Where is the model?

I was reading a review that came in Structure’s recent issue. The article is titled “Protein Modeling: What Happened to the ‘Protein Structure Gap’?” [1] It was very interesting to read, especially the section called “Know your limits“.

Wouldn’t it be a great idea to put all these homology modeled structures that were published (of course, in a peer-reviewed journal) in one place? For some researchers, homology models are usually considered with a pinch (sorry a bucket!) of salt. Still, why should I spend time on modeling the protein, if a model exists already?

ResearchBlogging.orgI have been in situations, where I would come across a paper that describes a structure that was homology modeled and made conclusions from that. Usually, my first stop is at ModBase. Would the structure in ModBase is exactly as the model discussed? So I would scurry to find the coordinates of it in the supplementary materials or in the respective lab website. And, I would not always be lucky. That would start an awkward journey of contacting the authors and explain my ulterior motive of looking at the structure. (Sometimes, I would think the authors must be misunderstanding my motive as to find faults. No! I am not that bad! 🙂 )

Enter Protein Model Portal (PMP) [2] in the picture and the Model archive (currently in beta version). In PMP, one can give a query and get a list of structures (experimentally determined and modeled) to view. In case of only modeled structures, the structures from ModBase, Swissmodel are also listed. The next step is where it gets interesting. After selecting the radio buttons against each structure, one can compare the structural variability between the structures.There are other features in the website that tells the reliability, parameters and constraints of the model.

Below is a screenshot of a query protein of my current research in PMP (http://www.proteinmodelportal.org/)

Screen Shot 2013-09-04 at 5.14.38 PMModel archive, on the other hand, provides a DOI for each model deposited, exactly as in PDB. This is important since, if a peer-reviewed publication had a homology modeled structure, it needs to be made available to the public and other scientific colleagues to look at it. The argument is the same that was put across journals when PDB was founded. If you are publishing a paper with a homology modeled structure, deposit in Model archive and mention it in the manuscript. That the structures will be available to start working form and add more parameters and constraints is great!

The archive is still being established and I think it will take some time before this also becomes a crucial step in publishing articles on homology modeled structures. Thanks to Prof. Torsten Schwede, here is a screenshot of the two homology models of DapE [4] that were deposited in Model archive and the paper describing the protein was published in Metallomics [5] Click on this link to access the models.

Screenshot of DapE homology models deposited in Model archive

Screenshot of DapE homology models deposited in Model archiveDo spread the word about Model archive.

Friends, I don’t want to sound patronizing, but next time you model a structure, you realize that the homology models had some contribution in the conclusion, do think of submitting the structures to Model archive. Plus, mention a sentence as to where the models have been uploaded to. 🙂

Since, this is a community based effort and if you have any suggestions/comments do send them to Prof. Torsten Schwede (http://www.biozentrum.unibas.ch/research/groups-platforms/overview/unit/schwede/)

I will touch more on homology modeled structures on the next post. Adios amigos!

References:

  1. Torsten Schwede (2013). Protein Modeling: What Happened to the “Protein Structure Gap”? Structure, 21 (9), 1531-1540 DOI: 10.1016/j.str.2013.08.007
  2. Haas J, Roth S, Arnold K, Kiefer F, Schmidt T, Bordoli L, & Schwede T (2013). The Protein Model Portal–a comprehensive resource for protein structure and model information. Database : the journal of biological databases and curation, 2013 PMID: 23624946
  3. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, & Wilson IA (2009). Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993), 17 (2), 151-9 PMID: 19217386
  4. http://www.modelarchive.org/doi/10.5452/ma-a1nb6
  5. Narasimha Rao Uda, Grégory Upert, Gaetano Angelici, Stefan Nicolet, Tobias Schmidt, Torsten Schwede, & Marc Creus (2013). Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE: implications of metal heterogeneity for evolution and antibiotic drug design
    Metallomics DOI: 10.1039/c3mt00125c
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