Danial

GitHub - Danialgharaie/mutant-landscape: using pLMs to extract the mutation landscape of protein sequence using pLMs to extract the mutation landscape of protein sequence - Danialgharaie/mutant-landscape

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code here: github.com/Danialgharai...

#proteinengineering #bioinformatics #evolutionaryalgorithms #multifitness #ParetoFront

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once you see the Pareto front, you can pick the kind of compromise that fits your goal.
not perfect, but intentional.

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stability trades off with packing.
solubility pushes in its own direction.
it’s less about finding an optimum, more about exploring the trade-off space.

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working on multi-objective protein design made it clear there’s rarely a “best” sequence.
improving one property often hurts another.

Staying ahead of the curve: a decade of preprints in biology When Cold Spring Harbor Laboratory announced the launch of bioRxiv in November 2013, only the braver or more radical amongst us would have predicted that it heralded a lasting change within the scienc...

Hard to remember that just 12 years ago there was no @biorxivpreprint.bsky.social and almost no one in the biology community preprinted their work. What a long way we’ve come. @reinierprosee.bsky.social and I wrote a thing about how @biologists.bsky.social embraced the preprint world

Hi everyone! I’m looking to join academic labs remotely to collaborate and discuss ideas in structural biology, focusing on computational protein design. I have relevant experience and can share details. Please DM me with any opportunities!

Clustering Proteins by Structure — The Ultimate Guide Explore structural protein clustering with ClusterProt and Kluster tools that classify proteins by their 3D structure. Discover applications in functional prediction, mutation analysis, and protein en...

Learn how to cluster proteins by structure with methods like RMSD and TM-score for comparing 3D shapes. My latest post: neurosnap.ai/blog/post/cl... #bioinformatics

Are these sessions open to the public? They sound super interesting! Also, are there any available recordings of the sessions?

GitHub - Danialgharaie/DSSP-Pre: A Simple Program For Making Predicted Protein Structures Compatible With DSSP A Simple Program For Making Predicted Protein Structures Compatible With DSSP - Danialgharaie/DSSP-Pre

Had trouble getting predicted protein structures to work with DSSP and StrucTFactor, so I wrote a simple C program to handle it. If you’re facing the same issue, here’s the code: github.com/Danialgharai...)
Hope it’s useful!

#MolecularBiology

Had some fun with Boltz!

Introducing Chai-1: A Commercial Alternative to AlphaFold3 Chai-1 is a powerful molecular structure prediction model, now available through Neurosnap for commercial use. Learn how Chai-1 rivals AlphaFold3 in accuracy while offering more flexible access for re...

🚀 Just published a new blog post on Chai-1: an open alternative to AlphaFold3 for commercial molecular modeling!

🔗 Read more: neurosnap.ai/blog/post/in...

#MolecularModeling #Chai1 #AlphaFold3 #DrugDiscovery #Neurosnap #AI #Biotech