News: Stay up-to-date!

We just moved from our old webserver to a new machine. Therefore, it is possible that some internal and external paths may be incorrect. If you find any inconsistencies please feel free to contact us.

Our last rollout caused some trouble with our database connections. Therefore requests from the searchbar as well as annotation tables for all datasets could not be processed correctly. This problem should be fixed now. We wish you happy holidays and a happy new year.

We had to shutdown our server multiple times this week for maintenance. We want to apologize for inconveniences, but everything should return to normal now.

Our energy profile search tool eSearch got some improvements regarding performance and sensitivity.

The website got some new styles due to the change to HTML5. Associated with this upgrade the visualization tools (eVis and jMol) are now available as HTML5 versions.
Furthermore, we added a section called ePfam, where the results of energetic analysis of protein families are visualized.

Although we are a bit sloppy with the maintenance of our news, our energy tools experiencing regular improvements. The adaption of data handling regarding to chain sensitivity provides a much more specific exploration of energy data from now on. Additionally, annotations from common databases as well as literature references to relevant articles are included and crosslinked for each data entry. A new and more precise version of eGor for globular proteins has been uploaded.
In general some minor adaptions and bugfixes have been made in preparation of a larger tool and code review this summer.

e2TMR is an Hidden Markov Model-based approach to predict membrane-spanning helices and intra/extra-cellular regions in alpha-helical membrane proteins starting from an energy profile predicted from sequence using eGOR. The algorithm shows promising results and we hope to deliver an implementation of e2TMR at eProS soon.

With the new annotation system running at the server, energy profiles of the entire PDB archive (excluding error-prone entries, beta-barrel membrane proteins and protein-nucleic acid complexes) have been recalculated and annotated. At the moment, eProS contains energy profile entries of about 76,145 globular and 1,264 alpha-helical transmembrane protein structures. Currently, we are working on an automated weekly-update system to guarantee keeping the eProS database, annotations and cross-links up-to-date.

Annotations from various sources such as CATH, SCOP and Pfam as well as GO-term descriptors have been integrated in the database. Cross-linking to other databases is now given.

The eProS database is now accessible via standard html pages. This allows a more ordered and intuitional way of browsing the energy profile database.

The eProS database now holds about 75,000 energy profile files of all known protein and protein-protein complex structures. However, entries of protein-nucleic acid complexes cannot be found at the database since the coarse-grained energy model is not applicable to such interactions.

eProS is now presented in a novel design.

Problems while parsing non-standard PDB-files (such as PDB-files obtained by molecular/comparative modeling etc.) have been fixed. If you still have problems calculating energy profiles from such files, please contact us!

After filtering our database for theoretical models, redundant and error-prone structures, statistics for globular and alpha-helical membrane proteins have been recalculated.

A novel approach for scoring energy profile alignments has been implemented. The scoring has shown to be faster and numerically and biologically more robust than the previously used z-scoring method.

On Wednesday, 20th of July 2011, bioservices.hs-mittweida.de is going to be shut down, due to maintenance. For the period from 6 p.m. until 12 a.m. CET the server won't be available. Thank you for your understanding.

Fully functional toolbox available. Enjoy your stay...

The statistic for globular proteins is now accessible. New content was submitted and tools have been improved.

The database structure has been rearranged and and the set of alpha-helical membrane proteins has been extended.

You can now access our dataset over the appropriate link in the menu. Some bugs and unexpected behaviors were fixed.

Bugfixing and the improvements of the tools is still in progress. Today a new design was applied.

The server is under reconstruction. Improvements are implemented and bugs are fixed.

After relying on PDBTM topology annotations, eProS has been updated to determine the (non-)membrane spanning regions in alpha-helical membrane protein structures via the TMDET service. Thus, energy profiles of theoretical alpha-helical membrane protein structures obtained from various sources can be calculated and scanned for similar profiles in our database.

Energy profile calculation and energy profile alignment algorithms for alpha-helical membrane protein structures have been improved.

The statistics for globular proteins are now accessible and can be viewed at the eProS-statistics page.

Today the energy profile suite went online. The move from a windows machine to unix ended up in some new interesting problems. Most of them should be solved, but if you find something currently not working, please contact us. The current version starts our alpha test phase.