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Just wondering if anyone has any information on what the general consensus on publishing/depositing online protein structure simulations is?

I've been doing a fair bit of work to characterise the 'quality' of the simulations I have (how well they approximate known homologous structures), but don't know what is generally thought of protein structure simulation methods. They do a lot of work in the CASP programs every couple of years to assess whether they simulate accurately, so a plausible structure simulation should be a valid surrogate for an otherwise unknown protein IMO?

Are the online databases purely for structures resolved experimentally?

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  • $\begingroup$ The consensus is "not publishing/depositing anything". Reproducability might be an issue throughout biology, but it's sad to see that in the one area that should be perfectly reproducable every time the standards are as low as they are. Please just put it somewhere, supplementary info or any kind of database is better than nothing. $\endgroup$ – VonBeche Sep 26 '16 at 18:03
  • $\begingroup$ Yeah I fear you're right...read a paper recently about the number of genomes that go unpublished...and my group is as guilty of that as any. They will be included in my thesis certainly, and can be made available through our HPC infrastructure. Really I was just wondering if you tried to publish a paper with simulated rather than experimented structures, whether you'd be opening yourself up to serious criticism... $\endgroup$ – Joe Healey Sep 27 '16 at 9:22
  • $\begingroup$ I published a protein engineering paper based on a model structure. I regret that we didn't publish the structure of the model (although it was just made with YASARA standard settings, nothing special). We had some troubles publishing it where we wanted, but using the model as the basis for protein engineering was never an issue. $\endgroup$ – VonBeche Sep 28 '16 at 8:04

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