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This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Bioinformatics

Open Access Proceedings

Mapping small molecule binding data to structural domains

Felix A Kruger, Raghd Rostom and John P Overington*

Author Affiliations

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK

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BMC Bioinformatics 2012, 13(Suppl 17):S11  doi:10.1186/1471-2105-13-S17-S11

Published: 13 December 2012

Additional files

Additional file 1:

Domain annotations for the ChEMBL target dictionary. Tab-delimited file. The column 'uniprot' provides the Uniprot identifier, the column 'pfam' the Pfam identifier, 'start' and 'end' the start and end positions of the respective domain in the Uniprot sequence.

Format: TXT Size: 277KB Download file

Open Data

Additional file 2:

Table of mapped interactions. Tab-delimited file. The column 'activity' provides the value of the ChEMBL field activity_id, 'domain' the mapped Pfam-A domain, 'molregno' the identifier for the small molecule, 'uniprot' provides the Uniprot identifier and 'maptype' indicates whether the protein target is a single- or multi-domain protein.

Format: TXT Size: 7MB Download file

Open Data

Additional file 3:

Renderings of small molecule binding at the interface of Pfam-A domains. This is a folder containing graphics in JPG format.

Format: ZIP Size: 572KB Download file

Open Data

Additional file 4:

Session files of small molecule binding at the interface of Pfam-A domains. Zipped folder containing Qt-MG session files and required PDB files.

Format: ZIP Size: 1.7MB Download file

Open Data

Additional file 5:

Outlier selection for PCA. Boxplots show distributions of descriptor values for all molecules in the analysis. Red lines indicate chosen cut-offs for outlier selection.

Format: PDF Size: 92KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

List of conflicts between 'seed' domains occurring within the same target. Tab delimited file. The column 'uniprot' provides the Uniprot identifier, the column 'conflict' the seed domains co-occurring in the specified protein.

Format: TXT Size: 1KB Download file

Open Data

Additional file 7:

Manually removed protein targets. This is a text file listing all entries that were manually removed before mapping small molecule binding. Reasons for the removal are indicated for each identifier.

Format: PDF Size: 49KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data