Paper was rejected today! Scanning through the reviews, there were some factual/scientific errors that need to be corrected before it can be published 😱 Happy that peer review caught this, would much rather publish a better paper later than rush one out with errors

Reviving this account to say that the last paper from my PhD is out in final form! Here, we look at how the timing of artificial tactile sensations (delivered via intracortical microstimulation/ICMS) is perceived relative to visual cues in two participants with spinal cord injuries. 🧠✋👀

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

Are you a grad student or postdoc at the bench in the UC system? If so, please DM. (for the record, this is a question about laboratory procedure, not any individual PI) #chemsky ⚗️

Here at the BV-BRC workshop - refreshing to be at a workshop without a set problem to solve. Learning just for the sake of learning 😉

Some crystal structures show evidence of multiple stable conformations, such as loops or side chains with two distinct regions of density. These can be correctly modeled by MD, but not modern protein ensemble prediction tools like AlphaFlow or DiG (BioEmu not tested) www.biorxiv.org/content/10.1...

This is a cool program I've worked with for a few years matching STEM professionals and students as pen pals; if you're a 5th-8th grade teacher interested in pen pals for the fall, check out prescientist.org/for-teachers/

every time I'm off blue sky for more than a day or two and return, my feed (I only follow scientists) morphs into a tsunami of political clickbait, worse than twitter. Blocking left and right but it never gets any better. Spending less and less time here because of all the political junk smh

not attending but met up with @leftymiller.bsky.social at #ACSSpring2025! I feel people are always excited about the science at conferences but I'm always excited about the connections and the people behind the science

happy to say it - our projects are hiring again!

Water-mediated interactions between glycans are weakly repulsive and unexpectedly long-ranged https://www.biorxiv.org/content/10.1101/2025.02.16.638483v1

Everything is chaos, but I wanted to share some awesome recent science from the lab that hints at where the future of biomolecular simulation is headed: Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.

exciting times! Will definitely be trying this out

#compchem Good read: Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias #compchemsky #biosky pubs.acs.org/doi/10.1021/...

🚨Preprint Alert!🚨 #ProteinDesign is advancing rapidly—wouldn't it be great to seamlessly combine design tools to achieve more than what each can do alone?🤔 Here, we introduce AI.zymes: A modular platform for evolutionary #EnzymeDesign.♻️🖥️ biorxiv.org/content/10.1... 1/🧵

We’re thrilled to announce the launch of Bind Research, the UK’s first not-for-profit Focused Research Organisation, with long-term support from the Department for Science, Innovation and Technology’s Research Ventures Catalyst Programme, industry, and charities.

We developed a computationally efficient method to predict hot spots driving conformational changes in small molecule sensing proteins. It can easily be generalized to explore allosteric couplings in a wide range of proteins. Code available in the preprint, check it out ! #compchem #compbio

CDR3 loop conformation, specifically whether the C-terminus is kinked or not, is a major determinants of whether a nanobody-antigen complex is correctly predicted using SOTA protein structure prediction software doi.org/10.1021/acs....

First new work from @moldynfr.bsky.social and me in collaboration with Sebastian Milster and Joe Dzubiella herein Freiburg: coarse-graining the transport dynamics of particles through responsive media via Langevin equation models. #Chemsky #compchem #softmatter arxiv.org/abs/2501.18484

Our colleagues in Prague have released a database for molecular biophysics data - mbdb-data.org! 🌍📊 A great step forwards FAIR data in biophysics. 🙌✨ @mosbri.bsky.social

MSKCC is looking for an AI Drug Discovery Lead to drive collaborations between researchers and pharma/biotech within the Office of Technology Development to accelerate the discovery and development of new therapeutics: www.linkedin.com/jobs/view/41...

There's just one week until the application period ends for the Frontera Fellowship! Collaborate with experts at the Texas Advanced Computing Center and use the powerful Frontera supercomputer to aid your research. Applications close February 7. Learn more: bit.ly/425QQc7

The Living Journal of Computational Molecular Science (LiveCoMS) is on BlueSky! Check out our recent blog post on why @livecomsjournal.bsky.social matters to find out more about us: livecomsjournal.org/index.php/li... #compchem #chemsky

Let’s stop treating "leaving academia" as negative. Scientists train for academia, industry, or what suits them. Industry isn’t an alternative; it’s a choice. In fields like engineering, most PhDs go to industry, and no one calls it "leaving academia." We should train scientists for diverse paths.

Our newest preprint is out. A PyMOL plugin giving access to a broad suite of high-performance, fast, and easy to use methods for virtual screening (50K molecules/h), docking, analysis of molecular interactions, dynamics, engineering permitting complex workflows.

Molecular simulations or AI models produce ever larger and more complex datasets. Comparing different conditions to find meaningful patterns is a bottleneck for many projects. We address this with PENSA, a flexible open-source analysis library. Now out in JCP: doi.org/10.1063/5.02... 🧪 #CompChem

We are excited to announce that the call for the new SciLifeLab PULSE postdoctoral program is now open! This unique program invites talented researchers to propose individually designed projects see : www.scilifelab.se/research/pul.... The deadline for applications is March 31, 2025.

1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce". Prepare to get cheesy, I'm glad to share the Cacio e paper preprint: arxiv.org/abs/2501.00536

Per an email from Google DeepMind: Alphafold 3 is not licensed for academics to use for work that leads to a vaccine (pandemic preparations, anyone?). If structure prediction performance is comparable, people will leave AF3 for competitors with more permissive licenses

Back by popular demand, I present PPI Prediction Challenge #2. My claim: I AM SKEPTICAL COMPUTATIONAL APPROACHES CAN PREDICT WHETHER TWO PROTEINS INTERACT. Someone prove me wrong (take two). docs.google.com/forms/d/e/1F... 1/n

While dockers are keep docking (now with diffusion and AI😀), Pat Walters and Ajay Jain show sobering assessment of ‘perceived’ accuracy of such methods! Diffdock shots fired 🔥 The conclusion is totally worth reading in full! #chemsky #compchemsky arxiv.org/abs/2412.02889

Another onymous, impact neutral review sent off. This time for J Comp Chem proteinsandwavefunctions.blogspot.com/2016/01/writ...

Quick introduction since things are taking off around here - I’m Isabelle, a researcher in sensorimotor neural prosthetics. My interests include brain computer interfaces, tactile sensation (real and artificial), neurostimulation, and motor intention 🧠🤖

Do you know of any AI for Drug Discovery skeptics or critical voices here? 🤖💊🤔 Trying to collect a starter pack with people one can follow to avoid being stuck in the #BioAI bubble. Feel free to nominate yourself! #ChemSky #DrugDiscovery #DrugDesign #CompChemSky #MedChem

Excited to share that we are hiring a Bridge to Faculty Postdoc in Microbiology and Immunology at the University of Illinois Chicago. Please reach out if you have any questions about the program. And please share broadly. uic.csod.com/ux/ats/caree...

Really fortunate to have had the honor of being featured as part of NVIDIA SC24 special address by Jensen Huang and Ian Buck. This summarizes a lot of the work that is ongoing in the group highlighting the role of LLMs, multi modality and generative AI. youtu.be/eKzNKxWUeCE

Heyo everyone, I'm Christian, a postdoc at @ramanathanlab.bsky.social. I use computers to study protein dynamics for vaccine design. Look forward to connecting!