This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities

Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich* and Gabriele Ausiello

Author Affiliations

Centre for Molecular Bioinformatics, Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, Rome 00133, Italy

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BMC Bioinformatics 2012, 13(Suppl 4):S17  doi:10.1186/1471-2105-13-S4-S17

Published: 28 March 2012

Additional files

Additional file 1:

Complete list of triplets along with their potentials. For each triplet with the same amino acid composition we report the total number of matches with the library of binding (BIND) and non-binding (non-bind) residues. In the last column the average PDBinder Propensity Value is calculated for each triplet. For clarity, the row describing the behaviour of the VAL triplet reports the "bind" and "non-bind" data for all triplets containing a Val, an Ala and a Leu in any order and conformation.

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Additional file 2:

AUC by using different distance thresholds. AUC achieved by PDBinder using different distance thresholds between the binding pockets residues and any atom of the bound ligand.

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