Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Methodology article

Quality assessment of protein model-structures based on structural and functional similarities

Bogumil M Konopka1, Jean-Christophe Nebel2 and Malgorzata Kotulska1*

Author Affiliations

1 Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland

2 Faculty of Science, Engineering and Computing, Kingston University, Kingston-upon-Thames, KT1 2EE, United Kingdom

For all author emails, please log on.

BMC Bioinformatics 2012, 13:242  doi:10.1186/1471-2105-13-242

Published: 21 September 2012

Additional files

Additional file 1:

CASP8 evaluation. The file has three worksheets “Overall”, “Per target” and “delta GDT”. The first worksheet provides “overall” correlations of quality predictions produced by all tested GOBA metrics with GDT-TS scores of protein model-structures submitted to CASP8. The second worksheet shows Pearson correlations calculated for model-structures of particular targets. The third worksheet provides the percentages of targets where ΔGDT fell into one of four GDT bins.

Format: XLS Size: 71KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

CASP 9–in-contest evaluation. The content of the file is analogical to the contents of Additional file 1. The file has three worksheets: “Overall”, “Per target” and “delta GDT”. The evaluated models were submitted to CASP9.

Format: XLS Size: 22KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

CASP 9 evaluation. The content of the file is analogical to the contents of Additional file 1 and 2. The file has three worksheets: “Overall, “Per target” and “delta GDT”. The evaluated models were submitted to CASP9.

Format: XLS Size: 30KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

comparison of CASP 8 MQAPs. The file has two worksheets: “Per target” and “Delta GDT”. It shows the performance of selected GOBA measures and the performance of groups that participated in Quality Assessment category of CASP8. The table in “Per target” is sorted by average “Per target” correlation acquired by groups. Average and quartile values along with Minimal and Maximal correlation values are given in the last columns of the table. The second worksheet provides “delta GDT” analysis analogical to those presented in Additional files 1, 2, 3.

Format: XLS Size: 102KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

comparison of CASP9 MQAPs. The file has two worksheets: “Per target” and “Delta GDT”. It shows the performance of selected GOBA measures and the performance of groups that participated in Quality Assessment category of CASP9. The contents of worksheets are analogical to those in Additional file 5.

Format: XLS Size: 79KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

dependence of GOBA performance on GO term annotations. The file shows the correlations between parameters describing protein GO term annotations (number of GO terms, the depth of the most specific GO term, average similarity of GO terms in the set) and GOBA “Per Target” performance in CASP8 and CASP9-in-contest validation sets.

Format: XLS Size: 11KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

CASP 8 validation set targets. The file lists all CASP 8 target domains that were used in our CASP8 validation set.

Format: LIST Size: 1KB Download file

Open Data

Additional file 8:

GO term availability. The file has two worksheets, “Annotations” and “Go_evidence”. In the first worksheet, the numbers of GO term annotations, available for protein entries in Uniprot and in PDB, are listed. In the second worksheet the distributions of evidence codes in Uniprot in PDB are presented. The legend for GO evidence codes is also provided.

Format: XLS Size: 14KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data