Open Access Highly Accessed Methodology article

Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences

Adam Amos-Binks1, Catalin Patulea3, Sylvain Pitre1, Andrew Schoenrock1, Yuan Gui2, James R Green3, Ashkan Golshani2 and Frank Dehne1*

  • * Corresponding author: Frank Dehne frank@dehne.net

  • † Equal contributors

Author Affiliations

1 School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada

2 Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada

3 Department of Systems and Computer Engineering, Carleton University, Ottawa, ON K1S5B6, Canada

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BMC Bioinformatics 2011, 12:225  doi:10.1186/1471-2105-12-225

Published: 2 June 2011

Additional files

Additional file 1:

Pairs of yeast proteins with lab-confirmed binding sites. This file contains 265 pairs of interacting yeast proteins, with associated amino acid ranges for the binding sites on each protein, extracted from DOMINO [26], and used as validation data. Each line represents one pair, with the following fields tab-separated: ORF name of protein A, ORF name of protein B, start position of binding site along protein A, end position of binding site along protein A, start position of binding site B, end position of binding site B.

Format: TXT Size: 9KB Download file

Open Data

Additional file 2:

Pairs of human proteins with lab-confirmed binding sites. This file contains 423 pairs of interacting human proteins, with associated amino acid ranges for the binding sites on each protein, extracted from DOMINO [26], and used as validation data. Each line represents one pair, with the following fields tab-separated: Uniprot accession of protein A, Uniprot accession of protein B, start position of binding site along protein A, end position of binding site along protein A, start position of binding site B, end position of binding site B.

Format: TXT Size: 13KB Download file

Open Data