Chemistry in 3D [message #1541] |
Thu, 17 March 2022 10:56 ![Go to next message Go to next message](/forum/theme/myThemeWithHFCSS/images/down.png) |
Christophe
Messages: 31 Registered: January 2022
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Member |
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Hello everyone,
I read the user manual concerning conformers and 3D chemistry in general and I would like to go a bit deeper.
Does anyone know any good tutorials and/or videos ?
For example I watched the videos of I. Giraud about DW (RSC CICAG Open Source Tools for Chemistry Workshops) and it was really great.
Is there anything comparable for 3D chemistry?
Many thanks
Also: two silly questions:
- When I add a new empty row in DW, it remains invisible and I can't edit it. How to visualize such a row?
- When you click on any rows, it becomes reference cell (red frame around it). How to undo this reference cell selection (to make this red frame disappear)?
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Re: Chemistry in 3D [message #1562 is a reply to message #1560] |
Tue, 22 March 2022 13:57 ![Go to previous message Go to previous message](/forum/theme/myThemeWithHFCSS/images/up.png) ![Go to next message Go to next message](/forum/theme/myThemeWithHFCSS/images/down.png) |
nbehrnd
Messages: 215 Registered: June 2019
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Senior Member |
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Dear Christophe,
the conformer generator's aim is the provision e.g., of starting geometries for (in silico) docking experiments and considers only the isolated, single molecule in question. Once the molecule experiences interactions with neighbouring molecules e.g., intermolecular hydrogen bonds may render these predicted energetic minima more shallow/more deep. Then, some conformations might be not longer favourable, and others are locked-in; both render a reliable prediction more demanding. (One reason for prediction contests like the ones by CCDC,[1] or CASP.[2])
The number of conformers per molecule one want to query equally depends on the number of bonds which are conformational flexible. In this perspective, the default of up to 16 is (an empiric) suggestion. DataWarrior neither is the only program to offer this functionality,[3] nor do the force fields provided aim to compete in accuracy and precision with higher level(s) of theory/specialized programs.
Because I have no working experience with the shape alignment and docking you refer to, my suggest were to screen the 500+ citations on ACS's landing page for the the primary publication about DataWarrior,[4] or/and collect advice by others.
Norwid
[1] Reilly et al. Acta Cryst. 2016, B72, 439-459; doi 10.1107/S2052520616007447
[2] https://en.wikipedia.org/wiki/AlphaFold
[3] Ebejer, J. P. et al. J. Chem. Inf. Model. 2012, 52, 1146-1158; doi 10.1021/ci2004658
[4] Sander T. et al. J. Chem. Inf. Model. 2015, 55, 460-473; doi 10.1021/ci500588j
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