Imprint and Data Protection

Principal investigator for this tool is Rebecca Wade.

For legal imprint and data protection information, please check our institute policy, also loaded for your convenience at the bottom of this page.

To contact the team from the tool development/maintainance, please use our Contact page.

Acknowledgement

Work on Prosat⁺ was supported by

• The Klaus Tschira Foundation
• The vitual liver network, a major system biology project supported by the BMBF

How to cite Prosat⁺

If you use Prosat⁺ in the course of generating work for publication you should cite the following article:

This tool uses the following databases and tools:

• RCSB PDB Database: www.rcsb.org

  H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.

  We use the REST-full webinterface of RCSB as well as download full entries.

• UniProt Database: https://www.uniprot.org

  UniProt: a hub for protein information Nucleic Acids Res. 43: D204-D212 (2015).

  UniProt information is retrieved via its XML entry format

• SIFTS database https://www.ebi.ac.uk/pdbe/docs/sifts/, see Velankar et al., Nucleic Acids Research 41, D483 (2013).

  The SIFTS database, maintained at the EBI, provides a mapping between PDB entries and a reference UniProt entry, as well as other datasources.

• BLAST tool: NCBI BLAST Download, described here: Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L.. (2009) "BLAST+: architecture and applications." BMC Bioinformatics. 10:421.

  The BLAST tool is used to search for related UniProt entries and to map features of these entries onto the reference entry. In addition the BLAST tool is used to find UniProt entries in case the user provides a sequence. From these UniProt entries PDB entries are mapped.

• JSMol visualization (version 14.4.2) is used for the interactive visualization of the protein structure. It does not require a Java plugin.
• BioJava version 4.2 is used for pairwise sequence alignment of similar sequences found by blast. This alignment is done using a PAM250 substitution matrix, a gap opening penalty of 6 and a gap extension penalty of 1.
• Play framework 2.4 is used to build the interactive web application.
• Twitter bootstrap 3 is used to generate the HTML user interface elements.
• AngularJS 1, the jQuery plugin Sidr, and the Angular-xeditable bundle were used for better usability and layout of the webserver.