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 only.

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


Copyright 2005-2011. Institute for Genomics and Bioinformatics. University of California, Irvine. USA.


1. SSpro, SSpro8, ACCpro, ACCpro20 : Protein Secondary Structure and Relative Solvent Accessibility Prediction

The 4 predictors are included in the SCRATCH suite of 1D predictors available for download here:

SCRATCH-1D release 1.1 (linux version, 2.7 GB), installation instructions, documentation, training sets. The package currently includes: Version 4.0 of SSpro and ACCpro is still available here: sspro4.tar.gz.

References:

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. [PDF] [PDF at Bioinformatics website]

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

References:
[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 & 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:
C. N. Magnan, A. Randall, & P. Baldi. SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics, vol. 25, 17, (2009). [PDF]



9. SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations

SIDEpro predicts side-chain conformations for protein backbones. SIDEpro can accommodate non-standard amino acids including PTMs.
Download Linux version | Installation instructions | Rotamer library | SIDEpro training set|FPTM set |NSA dataset
download/install sizes:(165 Mb, 210 Mb)

Reference:
K. Nagata, A. Randall, & P. Baldi. SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations. Proteins , vol. 80, 1, (2012).


10. Polymorphic Antigen Cross Reactivity Analysis

The archive file consists of Perl scripts and data files to replicate the computational analysis presented in the manuscript. Download | Download Windows version | Overview
download sizes:(1.0 Mb)

Manuscript submitted for review December 2012:
E. Baum, A. Randall, M. Zeller, P. Baldi, & A. Barbour. Quantifying cross-reactive antibody binding and inferring epitopes among Borrelia burgdorferi OspC variants using protein microarray data


11. VIRALpro: Prediction of capsid and tail proteins

VIRALpro release 1.0 (linux version, 25 MB) | installation instructions | Experimental Data

Manuscript submitted for review August 2015.



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

Contact:
For technical issues, please email pfbaldi@ics.uci.edu and yuzok [at] ics [dot] uci [dot] edu.
For commercial licenses, please email igb-license [at] ics [dot] uci [dot] edu.