Excited to share our new review on Proximity-Based Modalities for Biology and Medicine | Just out ASAP in ACS Central Science ACS Central Science pubs.acs.org/doi/10.1021/ac…

Now out in slightly shorter form :) nature.com/articles/s4158… Kotaro Tsuboyama Justas Dauparas Elodie Laine Sergey Ovchinnikov

I'm happy to announce that we've released the entire PocketMiner training and validation data on our Github with detailed instructions. This should make it much easier for others to train and test models for cryptic pocket prediction. (github.com/Mickdub/gvp/tr…)

👉We recently published Leonard's and Helmut's study explaining "Why solvent response contributions to #solvation free energies are compatible with Ben-Naim's #theorem" arXiv.org Feedback most welcome! Read it here: arxiv.org/abs/2306.09392

Toward docking and interface design, our latest DL tool is a graph neural net for protein interfaces, with the representation learned in different structural contexts. Work by Dr. Sai Pooja Mahajan, also with Jeff Ruffolo. biorxiv.org/content/10.110…

New paper led by Robinson Research Group and first author Haiping Tang. Delighted to have collaborated with the multidisciplinary team via Dheeraj Prakaash and Conrado Pedebos. Fun to work with David B Sauer and Katharina L. Duerr OMass Therapeutics

"Reliable protein-protein docking with AlphaFold, Rosetta and replica-exchange" Some promising results on antibody-antigen complex prediction biorxiv.org/content/10.110…

Now out in JCTC: Our paper on our Separated Topologies method for more flexible relative free energy calculations, combining benefits of relative and absolute calculations. pubs.acs.org/doi/10.1021/ac…

Online now! Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction dlvr.it/SvcNTG

Thrilled to have our genAI NeuralPLexer research featured on the cover of Nature Machine Intelligence. The pub shows how our model has set the standard for 3D protein-ligand structure prediction for drug discovery. Thanks to our collaborators NVIDIA AI and Caltech nature.com/natmachintell/…

It took a while but it's here: the Fragmenstein preprint! chemrxiv.org/engage/chemrxi… A big thank-you to everyone who helped in its creation, especially user feedback!

Extremely happy to present our work, a tour de force of 10+ years, where we show the structural analysis and conformational dynamics of a holo-adhesion GPCR and reveal interplay between extracellular and transmembrane domains. A thread: 1/8 tinyurl.com/mvwf7kan #gpcr #drgpcr

🎉🚀 Excited to share that my internship work, "Benchmarking Active Learning Protocols for Ligand Binding Affinity Prediction," has been published in ACS JCIM & JCTC Journals! 🔗 pubs.acs.org/doi/10.1021/ac… Find 🧵 below for a quick overview. Exscientia

Wow! Time-resolved cryo-EM of G-protein activation by a GPCR Congrats! nature.com/articles/s4158…

Excited that our #OpenFold is out! Following the recent #AlphaFold3 announcement, the need for a trainable, fast, and efficient pipeline for biomolecular modeling is becoming more critical! 1/5

Molecular generative models can *directly* optimize for synthesizability using retrosynthesis models! Check out initial results which can be an alternative to synthesizability-constrained generation Pre-print: arxiv.org/abs/2407.12186… Code: github.com/schwallergroup… (1/2)

Accelerating Fragment-Based Drug Discovery Using Grand Canonical Nonequilibrium Candidate Monte Carlo - The paper introduces the Grand Canonical Nonequilibrium Candidate Monte Carlo (GCNCMC) method, a cutting-edge approach designed to overcome limitations in molecular dynamics

FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling - FlexSBDD is a novel deep generative model designed to account for protein flexibility during drug design, offering a major leap in generating 3D ligand molecules that bind more effectively to target proteins.

Check out this review article the great Dave Nichols and I wrote on the "Chemistry/structural biology of psychedelic drugs and their receptor(s)". Online today! This is a big milestone as it represents the first independent publication from my lab! bpspubs.onlinelibrary.wiley.com/doi/epdf/10.11…