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Open Access Research article

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps

Kevin Y Yip12, Lukas Utz3, Simon Sitwell3, Xihao Hu2, Sachdev S Sidhu378, Benjamin E Turk4, Mark Gerstein156 and Philip M Kim3789*

Author Affiliations

1 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA

2 Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong

3 Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada

4 Department of Pharmacology, Yale University, New Haven, CT, USA

5 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA

6 Department of Computer Science, Yale University, New Haven, CT, USA

7 Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada

8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

9 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

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BMC Biology 2011, 9:53  doi:10.1186/1741-7007-9-53

Published: 11 August 2011

Additional files

Additional file 1:

Correlation between covariation score and physical proximity between each PRD site and each PWM position for the three types of PRDs when distances are computed between residue centers. Figure S1.

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Open Data

Additional file 2:

Correlation between covariation score and physical proximity between each PRD site and each PWM position for the three types of PRDs when distances are computed between alpha carbon atoms. Figure S2.

Format: PDF Size: 183KB Download file

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Open Data

Additional file 3:

Correlation between covariation score and physical proximity between each PRD site and each PWM position for the three types of PRDs when distances are computed between the closest atoms minus their van der Waal's radii. Figure S3

Format: PDF Size: 183KB Download file

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Open Data

Additional file 4:

Correlation between covariation score and physical proximity between each PRD site of a PDZ domain and each PWM position when distances are computed between alpha carbon atoms in four different PDB structures. Figure S4

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Open Data

Additional file 5:

Conservation and distance to the closest peptide residue of each PDZ domain site. For each site on the domain, we computed the total sequence weight of the sequences having a particular amino acid at the site. The conservation of the site is defined by the maximum of such total weights normalized by the total sequence weight of all sequences in the MSA. Figure S5.

Format: PDF Size: 22KB Download file

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Open Data