Very informative post! You did a good job explaining replica exchange. The analogy of multiple parallel universes, each of which has different physical laws, was very effective. I especially liked your use of the word "alchemical" to describe these deviations from physical constraints.
If I correctly understand the figure comparing different techniques for cryptic pocket discovery, it's saying that SWISH-X is successful at identifying confirmed cryptic pockets. However, how effective is this method for identifying *novel* pockets? Considering that the replica exchange approach involves deviating from physical laws, I would expect a fairly high rate of false positives. Has this been estimated?
Fascinating work. I'm curious if organisms that persist in several distinct environments over their life (like parasites) have proteins that exhibit more cryptic switches? A tool like SWISHX will be invaluable for systematically testing these kinds of hypotheses.
Very informative post! You did a good job explaining replica exchange. The analogy of multiple parallel universes, each of which has different physical laws, was very effective. I especially liked your use of the word "alchemical" to describe these deviations from physical constraints.
If I correctly understand the figure comparing different techniques for cryptic pocket discovery, it's saying that SWISH-X is successful at identifying confirmed cryptic pockets. However, how effective is this method for identifying *novel* pockets? Considering that the replica exchange approach involves deviating from physical laws, I would expect a fairly high rate of false positives. Has this been estimated?
Fascinating work. I'm curious if organisms that persist in several distinct environments over their life (like parasites) have proteins that exhibit more cryptic switches? A tool like SWISHX will be invaluable for systematically testing these kinds of hypotheses.