Asklemmy

Here is an AI based summary of top breakthroughs:

Here are some of the biggest breakthroughs mentioned in the provided references:

1. 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) .

2. 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) .

3. 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) .

4. RNA Polymerase II Dynamics:

   • Investigated the dynamics of RNA polymerase II translocation at atomic resolution, elucidating mechanisms of transcription elongation (Silva et al., 2014) .

5. 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) .

6. 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) .

7. 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) .

8. 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) .

9. 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) .

10. GPCR Activation Pathways:

    • Revealed ligand modulation of GPCR activation pathways through extensive simulations, providing insights into receptor function (Kohlhoff et al., 2014) .

intarrwebs

Sounds like an intranet for pirates!

I forgot there is also the SETI@home project working on the same principle. Searching Extra Terrestrial Intelligence 👽👽👽

It's basically a software you install to donate your computer's idle power (ie typicallywhen the CPU does nothing) to help scientists with the huge amount of calculations that simulating the folding of protein requires and that not even the best supercomputers can achieve alone in a reasonable time. It's distributed science. I'll admit I still don't grasp what folding means in the context of proteins. The programme folding@home started around 2000 and is still running ie you can still donate CPU time today

Folding@Home uses your computer trying to find new therapeutics by simulating protein dynamics.

If 10,000 people work one hour in one day, then that day still had 10,000 hours worked even if a day is only 24 hours. Same with CPUs, many of them run on more than just one core.

I mean I had the programme running for 10 years, donating whenever it was on and idle or on a low load. It was not necessary to be perfectly idle, the programme could take just e.g. 50% of the CPU. (Famously on a core2duo running programmes that were not multi-core). All in all my computer was probably on 12 hours per day