Hi,
I'm very new to IMP and have perhaps a naive question. We are working on a protein that is partially intrinsically disordered. We have a conformational ensemble that nicely fits to SAXS data set, but our aim is to include data from other methods to refine the ensemble. We have CD spectroscopy data and CCS from ion mobility MS. We were wondering whether IMP is suited to calculate the conformational ensemble using all three data sources (SAXS, CD spectroscopy, CCS by ion mobility MS) as input restraints? Clearly, IMP can handle the SAXS, but handling of CD and CCS was less clear to us.
Thank you and best wishes,
Yann
On 12/9/23 1:40 AM, yann.sterckx--- via IMP-users wrote: > We were wondering whether IMP is suited to calculate the > conformational ensemble using all three data sources (SAXS, CD > spectroscopy, CCS by ion mobility MS) as input restraints?
There is no specific support for CD or CCS, so you would certainly not just be able to give IMP your data straight from the instrument. But if you can think of a way to represent your experimental data as spatial restraints, you can add them to the IMP scoring function.
Ben
Dear Ben,
thank you for your reply. I’ll think of how we could represent the CD and CCS data as spatial restraints.
Best wishes,
Yann
> On 11 Dec 2023, at 21:28, Ben Webb ben@salilab.org wrote: > > CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. > > > On 12/9/23 1:40 AM, yann.sterckx--- via IMP-users wrote: >> We were wondering whether IMP is suited to calculate the >> conformational ensemble using all three data sources (SAXS, CD >> spectroscopy, CCS by ion mobility MS) as input restraints? > > There is no specific support for CD or CCS, so you would certainly not > just be able to give IMP your data straight from the instrument. But if > you can think of a way to represent your experimental data as spatial > restraints, you can add them to the IMP scoring function. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle
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Ben Webb -
Yann Sterckx -
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