Difference between revisions of "Team:Heidelberg/Software/Contact"

 
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Latest revision as of 02:04, 19 September 2015

What is this site about?

We, the iGEM Team Heidelberg 2015 have developed a software, that can calculate aptamer sequences for virtually any molecule with a known crystal structure. Read more about the software here (LINK) and inform yourself about the project itself here (LINK). Table below displays the requests that have already arrived us.
Processing time may vary depending on the grade of preprocessing required. Please read instruction below for further information.

Need an aptamer?

Use this form to send a request for an aptamer. Please read the intructions listed below on how to modify the .pdb file before.

Ligand Name:

Name or institution:

Email to notify:

.pdb file of ligand:

Overview of requests

Requester Ligand .pdb file Aptamere sequence Status
iGEM Heidelberg 2015 Ketamin CCACCC; CCGATG; GGGATT Done
iGEM Michigan 2015 Kanamycin TTCTCTC; CGGGGAT; CGGGGGT; GCTGTCG Evaluated
iGEM Heidelberg 2015 p53 AAGGTGGG; TTCTGGGTGTG; TTCTGGGTGTT; TTAATGATATGTC; TTAATGATATCAT; TTAATGATATAGT; TTAATGATCGGGT; TTAATGATCGGGA Evaluated
iGEM Michigan 2015 L-Lactate dehydrogenase Calculating
Division of Optical Nanoscopy, dkfz Vimentin Pending
iGEM Heidelberg 2015 SaCas9 ATAGGTGGAAAGGGGCGT; ATAGGTGGAAAGGGGCGG Done
Dr. Stefan Kallenberger Actin ACGTCCTTTGAGGGAC Done
iGEM Heidelberg 2014 Xylanase Pending
Prof. Dr. Michael Wink Ranalexin Pending
Dr. Holger Schäfer Snakin-2 Pending

Further information

Aptamers, originally having been conceived as an alternative to antibodies have proven notoriously difficult to properly select, against the multitude of targets available in nature. With our software [INSERT_NAME] you can find your own aptamer to target the ligand you want. To acheive this, we use an algorithm to find the nucleotide sequence minimizing the entropy of binding to the ligand. What enables this, is a combination of stratified sampling and Markov Chain Monte Carlo methods. With this contact form, you can send us ligands, which for we will then compute aptamer candidates. To do this, we need crystal structures of those ligands, which have to follow a few rules for swift processing.

  1. The format should be .pdb for proteins, and .pdb or .mol2 for small molecules.
  2. In the case of small molecules, please take the time to run a semi-empirical quantum chemical calculation of its parameters using the following command in ambertools: antechamber -i [INPUT_NAME].pdb -fi pdb -o [OUTPUT_NAME].mol2 -fo mol2 -c bcc -s 2 where you substitute [INPUT_NAME] and [OUTPUT_NAME] with the respective filenames. Please then submit the .mol file.
  3. The files should contain no waters, unless you need, for some reason, an aptamer for water (which would not work).
  4. Protein files should contain no prosthetic groups or cofactors. This would require separate quantum-chemical handling for parameter estimation before processing.
  5. Proteins should contain no nonstandard amino acids, not contained in Amber parameters.
  6. For proteins, which are very large, please consider, if targeting a specific domain of that protein would be sufficient, or even beneficial to your project. Very large proteins could incur penalties on the software's performance.

For us to be able to efficiently process your requests, it is vital that your parts have been processed in conformance with the above guidelines. Input files not conforming to those guidlines would take a lot of work to process, due to the fact, that anything non-standard has to be parametrised by hand, using quantum chemistry software.

We still encourage you to submit your targets, even if they do not fit the guidelines. Currently, the processing of those files will be handled with lower priority, and their processing itself might take a lot of time. That said, we will inform you of all possible complications regarding your submission. Just bear in mind that it could take a very long time to process your request.