Structural footprinting in protein structure comparison: the impact of structural fragments

doi:10.1186/1472-6807-7-53

BMC Structural Biology

Volume 7

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Islamaj Dogan R
Wilbur WJ
O'Leary DP
Przytycka TM

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Wilbur WJ
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Research article

Structural footprinting in protein structure comparison: the impact of structural fragments

Elena Zotenko¹^,3 , Rezarta Islamaj Dogan¹^,3 , W John Wilbur³ , Dianne P O'Leary¹^,2 and Teresa M Przytycka³

¹Department of Computer Science, University of Maryland, College Park, MD 20742, USA

²Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA

³National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

author email corresponding author email

BMC Structural Biology 2007, 7:53doi:10.1186/1472-6807-7-53


Published:	9 August 2007

Additional files

Additional file 3:

The Python code for the SSEF and SEGF methods. An archive that contains the Python code and auxiliary files necessary to compute: (i) the SEGF footprint from a PDB file of a structure; (ii) the SSEF footprint from a PDB file of a structure; (iii) structural similarity score given PDB files of structures using either SSEF, SEGF or SSEF+SEGF method.

Format: ZIP Size: 140KB Download file

Additional file 4:

The set of training examples used to learn linear combination coefficients. A text file that contains the set of training examples used to learn linear combination coefficients.

Format: TXT Size: 101KB Download file

Additional file 1:

ROC scores for all superfamilies included in the study. An Excel file with performance, in terms of ROC₃₀₀scores, for all superfamilies included in the study and across different methods: SSEF, SEGF, LFF, voting, SSEF+SEGF, SSEF+LFF, SEGF+LFF, SSEF+SEGF+LFF.

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Affinity graphs and affinity scores for all three methods. An archive that contains the affinity graphs for all three methods. The graphs are given in Cytoscape's GML format. We also include a separate file for each method giving the affinity scores.

Format: ZIP Size: 599KB Download file