Linking integrative models out to experimental data
Hi all,
As you know, whenever we build an integrative or hybrid model we need to point to multiple sources of input experimental data. It doesn't make sense to embed that data directly in an mmCIF file because that would be very inefficient, so instead we need to link out to wherever the raw and/or processed experimental datasets are stored, ideally in a repository maintained by experts in the field (e.g. PDB, EMDB, SASBDB). I've summarized the kinds of data that we've been dealing with so far in our own modeling, with pointers to repositories where available, in the wiki: https://github.com/ihmwg/IHM-dictionary/wiki/External%20data
Please take a look and add to it (or reply to this email). It seems likely that there are many modeling scenarios that neither RCSB nor the Sali lab have considered thus far.
Ben
Dear Ben, I've noticed that you haven’t included NMR data in to your integrative or hybrid modeling system. BMRB maintains the archive of all kind of NMR experimental data. It is available in NMR-STAR format. We have different kind of distance restraints extracted from different NMR experiments, which could be effectively used for IHM. Thanks, Kumaran form BMRB
> On Feb 27, 2017, at 6:41 PM, Ben Webb ben@salilab.org wrote: > > Hi all, > > As you know, whenever we build an integrative or hybrid model we need to point to multiple sources of input experimental data. It doesn't make sense to embed that data directly in an mmCIF file because that would be very inefficient, so instead we need to link out to wherever the raw and/or processed experimental datasets are stored, ideally in a repository maintained by experts in the field (e.g. PDB, EMDB, SASBDB). I've summarized the kinds of data that we've been dealing with so far in our own modeling, with pointers to repositories where available, in the wiki: > https://github.com/ihmwg/IHM-dictionary/wiki/External%20data > > Please take a look and add to it (or reply to this email). It seems likely that there are many modeling scenarios that neither RCSB nor the Sali lab have considered thus far. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IHM-repval mailing list > IHM-repval@salilab.org > https://salilab.org/mailman/listinfo/ihm-repval
On 2/28/17 9:30 AM, Kumaran Baskaran wrote: > I've noticed that you haven’t included NMR data in to your > integrative or hybrid modeling system. BMRB maintains the archive of > all kind of NMR experimental data. It is available in NMR-STAR > format. We have different kind of distance restraints extracted from > different NMR experiments, which could be effectively used for IHM.
Thanks for the info! The only reason why we didn't list NMR in the wiki is that we don't currently have any use cases where people have generated integrative models including NMR data. Are you aware of any?
Ben
Thanks Ben. I am aware of at least one used case in RNA structural analysis using NRM-SAXS/WAXS.
https://www.ncbi.nlm.nih.gov/pubmed/26655855
I hope there may be many .
-Kumaran
On 03/06/2017 07:36 PM, Ben Webb wrote: > On 2/28/17 9:30 AM, Kumaran Baskaran wrote: >> I've noticed that you haven’t included NMR data in to your >> integrative or hybrid modeling system. BMRB maintains the archive of >> all kind of NMR experimental data. It is available in NMR-STAR >> format. We have different kind of distance restraints extracted from >> different NMR experiments, which could be effectively used for IHM. > > Thanks for the info! The only reason why we didn't list NMR in the > wiki is that we don't currently have any use cases where people have > generated integrative models including NMR data. Are you aware of any? > > Ben
Hi Ben and Kumaran,
Thanks for starting the thread. There is also a nice example of NMR, SAXS, SANS and even EM used in generating a protein/RNA complex: PDB entry 4by9, BMRB entry 19400: http://europepmc.org/abstract/MED/24121435, pdbe.org/4by9
Best, Aleks
On 13/03/2017 15:21, Kumaran Baskaran wrote: > Thanks Ben. I am aware of at least one used case in RNA structural > analysis using NRM-SAXS/WAXS. > > https://www.ncbi.nlm.nih.gov/pubmed/26655855 > > I hope there may be many . > > -Kumaran > > > On 03/06/2017 07:36 PM, Ben Webb wrote: >> On 2/28/17 9:30 AM, Kumaran Baskaran wrote: >>> I've noticed that you haven’t included NMR data in to your >>> integrative or hybrid modeling system. BMRB maintains the archive of >>> all kind of NMR experimental data. It is available in NMR-STAR >>> format. We have different kind of distance restraints extracted from >>> different NMR experiments, which could be effectively used for IHM. >> >> Thanks for the info! The only reason why we didn't list NMR in the >> wiki is that we don't currently have any use cases where people have >> generated integrative models including NMR data. Are you aware of any? >> >> Ben > > _______________________________________________ > IHM-repval mailing list > IHM-repval@salilab.org > https://salilab.org/mailman/listinfo/ihm-repval
participants (3)
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Aleksandras Gutmanas -
Ben Webb -
Kumaran Baskaran