1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

📣 ❗2nd Preprint of the Summer ❗ 📣 "Kinase inhibitors can change protonation or tautomeric state upon binding." LInk: doi.org/10.64898/202... We find that kinase-inhibitors can change in net-charge and tautomer state upon binding (from solution-state to kinase-bound), affecting med-chem choices!

In collaboration with Jiwon Seo‘s group at GIST, we are pleased to be co-authors on a new paper describing the structure of peptoid oligomers in nonpolar solvent! doi.org/10.1021/acs.... 1/n

Noncanonical Folding of Peptoid Oligomers: Formation of a Closed Conformation in Nonpolar Solvent

Conformational behavior of peptoids in low-dielectric solvents remains poorly understood despite its relevance to membrane environments. Here, conformations of N-(S)-1-phenylethylglycine (Nspe) homo-o...

doi.org

Just submitted my public comment on the new proposed OMB rules before the July 13 deadline. You can too, here: www.federalregister.gov/documents/20... Helpful guidance found here: * www.acs.org/policy/washi... * elizabethginexi.substack.com/p/what-we-ne... * www.biophysics.org/blog/what-is...

📢 We're hiring a PhD student (4 years) in computational chemistry at Freie Universität Berlin. Research on molecular dynamics, molecular kinetics, rare events & machine learning. Apply by 3 Aug 2026: jobs.fu-berlin.de/job/Research... #CompChem

Our lab's paper on the de novo design of small-molecule binding proteins is out! In it, we show how neural nets can be trained and used to design binders to drugs with very high success rates. www.nature.com/articles/s41...

Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature

 By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing p...

nature.com

New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)

Excited to share our work describing structural ensembles of protein folding intermediates on the ribosome is now published in @natsmb.nature.com ! www.nature.com/articles/s41... Very grateful to co-first author @sammyhschan.bsky.social, our supervisor John Christodoulou and all our co-authors.

Structures of protein folding intermediates on the ribosome - Nature Structural & Molecular Biology

Atomistic structural ensembles of protein folding intermediates on the ribosome are resolved by comprehensive 19F nuclear magnetic resonance analyses integrated with molecular dynamics simulations, pr...

nature.com

In May, the @openbind.bsky.social project (hosted at @diamondlightsource.bsky.social , part of Instruct-UK) produced its first public release of experimental data. This represents a crucial milestone for open science! You can read more on our website: instruct-eric.org/news/openbin...

OpenBind's First Public Release

Instruct-ERIC is a pan-European research infrastructure in structural biology, making high-end technologies and methods available to all European researchers.

instruct-eric.org

🧪⚛️ Our paper is finally published in Phys Rev Research! doi.org/10.1103/cnfz... Can cells make decisions using equilibrium physical principles, without resorting to irreversible, energy-consuming signaling cascades? We say yes, with the help of self-assembling membrane proteins! 🧵(1/7)

Time-resolved experiments are powerful, but difficult to interpret ⏱️💃 In "A Bayesian Approach to Interpret Time-Resolved Experiments Using Molecular Simulations" Carl Henning Hansen and Simone Orioli developed an approach to use MD to interpret time-resolved experiments doi.org/10.1021/acsp...

Why is it so difficult to predict accurate mutational effects on protein stability? We explored the contribution from changes in native state configurational entropy in this paper, which also happens to be the last from my PhD. A short thread of why this matters. 1/n doi.org/10.48550/arX...

arXiv q-bio.BM Biomolecules@qbiobm-bot.bsky.social · 3mo ago

Lindorff-Larsen, Best, Mittermaier, Kay, Dobson, Vendruscolo: Detection of residual native state entropy changes upon mutation in Fyn SH3 https://arxiv.org/abs/2605.14496 https://arxiv.org/pdf/2605.14496 https://arxiv.org/html/2605.14496

Now published in NSMB! Paper: doi.org/10.1038/s415... Full PDF: rdcu.be/fhBtI Overview of additions since the preprint👇 (1/5)

Evaluating generalization in protein–ligand cofolding methods - Nature Structural & Molecular Biology

This work introduces the Runs N’ Poses dataset for benchmarking deep learning methods on the protein–ligand complex prediction task. It shows that current methods rely on memorization, challenging the...

doi.org

Peter Škrinjar@peterskrinjar.bsky.social · last yr.

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹! www.biorxiv.org/content/10.1... 🧵👇 (1/n)

Have you read about our GNN model for assigning partial charges? It's at the heart of both our Sage 2.3.0 force field and the protein force field we're developing. The paper was published last month in JCTC. pubs.acs.org/doi/10.1021/...

Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model

Partial atomic charges are a fundamental component underlying classical molecular simulations, but assigning charges remains a computational bottleneck; many common methods rely on quantum mechanical ...

pubs.acs.org

openfe now supports simulations of membrane proteins! openfree.energy/science/upda...

