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A diffusion model for programmable protein structure generation, with code and wet-lab experiments. Andrew Beam Wujie Wang Generate:Biomedicines nature.com/articles/s4158…

My first paper in the Alberto Perez group! Opportunities, strategies, and challenges in peptide-based drug discovery wires.onlinelibrary.wiley.com/doi/10.1002/wc… Bright future ahead for the marriage between physics-based and AI models #compchem #drugdesign #MachineLearning UF Chemistry

A new version of AlphaPulldown by DingquanYu. Includes experimental support for multimeric templates in AlphaFold by Dmitry Molodenskiy and interface to crosslink-based modeling AlphaLink2 of Rappsilber laboratory github.com/KosinskiLab/Al…

pubs.acs.org/doi/full/10.10…

For anybody interested in the conformational dynamics and interactions of intrinsically disordered proteins may want to check our recent short review in COSB sciencedirect.com/science/articl…

Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling pubs.acs.org/doi/10.1021/ac… #JCIM Vol63 Issue23 #Bioinformatics

🥳 The paper on using AF2 for protein interaction interface discovery has been published at Molecular Systems Biology! Congratulations to all the authors! Have a look 👉 embopress.org/doi/full/10.10…

Happy to share the publication of our paper in nature Conformational ensembles of the human intrinsically disordered proteome Work led by Giulio Tesei and Anna Ida🕊. I'll post more later, but for now here is a link: nature.com/articles/s4158… and a short movie about the work

Our Manscript "Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model" led by graduate student Tommy Sisk is now out in PNASNews pnas.org/doi/full/10.10…

CombFold from Ben Shor and Dina Schneidman is a combinatorial and hierarchical assembly algorithm for predicting structures of large protein complexes that makes use of pairwise interactions between subunits as predicted by AlphaFold2. nature.com/articles/s4159…

We've got a cool paper out with Grzegorz Grabe and Sophie Helaine lab! This bacterial🦠toxin-antitoxin system is doing some crazy stuff, and we could help explain the structural role of DNA in the whole process: nature.com/articles/s4159… Check out the long explainer movie I made

Happy to share preprint from our group on understanding the binding pocket dynamics of nuclear receptor REV-ERB. Shriyansh led the work. biorxiv.org/content/10.110…

AlphaFold lecture slides are here: amyxlu.github.io/data/alphafold… Truly believe in AlphaFold as an AlexNet moment for biology, to endure for its empirical validation of the computational ingredients it propounds rather than (just) as a tool. Super fun to do this deep dive 🧬

As Computational Biology @IITGN group starts its exploration of modeling plant circadian rhythms, some interesting results soon. In the mean time, check out a comprehensive review of differential equation based models in this area by PhD student Shashank Kumar Singh doi.org/10.1007/s11103…

Exciting new work from Qian Cong's group on predicting human protein interactome. Leveraging new eukaryotic genomes, new RoseTTAFold2 trained on +/- pairs of PPI and large distilled dataset of domain-domain interactions! 🤩 biorxiv.org/content/10.110…

BREAKING NEWS The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”

In 2003, this year’s chemistry laureate David Baker succeeded in designing a new protein that was unlike any other protein. This was the first step in something that can only be described as an extraordinary development. A few of the many spectacular proteins created in Baker’s

This year’s #NobelPrize laureates in chemistry have revealed proteins’ secrets through computing and artificial intelligence. Chemists have long dreamed of fully understanding and mastering the chemical tools of life – proteins. This dream is now within reach. 2024 chemistry

One of my favourite works in the lab is out now! Classical modeling approaches are still the key to understanding complex structures like NOTCH. It’s amazing how these structural models can help us capture the perturbations caused by disease mutations in finer detail.

Wrapping the year by a new preprint from the lab. Saman and Deepak found that LC3 clusters as islands on autophagosomes that overlay with PI lipids! Great collaboration with the awesome Nitin Mohan lab! LC3 forms functional nanocluster on autophagosome biorxiv.org/content/10.110…