search

opensourceantibiotics / murligase

Everything to do with the Mur Ligase Project
29 stars 6 forks source link

Protein Structure Prediction Tools More Generally Available #48

Open mattodd opened 3 years ago

mattodd commented 3 years ago

Both published yesterday:

Alphafold paper: https://www.nature.com/articles/s41586-021-03819-2 David Baker's paper: https://science.sciencemag.org/content/early/2021/07/14/science.abj8754

I guess what we need is volunteers to try out the code (available in both cases) on e.g. MurC to compare with xstal structure?

drc007 commented 3 years ago

@mattodd You can access the David Baker solution using this website https://robetta.bakerlab.org/submit.php.

Is the MurC crystal structure in the PDB that was part of the training set?

mattodd commented 3 years ago

@drc007 good question. Don't know. If yes, then the chances are, I guess, a lot better for the prediction of other murs and other species of MurC.

mattodd commented 3 years ago

The Alphafold team kindly emailed to alert us to the publication of the papers and database, and specifically to say this re the proteins we'd highlighted:

"I’m also very happy to share the structures for the antibacterial targets you sent over. I’ve added a link to all but one of them below, which will take you to their structure page including a 3D viewer with the confidence metrics and PDB/mmCIF files.

MurC- E.coli | link to structure

MurC- M. tuberculosis | link to structure

MurD E.coli | link to structure

MurD- M. tuberculosis | link to structure

MurE- E.coli | link to structure

The structure for MurE - P, aeruginosa sequence is not yet part of the AlphaFold databaset. You can try searching for it using the EBI Protein Similarity Search tool against the sequence in the AlphaFold Database, and there may be a structure prediction available that has a similar sequence (see also the FAQs). The AlphaFold database will also continue to expand and be updated over time. In the meantime the AlphaFold source code and Colab notebook can be used to predict the structures of proteins not yet in AlphaFold DB."