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20 ms·

1.
by cing 3mo ago
There have been efforts to standardize antibody reagent testing that are sorely underfunded/undervalued, https://ycharos.com/ ( https://www.nature.com/articles/s41596-024-01095-8 )
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by cing 8mo ago
Github issues will be the real social network for AI agents, no humans allowed!
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by cing 1y ago
Author made it clear this was an educational essay, but concluding the problem has very limited therapeutic applications comes across like a bit of a take down for Atomic AI's platform.
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by cing 3y ago
Heck yes. Music pirates have done a whole lot to help preserve hip-hop history by ripping/archiving countless rare/underground 12" and cassettes that are definitely not available on streaming platforms; we're talking alt
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by cing 4y ago
This has been a previous area of research for Google ( https://ai.googleblog.com/2017/04/predicting-properties-of-m... ). It remains routine to benchmark GNNs and other molecular machine learning models on predictin
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by cing 5y ago
I agree with the sentiment of this paper (AF can enable drug discovery), but in this specific instance, the authors had a real opportunity contribute a general finding to the scientific community but instead they put in the lowest amount of
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by cing 5y ago
Not saying it's easy but ribosomal synthesis of consecutive non-canonical amino acids has been achieved by some groups ( https://www.cell.com/cell-chemical-biology/fulltext/S2451-94... , https://pubs
8.
by cing 5y ago
Our startup routinely orders the synthesis of hundreds of peptides for technology validation and drug discovery research (not suitable for human consumption). Costs for a small quantity through a contract research organizion can be $200-$20
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by cing 5y ago
There is innovation in this space. From green chemistry initiatives to replace hazardous solvents by CROs/industry invested in large-scale production of peptides, https://www.bachem.com/news/bachem-novo-nordisk-red
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by cing 5y ago
One of the reasons we don't have them all is that individual genes can encode for multiple protein isoforms through alternative splicing. AlphaFold was only run on one. Otherwise, there's lots of important biochemical/biophys
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by cing 5y ago
Just in case you're not joking, it's worth noting that the majority of distributed molecular simulation (past and present) is spent studying "folded proteins" to discover structures of proteins that are often hidden from
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by cing 5y ago
Everything between the BRCT and RING domains of BRCA1 is an intrinsically unstructured region which DeepMind correctly predicts, https://pubmed.ncbi.nlm.nih.gov/15571721/ Another famous one would be R-domain of CFTR, w
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by cing 5y ago
Yet, there were still 136 human teams who competed in CASP14 ( https://predictioncenter.org/casp14/docs.cgi?view=groupsbyna... ), including DeepMind. Even if a significant fraction of these projects were done piggy-backi
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by cing 5y ago
The process is described in Supplementary, but where do you see the code to train the model? The repository is the inference pipeline.
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by cing 6y ago
There's quite a nice plot from a review paper of D.E. Shaw Research that lists the timescale of several biological processes (and compares it to other experimental methods), https://www.annualreviews.org/doi/full&#
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by cing 7y ago
So what you're saying is: https://xkcd.com/1831/ , except that CS/ML practitioners have a negative impact by trying to contribute without understanding the nuance. I think the next logical question is: how man
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by cing 7y ago
Best of luck. Although not in the majority, there have been many academic recruiting posts on HN in the past.
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by cing 8y ago
I know that docking using GPU is about an order of magnitude faster than CPU (see today's Schrodinger 2019-1 release notes, https://youtu.be/K4AYdBvuOe4?t=90 ). Is there a way of doing GPU accelerated precomputation tho
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by cing 8y ago
The majority of ongoing Folding@Home tasks are not aimed at structure determination, but rather simulating the conformational dynamics of folded proteins (exploring the energy landscape rather than searching for the global minimum). Very fe
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by cing 8y ago
The path is most likely through reliable structure prediction of drug targets. That would open up rational drug design projects that may have previously been impossible. The only problem is that experimental structure determination is so go
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by cing 8y ago
This reminded me of a nice article about how blindness evolved in the Mexican cavefish, http://seedmagazine.com/content/article/pz_myers_on_how_the_...
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by cing 8y ago
I'm a cofounder of a start-up working on near-term applications of quantum computing in biology, specifically on the protein structure side of things ( https://www.proteinqure.com ). There are many self-contained subproblems
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by cing 8y ago
ProteinQure | Machine Learning Engineer, Computational Biologist | On-site, full-time | Toronto, Canada ProteinQure is an early stage deep techy startup building the next generation of computational drug design tools helping to reimagine h
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by cing 8y ago
I'm confused as to why you're addressing this commenter using "argument from authority" when you seem to be weakening your position, suggesting that studying protein dynamics has led to significant advances in the field.
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by cing 8y ago
Relay is not doing protein engineering or working on predicting protein structure. They are making models of protein dynamics to assist in drug discovery (often using already determined structures). We both disagree with the parent commente
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16 Pitfalls to Avoid When Building a Computational Therapeutics Company(a16z.com)
3 points by cing 8y ago|0 comments
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by cing 9y ago
The PDB represents the best we have, but I wouldn't call it a great dataset for learning. The 150,000 known structures are a drop in the ocean when it comes to the space of possible sequences/structures.
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by cing 9y ago
DeepMind and others are trying. "Hassabis said the company is now planning to apply an algorithm based on AlphaGo Zero to other domains with real-world applications, starting with protein folding." [1] https://www.bloom
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The business of improving global health(gatesnotes.com)
2 points by cing 9y ago|0 comments
30.
by cing 9y ago
Not sure what OP is thinking, but you can look at this example of a commercial product designed for the prediction of off-target effects ( https://cyclicarx.com/ligandexpress/ ).

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