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"optimize a predicted structure of their molecule using density functional theory (DFT), then draw it like a crystal structure would be displayed (a 3D plot wit

"optimize a predicted structure of their molecule using density functional theory (DFT), then draw it like a crystal structure would be displayed (a 3D plot with error ellipsoids at each atom, with probable bonds shown)" why not just publish this instead. surely an optimized model is still valuable.

opticfluorine 4y ago
Typically not on their own - it's very easy to calculate an optimized structure that is incorrect, so you typically want some sort of justification for your structure. Typically you would be calculating one of these geometries along the way to calculating other interesting properties to either compare with experiment or make new predictions (or both). The "gold standard" is... comparison with a crystal structure from X-ray diffraction. In my field (small inorganic molecules used as catalysts), I typically calculated the structure along the way to calculating the molecular orbitals for describing the electronic structure (important for understanding many properties of the catalyst and its reactivity) and predicting the infrared and visible spectra (useful for comparison with experiment and for explaining the electronic and magnetic properties of the molecule). It's the whole picture that's valuable, not just the structure - and the more experimental properties you include, the harder it is to fake the whole thing.
chaxor 4y ago
I absolutely agree. Most of the time, getting very good DFT results is actually far more difficult that getting the experimental results of cystollography itself. They're both quite hard, and it depends on which techniques are applied, but getting computational methods to match with great quantum accuracy is very, *very* difficult. I know more about condensed matter physics and GW Bethe Salpeter approaches etc, than proteins, but the difficulty in getting good computational methods to work is still out of reach for ~95% of scientists even in that field.

opticfluorine 4y ago

Typically not on their own - it's very easy to calculate an optimized structure that is incorrect, so you typically want some sort of justification for your structure. Typically you would be calculating one of these geometries along the way to calculating other interesting properties to either compare with experiment or make new predictions (or both). The "gold standard" is... comparison with a crystal structure from X-ray diffraction. In my field (small inorganic molecules used as catalysts), I typically calculated the structure along the way to calculating the molecular orbitals for describing the electronic structure (important for understanding many properties of the catalyst and its reactivity) and predicting the infrared and visible spectra (useful for comparison with experiment and for explaining the electronic and magnetic properties of the molecule). It's the whole picture that's valuable, not just the structure - and the more experimental properties you include, the harder it is to fake the whole thing.

chaxor 4y ago

I absolutely agree. Most of the time, getting very good DFT results is actually far more difficult that getting the experimental results of cystollography itself. They're both quite hard, and it depends on which techniques are applied, but getting computational methods to match with great quantum accuracy is very, *very* difficult. I know more about condensed matter physics and GW Bethe Salpeter approaches etc, than proteins, but the difficulty in getting good computational methods to work is still out of reach for ~95% of scientists even in that field.