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Can anyone give an ELI5 for what the limitation is in terms of processing these computationally? Is the challenge that it's difficult to model how a molecule wi

Can anyone give an ELI5 for what the limitation is in terms of processing these computationally? Is the challenge that it's difficult to model how a molecule will interact with another molecule, so you have to do it with atoms and test the interaction across every other molecule in the search space? For context I got a B- in high school chemistry and haven't looked back. *Edit: "do it with atoms" is confusing in this context. I mean do it in the real world outside of bits.

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whatshisface 5y ago
Molecules obey known laws of physics and can in principle be simulated exactly. That is not practical with present-day computers because it's quantum-mechanical and has an exponentially large state space. Heuristic and approximate methods are used to pare this down, sacrificing absolute truth, leading to results that are not very reliable. That is why experiments are still done in chemistry labs even though everything that happens in a chemistry lab has been "understood" since the 1930s. Chemists focus in on the least simulatable problems because most interesting chemistry happens right on the border of not happening at all. Molecules that are very easy to calculate are ones that small energy errors don't matter for. That makes them either incredibly stable or incredibly unstable, but chemistry happens near the boundary.
- dmurray 5y ago
  I upvoted this because it's an interesting take, but it doesn't feel like it's true. Chemists pick new molecules to experiment with primarily because they're similar to old ones that solve a particular problem (cure a disease, colour an emulsion, explode very fast...), not because they tried computational simulation of those molecules and couldn't overcome precision/chaos issues.
  - 41b696ef1113 5y ago
    >...not because they tried computational simulation of those molecules and couldn't overcome precision/chaos issues. Existing simulations are slow and inaccurate. Why waste your time generating computational results that you do not trust when you can just iterate on existing molecules and have them in hand, ready for testing?
  - whatshisface 5y ago
    If a molecule solves a particular problem, then it is neither so unstable that a poor simulation could predict its instability, nor so stable that a poor simulation could predict its stability. The molecules that are the easiest to predict computationally tend to be the least interesting. The energy difference between the bound and unbound states has to be small for it to be interesting which automatically puts it in the realm of difficult simulation. So no, chemists do not pick difficult molecules on purpose - they do so because difficulty and interestingness originate from the same place.
t3po7re5 5y ago
There's an open-source project run by a team out of IBM thats trying to use RL to navigate the space more effectively looking for anti cancer molecular compounds https://github.com/PaccMann/paccmann_rl https://github.com/PaccMann/paccmann_rl
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whatshisface 5y ago

Molecules obey known laws of physics and can in principle be simulated exactly. That is not practical with present-day computers because it's quantum-mechanical and has an exponentially large state space. Heuristic and approximate methods are used to pare this down, sacrificing absolute truth, leading to results that are not very reliable. That is why experiments are still done in chemistry labs even though everything that happens in a chemistry lab has been "understood" since the 1930s. Chemists focus in on the least simulatable problems because most interesting chemistry happens right on the border of not happening at all. Molecules that are very easy to calculate are ones that small energy errors don't matter for. That makes them either incredibly stable or incredibly unstable, but chemistry happens near the boundary.

dmurray 5y ago
I upvoted this because it's an interesting take, but it doesn't feel like it's true. Chemists pick new molecules to experiment with primarily because they're similar to old ones that solve a particular problem (cure a disease, colour an emulsion, explode very fast...), not because they tried computational simulation of those molecules and couldn't overcome precision/chaos issues.
- 41b696ef1113 5y ago
  >...not because they tried computational simulation of those molecules and couldn't overcome precision/chaos issues. Existing simulations are slow and inaccurate. Why waste your time generating computational results that you do not trust when you can just iterate on existing molecules and have them in hand, ready for testing?
- whatshisface 5y ago
  If a molecule solves a particular problem, then it is neither so unstable that a poor simulation could predict its instability, nor so stable that a poor simulation could predict its stability. The molecules that are the easiest to predict computationally tend to be the least interesting. The energy difference between the bound and unbound states has to be small for it to be interesting which automatically puts it in the realm of difficult simulation. So no, chemists do not pick difficult molecules on purpose - they do so because difficulty and interestingness originate from the same place.

t3po7re5 5y ago

There's an open-source project run by a team out of IBM thats trying to use RL to navigate the space more effectively looking for anti cancer molecular compounds https://github.com/PaccMann/paccmann_rl https://github.com/PaccMann/paccmann_rl

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