Using a bunch of signals to create a 3d representation of the system
features
- cyro-EM
- x-ray
- tomo
- glynomics/libidomics
- genetics
studying large-scale viron surface protein behavior using MD
“we are so biased by what we can see experimentally, so do MD”
“breathing” motion
- proteins of specific virons “breath”: oning and closing an entire backbone group; this is not yet quantified in physical modeling
- when its open, the “breathing open” motion causes the virus to be vunerable
- so some antibodies jam into the open position
“head tilting” motion
- when its tilted, there is an epitope that becomes exposed
- this is a site that’s possible for introduction of what’s needed
overall architecture
- use conventional MD
- discover regions of instability (see above for examples) for possible binding surfaces
- bam inhibition!
maybe at some point run a cyro-EM to experimentally run some