Open Access Highly Accessed Methodology article

A novel method to compare protein structures using local descriptors

Paweł Daniluk1,2 and Bogdan Lesyng1,2*

1 Faculty of Physics, Department of Biophysics and CoE BioExploratorium, University of Warsaw, Żwirki i Wigury 93, Warsaw, Poland

2 Bioinfomatics Laboratory, Medical Research Centre, Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland

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BMC Bioinformatics 2011, 12:344 doi:10.1186/1471-2105-12-344

Published: 17 August 2011

Additional files

Additional file 1:

Pruned SISYPHUS alignments - SCOP dataset. The file contains SISYPHUS alignments chosen for the SCOP dataset.

Format: TXT Size: 146KB Download file

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Additional file 2:

Pruned SISYPHUS alignments - MD dataset. The file contains SISYPHUS alignments chosen for the MD dataset.

Format: TXT Size: 27KB Download file

Open Data

Additional file 3:

Pruned SISYPHUS alignments - MC dataset. The file contains SISYPHUS alignments chosen for the MC dataset.

Format: TXT Size: 51KB Download file

Open Data

Additional file 4:

Figures S1 and S2.

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This file can be viewed with: Adobe Acrobat Reader

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Additional file 5:

Comparison of DALI and DEDAL performance on the SCOP subset. Percentage scores of reconstructing the reference alignments on the SISYPHUS alignments SCOP subset.

Format: TXT Size: 10KB Download file

Open Data

Additional file 6:

Comparison of DALI and DEDAL performance on the MD subset. Percentage scores of reconstructing the reference alignments on the SISYPHUS alignments MD subset.

Format: TXT Size: 2KB Download file

Open Data

Additional file 7:

Comparison of DALI and DEDAL performance on the MC subset. Percentage scores of reconstructing the reference alignments on the SISYPHUS alignments MC subset.

Format: TXT Size: 2KB Download file

Open Data

Additional file 8:

Comparison of DEDAL and other methods preformance on the SISY set. Percentage scores of reconstructing the reference alignments on the SISY set. Results for other methods (except FlexSnap) cited after Mayr et al. [7].

Format: TXT Size: 11KB Download file

Open Data

Additional file 9:

Comparison of DEDAL and other methods preformance on the RIPC set. Percentage scores of reconstructing the reference alignments on the RIPC set. Letters in the type column denote: R - repetitions, I - extensive indels, P - permutations, C - conformational changes. Results for other methods (except FlexSnap) cited after Mayr et al. [7].

Format: TXT Size: 4KB Download file

Open Data