, beta-strand pairs, strand alignment, pairing direction, and beta-sheet topology.

Download BETApro1.0 here (Linux version) | Access BETApro Web Server| Download Dataset

Reference:
J. Cheng and P. Baldi, Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms, Bioinformatics, vol. 21, Suppl 1, pp. i75-84, 2005. [PDF] [PDF at Bioinformatics website]

6. DISpro1.0: Prediction of disordered regions from protein sequences.

Download DISpro1.0 here (Linux version) |Access DISpro Web Server |Download Dataset
Click here or see readme.txt in the zip file for the installation instructions.

Reference:
J. Cheng, M. Sweredoski, P. Baldi, Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data, Data Mining and Knowledge Discovery, vol. 11, no. 3, pp. 213-222, 2005. [PDF] [PDF at DAMI website]


7. SELECTpro: Protein Model Scoring/Selection and Side-Chain Prediction.
Access SELECTpro Web Server

SELECTpro 1.0: full version includes bundled feature predictors
download/install sizes:(680 Mb, 1.6 Gb)
Download SELECTpro1.0 (Linux version)| Overview and Installation Instructions

SELECTpro Solo: does not include feature predictors
download/install sizes:(3 Mb, 13 Mb)
Download SELECTpro Solo (Linux version)| Overview and Installation Instructions
Reference:
A. Randall, P. Baldi, SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERS, BMC Structural Biology, vol. 8, 52, 2008. [PDF]


8. SOLpro: Prediction of protein solubility upon overexpression

Download SOLpro (12Mb, Linux version) | Installation instructions | Access SOLpro server | Download Dataset | Cross-validations

Reference: manuscript submitted.

Acknowledgements
Third-party tools used in the software: BLAST, PSI-BLAST, and SVM-light.

Contact:
For technical problems, please contact Paul Rigor at prigor@ics.uci.edu
For commercial license, please contact Pierre Baldi at pfbaldi@ics.uci.edu