Vorolign Server

Welcome to the Vorolign Server for protein structure alignment. To use Vorolign, please do the following:

• In order to retrieve your results, please enter your E-mail adress and your job name in the corresponding text fields.
• Decide what you want to do
• If you want to align two or more protein structures please provide two or more space separated ASTRAL ids (example: d1mbn__) or PDB ids (including a chain id if you like, example: 1tim or 1timA) in the Your ids field and press the button Align structures
• To scan a target protein against the a protein database (currently the ASTRAL40, version 1.69), please enter one ASTRAL (example: d1mbn__) or PDB id (including a chain id if you like, example: 1tim or 1timA) of your target in the Your ids field and press the button Find similar structures
• After pushing the button, you'll see a confirmation that your request has been sent to the server.
• As soon as your results are available, you'll recive an e-mail with the link to your result page

Please enter your return email adress, the job name as well as the ASTRAL ids of your request below:

Version and News

• 25.09.2007: Vorolign is now part of the ProCKSI-Server deployed at the University of Nottingham.
• 01.02.2007: The Vorolign Paper is recommended by Adam Godzik in the Faculty of 1000 Biology community: Adam Godzik: Faculty of 1000 Biology, 1 Feb 2007
• 29.01.2007: Our paper about Vorolign (see reference below) has been awarded the Best student paper award (1st prize) at the European Conference on Computational Biology (ECCB) 2006
• 19.01.2007: There is currently a small bug in the superposition routine to superpose multiple structures. Therefore the superposition might look strange. We will fix this problem as soon as possible! The problem has no effect on the alignment quality or Vorolign scan results!
• 09.01.2007: New template database: now we use the Astral40 database, SCOP version 1.69
• 07.01.2007: Now Vorolign also provides normalized alignment scores which can judge the quality of the hits identified by VorolignScan.
• 20.12.2006: Server now uses a domain partitioning tool (PDP) before starting the scan. This especially improves the prediction accurracy for complete protein chains that might contain several SCOP domains

Contact

If you have any problems in using the server or questions regarding Vorolign please send your request to Fabian Birzele.

Larger jobs

We are happy that you are interested in using Vorolign. If you find Vorolign useful and want to send many requests please contact us such that we can process your requests faster and more convenient for both sides. Also, if you want to get multiple alignments of more than 20 structures, feel free to contact us and we'll see what we can do.

Reference

If you find Vorolign useful for your own research please cite:
Fabian Birzele, Jan E. Gewehr, Gergely Csaba and Ralf Zimmer. Vorolign - Fast Structural Alignment using Voronoi Contacts Bioinformatics, Vol. 23, No. 2, 2007, e205-e211 (Journal Article).

Supplementary material