Interrogating domain-domain interactions with parsimony based approaches

Katia S Guimarães¹^,2 and Teresa M Przytycka¹

¹National Center of Biotechnology, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

²Center of Informatics, Federal University of Pernambuco, Recife, PE 50732, Brazil

author email corresponding author email

BMC Bioinformatics 2008, 9:171doi:10.1186/1471-2105-9-171


Published:	26 March 2008

Additional files

Additional file 1:

Mapping of Supra-domains to domains. This file contains 162 rows, each containing one supra-domain name followed by the names of the original domains included in it, separated by a blank character.

Format: TXT Size: 5KB Download file

Additional file 2:

Set of gold standard pairs. This file contains the 691 generalized domain pairs in the gold standard set. Each line contains the names of two domains that comprise a pair, separated by a TAB character.

Format: TXT Size: 13KB Download file

Additional file 3:

GPE predictions. This file contains a heading line and 1399 rows with the GPE predicted domain pairs ordered by LP-score. All pairs listed have LP-score ≥ 0.60 and pw-score ≤ 0.01. Each row contains five fields: Generalized Dom A, Generalized Dom B, GPE LP-score, GPE pw-score, and Gold Std (1 if pair is in GPE benchmark set, 0 otherwise).

Format: XLS Size: 164KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

GPE LP-scores ≥ 0.50. This file contains the 7,554 generalized domain pairs that had GPE LP-score ≥ 0.50, regardless of their pw-scores. Each row contains five fields: Generalized Dom A, Generalized Dom B, GPE LP-score, GPE pw-score, and Gold Std (1 if pair is in GPE benchmark set, 0 otherwise).

Format: XLS Size: 751KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

Impact of pw-score cut-off on the quality of predictions. This file contains the numbers of domains pairs predicted and the fraction of those that are in the benchmark set, for different values of pw-score cut-off. As the cut-off becomes more stringent, the accuracy of the predictions improves.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 6:

Impact of reliability cut-off on the quality of predictions. This file contains five tables for five different reliability cut-offs, showing the number of predictions and the number of predicted pairs in the benchmark set as a function of LP-score cut-off.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 7:

Set of protein-protein interactions used to compare methods. This file contains the 192 interacting protein pairs used in the experiment of predicting the mediating domain pairs, used to compare GPE with other state-of-the-art methods. Each line contains two integer numbers, separated by a TAB character, that represent the DIP identifiers of the interacting proteins.

Format: TXT Size: 5KB Download file

Additional file 8:

Pairs Predicted By GPE and not by IB. This file contains the 50 top-scored original domain pairs that were predicted by GPE but had IB-score < 4.0. Each row contains six fields: ORIGdom A, ORIGdom B, GPE LP-score, GPE pw-score, IB-score, and number of Witnesses of that pair in GPE dataset in Generalized format.

Format: XLS Size: 30KB Download file

This file can be viewed with: Microsoft Excel Viewer