Here are some of the biggest breakthroughs mentioned in the provided references:
Exascale Simulations for SARS-CoV-2:
Conducted exascale simulations of SARS-CoV-2 spike protein, revealing dramatic spike opening and cryptic pockets, which have implications for drug design and understanding viral infectivity (Zimmerman et al., 2021) .
Ab Initio Protein Folding Simulations:
Achieved molecular simulations of ab initio protein folding for the NTL9 protein, providing insights into the protein folding process (Voelz et al., 2010) .
Markov State Models for Protein Dynamics:
Developed Markov State Models (MSMs) to study protein folding kinetics and dynamics, providing a framework to understand protein conformational changes over long timescales (Bowman et al., 2009; Lane et al., 2011) .
RNA Polymerase II Dynamics:
Investigated the dynamics of RNA polymerase II translocation at atomic resolution, elucidating mechanisms of transcription elongation (Silva et al., 2014) .
Ligand Modulation of GPCR Activation:
Used cloud-based simulations to reveal how ligands modulate G protein-coupled receptor (GPCR) activation pathways, advancing the understanding of GPCR function and drug targeting (Kohlhoff et al., 2014) .
Nanotube Confinement Effects on Proteins:
Demonstrated that nanotube confinement can denature protein helices, providing insights into the effects of nanoscale environments on protein structure (Sorin & Pande, 2006) .
Simulation and Experiment in Protein Folding:
Combined simulation and experimental approaches to reveal slow unfolded-state structuring in acyl-CoA binding protein folding, highlighting the interplay between simulations and experiments (Voelz et al., 2012) .
Advances in Markov State Models:
Improved coarse-graining and adaptive sampling techniques in MSMs, enhancing the modeling of biomolecular dynamics (Bowman, 2012; Zimmerman et al., 2018) .
Insights into Allosteric Sites:
Identified potential cryptic allosteric sites within folded proteins using equilibrium fluctuation analysis, suggesting new targets for drug discovery (Bowman & Geissler, 2012) .
GPCR Activation Pathways:
Revealed ligand modulation of GPCR activation pathways through extensive simulations, providing insights into receptor function (Kohlhoff et al., 2014) .
I don’t see much in there. Doing the simulations is not the same as confirming the simulations.
The question wasn’t did they do they simulation but rather was any major usable outcome validated. Seems very little if anything.
The thing is that many of these things just can’t be measured directly. You can use the information from the simulation to get a deeper understanding of e.g. some receptors (as was done), and use that information for something else. For example to optimize a binder for the receptor, or to manipulate the tonic signalling. But that’s then often a paper building onto the findings from the simulation.
In 1990, they started to sequence the human genome. About a decade later, the shotgun sequencing technique was advanced enough to be used on the human genome. A few years later, it was declared complete. In 2022, it was considered to be gapless, almost 2 decades later.
All of this, plus some other discoveries, led to CRISPR and the ability to edit genes in fully formed beings rather than just a few cells. After decades of research in a number of fields.
One of the things DNA does is make protein. (If you want to look at it a certain way, all it does is determine where and when to make protein.) Part of what makes protein do the thing it does is the shape it takes. (For instance, prions are misfolded proteins that cause other proteins to misfold, and then other weird things happen, like holes in your brain.)
So we have this massively complicated process that makes slightly less complicated things that behave in a variety of ways depending on their shape, which is dependent on the myriad ways they can fold, at the molecular level. And you wonder why they haven’t done a lot when we’re still to a large degree in the data-collecting and validation portion of this massive undertaking. As for what it can lead to, I expect it will be no less revolutionary than CRISPR is and will be, but that could still be decades away.
Here is an AI based summary of top breakthroughs:
Here are some of the biggest breakthroughs mentioned in the provided references:
Exascale Simulations for SARS-CoV-2:
Ab Initio Protein Folding Simulations:
Markov State Models for Protein Dynamics:
RNA Polymerase II Dynamics:
Ligand Modulation of GPCR Activation:
Nanotube Confinement Effects on Proteins:
Simulation and Experiment in Protein Folding:
Advances in Markov State Models:
Insights into Allosteric Sites:
GPCR Activation Pathways:
Sweet
I don’t see much in there. Doing the simulations is not the same as confirming the simulations. The question wasn’t did they do they simulation but rather was any major usable outcome validated. Seems very little if anything.
The thing is that many of these things just can’t be measured directly. You can use the information from the simulation to get a deeper understanding of e.g. some receptors (as was done), and use that information for something else. For example to optimize a binder for the receptor, or to manipulate the tonic signalling. But that’s then often a paper building onto the findings from the simulation.
Yeah so that’s the question, was any drug or other technique successfully optimized
In 1990, they started to sequence the human genome. About a decade later, the shotgun sequencing technique was advanced enough to be used on the human genome. A few years later, it was declared complete. In 2022, it was considered to be gapless, almost 2 decades later.
All of this, plus some other discoveries, led to CRISPR and the ability to edit genes in fully formed beings rather than just a few cells. After decades of research in a number of fields.
One of the things DNA does is make protein. (If you want to look at it a certain way, all it does is determine where and when to make protein.) Part of what makes protein do the thing it does is the shape it takes. (For instance, prions are misfolded proteins that cause other proteins to misfold, and then other weird things happen, like holes in your brain.)
So we have this massively complicated process that makes slightly less complicated things that behave in a variety of ways depending on their shape, which is dependent on the myriad ways they can fold, at the molecular level. And you wonder why they haven’t done a lot when we’re still to a large degree in the data-collecting and validation portion of this massive undertaking. As for what it can lead to, I expect it will be no less revolutionary than CRISPR is and will be, but that could still be decades away.