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AMR
AMR
2:27 AM
Why in the 21st century, when we know all that we know about human origins and genetics do people make such an inordinately big deal over skin color. It is just tedious. The link I posted has a very good description of the science behind why skin color is what it is. It all and only has to do with the intensity of UV radiation. UV can destroy folate which causes birth defects, but not having enough of the right UV causes Vit. D difficiency if not supplemented.
 
James
James
3:28 AM
 @m1clee You've raised 2 really good points.

 1. Conserved regions imply selective pressure for those residues. Selective pressure usually comes from the region being key for structure or function that without would be fatal for the cell.

    2. You're right, the visuals aren't always the interesting part of MD, but you are underestimating the potential of these simulations. A pharmacokineticist and other molecular scientists are more interested in the quantified data that comes out of these simulations rather than the visuals. Example - I was involved in a "steered MD" project that aimed…
 
TanMath
TanMath
@James huh?
 
James
James
Hi @TanMath. That rambling of mine was in response to comments on this answer. biology.stackexchange.com/a/42303/3553
 
TanMath
TanMath
Oh...
 
 
8 hours later…
m1clee
m1clee
11:54 AM
@James Of course.
This is my futuristic view of pharmaceutical studies, that, biologic macromolecules have "core design principles" that will be discovered. By "design", I try to emphasize that they aren't just evolutionarily conserved random combinations of monomers which gained functions over thousands of years. Or, are they?

So I tried to say, discovering these design principles is enough to calculate screening results. Leaving simulations unnecessary to deal with. But you said that currently simulations are used to roughly eliminate terrible candidates. So I am o.k. with simulations no…
 
 
4 hours later…
Resonating
Resonating
3:38 PM
@m1clee There aren't core design principles. To summarize bluntly: Things do stuff, but mostly by accident.
2
One really interesting MD application that Klaus Schulten is working on is kind of 'reverse MD'. He calls it the computational microscope, and the case study is a simulation of the lipid bilayer
stability of the bilayer in certain temperature and pH ranges is experimentally easy to test, but a consequence of emergent properties of the lipids in the bilayer. Different inter-molecular forces that are really hard to measure directly can be simulated and if the simulation has similar properties to reality, that hints that information provided to the simulation is correct.
It's exactly equivalent to 'well this membrane is made of an unknown material, but C18 phospholipid membranes have those properties also, so it's probably made of C18 phospholipids'
They're not accurate enough to do anything but improve the accuracy of MD simulations yet, but that's an important first step. :D
 

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