I am happy to share a review I recently wrote on the design of peptide binders. It gives an overview of experimentally validated tools and discusses the challenges of why peptide design is more difficult than the design of classical protein binders. www.chimia.ch/chimia/artic...

Very excited to share MIMIC: check it out! An amazing team effort!

Samuel Sledzieski@samsl.io · 3mo ago

Introducing MIMIC: a new foundation model trained natively across DNA, RNA and proteins. MIMIC is multimodal and generative: it can use structure, regulation, evolution, and experimental context to infer missing biology or design new sequences. 🧵⬇️

We are inviting applications for a research scientist/postdoctoral associate position in the broad field of computational chemistry/biophysics/AI-driven drug discovery. Please DM your CV and 2 reference names

We just preprinted one of my favorite studies @FlatironInst . I was lucky to be part of an amazing team studying the effects of rapid cooling to preserve samples in cryoEM. Read on to learn about the limits of cryoEM for biophysics and how to overcome them www.biorxiv.org/content/10.6...

Our latest Science Update video is here, and it's a big one! Science Lead @lilyminium.bsky.social, in spite of a cough, delivers 25 minutes of non-stop scientific action and high-octane thrills across all our areas of force field science. youtu.be/ZIw2JlCfSso

April 2026 Science Update

YouTube video by Open Force Field Initiative

youtu.be

We introduce ConforNets, a mechanism for conformational control in AlphaFold3 models - SoTA at producing diverse conformations on every multistate benchmark (N=104) - Novel capability: transfer state from one protein to another Outperforms BioEmu, ConforMix and AFsample3 🧵1/8

Our new FEP sampling engine GrandFEP is now on GitHub and Chemrxvi. We implemented GCMC, Water-Swap MC, REST2, and terminal-flip MC in OpenMM. Github github.com/deGrootLab/G... Chemrxiv doi.org/10.26434/che...

something to digest... ;-)

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 6mo ago

Isomorphic Labs Drug Design Engine (IsoDDE), a unified computational drug-design system Announcement: www.isomorphiclabs.com/articles/the... Report: storage.googleapis.com/isomorphicla...

Our recent preprint shows that metastable, short-lived PPIs captured by MD and IGME define key design targets for PROTACs, enabling rational discovery of sub-nanomolar RIPK1 degraders. Great collab w/ Weiping Tang! Congrats to Yue & co-authors! chemrxiv.org/doi/full/10.... -

"In contrast to previous attempts at iterative optimization, we employ a validation set to determine convergence. Using a validation set circumvents problems with parameter convergence and flags when overfitting occurs" pubs.acs.org/doi/full/10....

Robust and Automated Force Field Parameterization Using Validation Sets and Active Learning

Molecular mechanics force fields enable atomistic simulations of complex systems that are too large for a quantum mechanical treatment. Simulation accuracy depends on the parameters employed in the fo...

pubs.acs.org

New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...

Third preprint of the year is from @julianstreit.bsky.social who, with our collaborators at Peptone, show that multithermal On-the-fly Probability Enhanced Sampling (OPES) enables efficient generation of atomistic ensembles for disordered peptides and proteins 🍝 www.biorxiv.org/content/10.6...

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 7mo ago

Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling https://www.biorxiv.org/content/10.64898/2026.01.17.700112v1

The work by @danialv.bsky.social is now out in @pnas.org with a few changes after peer-review. Have a look if you are interested in lipid transport by bridge lipid transfer proteins (BLTPs)... www.pnas.org/doi/10.1073/...

Vanni Lab at UNIFR, Switzerland@labvanni.bsky.social · 12mo ago

Happy to share the latest from the lab, led by Daniel Alvarez, in collaboration with @lizconibear.bsky.social‬. In this AA-MD tour-de-force, we delve deep into the mechanism and energetics of lipid uptake by bridge-like lipid transfer proteins, and we learn a few interesting things along the way...

When I wrote my latest for @natchem.nature.com on the appropriation of the quantum mechanical lexicon by scam artists, could I have imagined that the surgeon general of Florida would be peddling the woo? Alas, probably. rdcu.be/eXQL (1/3)

Quantum quacks

Nature Chemistry - It is 100 years since the initial development of quantum mechanics, and not only did it bring with it a greater understanding of the world around us, it also introduced a new...

rdcu.be

New Preprint dropped. LAMMPS + ANI, a super fast implementation of MLIPs. Highly parallel (> 1000 GPUS) and much faster than anything else out there ! Work done by the amazing @ignaciopickering.bsky.social, @nickterrel.bsky.social , and Jinze (Richard) Xue. chemrxiv.org/engage/chemr...

LAMMPS-ANI: Large Scale Molecular Dynamics Simulations with ANI Neural Network Potential

Machine Learning Interatomic Potentials (MLIPs), trained with Quantum Mechanics data, can model potential energy surfaces for molecular systems with very high accuracy and extreme speedups compared to...

chemrxiv.org