Sharing our press release on the significance of our recent Nature Communications article, along with my personal perspective on its impact. Hope you enjoy the read! 🔗 pan.pl/en/ippt-pas-sc… Thoughts and feedback welcome!

ProteinsPlus: a publicly available resource for protein structure mining Nucleic Acids Res 1. ProteinsPlus is an open-access web server offering a comprehensive suite of tools for protein structure analysis, protein-ligand modeling, and PDB mining—making it one of the most versatile

Investigation of Electrostatic Effects on Enyzme Catalysis: Insights from Computational Simulations of Monoamine Oxidase A Pathological Variants Leading to the Brunner Syndrome #MolecularDynamics pubs.acs.org/doi/10.1021/ac… #JCIM Vol65 Issue7 #compchem

Next Tues (5/13) at 4PM ET, we will have Anna Lauko and Sam Pellock present "Computational design of serine hydrolases" Paper: science.org/doi/10.1126/sc… Sign up on our website for zoom links!

🚨 Major Update: We’ve released ColabSeprot, the sister of ColabSaprot, featuring ESM1b, ESM2, ProTrek, ProtBert! 🎉 Fine-tune protein language models in just a few clicks—no coding required! 🧬✨ 🔗 ColabSeprot: colab.research.google.com/github/westlak… ColabPLM video: youtube.com/watch?v=nmLtjl…

Guide your favorite protein sequence generative model １．This paper introduces ProteinGuide, a general framework for conditioning pre-trained protein generative models—like ProteinMPNN and ESM3—on arbitrary user-defined properties, without retraining the models.

Co-folding, the Future of Docking – Prediction of Allosteric and Orthosteric Ligands １．This study benchmarks emerging protein-ligand co-folding methods for predicting both orthosteric and allosteric binding modes, revealing that current deep learning models still strongly

Nice study from AstraZeneca (EvaNittinger, Özge Yoluk, Alessandro Tibo, Gustav Olanders) on the prediction of allosteric vs orthosteric ligands using a curated set of 17 targets! I've always been curious about the performance of cofolding models on allosteric interactions and

Reading group tomorrow: Jason Yim and Woody Ahern present "Atom level enzyme active site scaffolding using RFdiffusion2" biorxiv.org/content/10.110… Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeaking

New publication out! doi.org/10.1093/bioinf… VTX is open source and freely accessible for non commercial use Builds available at vtx.drugdesign.fr

MDML: Deep Learning for Molecular Simulation is officially here! 🎉 Streamline your workflow with powerful features: Featurization, SFA, ML-based RCs, PLUMED integration & hotspot identification. Get ready to accelerate your simulation analysis! github.com/svats73/mdml/t…

If you missed out on Sarel Fleishman's extraordinary talk last night, have no fear - you can check out the recording 👇 youtu.be/2aaWh8yVq8U

Artificial Intelligence And First Principle Methods In Protein Redesign: A Marriage Of Convenience? １．This study systematically compares modern AI-based tools and first-principle force field methods for multi-site protein redesign, focusing on structure, stability, and

Predicting Protein Function in the AI and Big Data Era １．This perspective provides a comprehensive overview of how deep learning and big data are reshaping the prediction of protein function—transitioning from homology-based inference to AI-driven structural and interaction

A deep learning method enables the design of proteins with distinct conformational states, mimicking the dynamic properties of natural signaling proteins #NBThighlight science.org/doi/10.1126/sc…

Download our 2024 Annual Report for an overview of recent activities and the global impact of PDB data and RCSB PDB services. pdb101.rcsb.org/news/681cb4613…

Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules #machinelearning #compchem pubs.acs.org/doi/abs/10.102…

Guide your favorite protein generative model with experimental data? Meet ProteinGuide - a method to condition pre-trained models on properties without retraining. We validated it both in silico by guiding ProteinMPNN and ESM3 on 3 tasks and in vitro by engineering base editors.

🚀 Excited to release BoltzDesign1! ✨ Now with LogMD-based trajectory visualization. 🔗 Demo: rcsb.ai/ff9c2b1ee8 Feedback & collabs welcome! 🙌 🔗: GitHub: github.com/yehlincho/Bolt… 🔗: Colab: colab.research.google.com/github/yehlinc… Sergey Ovchinnikov Martin Pacesa

We just published a quick write-up on BoltzDesign1—the open-source all-atom protein design tool from Yehlin Cho, Sergey Ovchinnikov , Martin Pacesa & Bruno Correia . Congrats to the team for pushing accessible binder design forward! ariax.bio/resources/bolt…