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SasView / sasview

Code for the SasView application.
BSD 3-Clause "New" or "Revised" License
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Deuterium exchange calculator #2590

Open lucas-wilkins opened 10 months ago

lucas-wilkins commented 10 months ago

A tool to calculate deuterium exchange on macromolecules.

At ISIS we've been looking into the capabilities of RDKit (https://www.rdkit.org/), and it seems it can handle most of the stuff we would need to implement this.

I think @wpotrzebowski and @yunliu01 would probably be interested in this.

pkienzle commented 10 months ago

The sld calculator will handle labile hydrogen if they are marked in the formula as H[1].

The periodictable.fasta module includes a number of molecules of interest taken from [1]. Even for molecules which are included in the tables the answers will be incorrect when the labile hydrogen is inaccessible, for example, because it is buried deep within a protein. You won't be able to fix that without a lot of MD simulation.

[1] Perkins, S.J., 1985. Chapter 6 X-Ray and Neutron Solution Scattering, in: New Comprehensive Biochemistry. Elsevier, pp. 143-265. https://doi.org/10.1016/S0167-7306(08)60575-X

lucas-wilkins commented 10 months ago

There's multiple things that need to be done to get an answer (most of them implemented in RDKit), but you don't need an MD simulation to get a reasonable answer.