iiinova — where your digital self keeps evolving

Christian Seitz @chemchristian.bsky.social · 20/04/2026

It's about time I make this official, I'm super honored to be awarded Elon University's Top 10 under 10 awards for the most exciting alumni from the past 10 years. 1/3

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Christian Seitz @chemchristian.bsky.social · 05/03/2026

Hello everyone, I am looking for my next role in the computational chemistry/biophysics space 🛫 I have 12 years of research experience in protein simulations/SBDD, looking for national lab/industry scientist positions anywhere in the world. Any connections/leads welcomed - thanks in advance! 🙏🏻

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Christian Seitz @chemchristian.bsky.social · 24/11/2025

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

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David Pfau @davidpfau.com · 28/05/2025

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.

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Chemjobber @chemjobber.bsky.social · 22/05/2025

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 ⚗️

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Christian Seitz @chemchristian.bsky.social · 05/05/2025

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 😉

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Diego del Alamo @delalamo.xyz · 23/04/2025

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...

Examples of alternate conformations with environmental explanations.
(A) a protein in two states (open and closed) mediated by allosteric effects; (B) a population of two discrete rotamer states of a sidechain; (C) bound and unbound states due to ligand interaction; (D) different oxidation states of a cysteine pair. Furthermore, some regions in many protein structures exhibit such a degree of flexibility, that no accurate modelling is possible (dashed lines, E). The backbone conformation cannot be determined with crystallographic methods in such cases.

Failure of ensemble prediction algorithms in altloc segments.
Although structure and ensemble prediction techniques based on amino acid sequences are capable of accurately reconstructing the overall backbone structure (left column), they consistently fail to produce viable samples corresponding to one of the two altloc conformations (as shown in the magnified regions in the second through fourth columns).

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Christian Seitz @chemchristian.bsky.social · 16/04/2025

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/

prescientist.org

For Teachers - Letters to a Pre-Scientist

Overview Are you a 5-8th grade STEM teacher in the US who wants to bring Letters to a Pre-Scientist into your classroom? We would love to hear from you! Teacher ...

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Christian Seitz @chemchristian.bsky.social · 11/04/2025

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

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Christian Seitz @chemchristian.bsky.social · 25/03/2025

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

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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 21/02/2025

Water-mediated interactions between glycans are weakly repulsive and unexpectedly long-ranged www.biorxiv.org/content/10.1101/202…

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John Chodera @jchodera.bsky.social · 19/02/2025

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.

Figure 1 from arXiv preprint https://doi.org/10.1101/2025.01.06.631610

Fig. 1 Espaloma is an end-to-end differentiable molecular mechanics parameter assignment scheme for arbitrary organic molecules. Espaloma (extensible surrogate potential optimized by message-passing) is a modular approach for directly computing molecular mechanics force field parameters FFF from a chemical graph G such as a small molecule or biopolymer via a process that is fully differentiable in the model parameters FNN. In Stage 1, a graph neural network is used to generate continuous latent atom embeddings describing local chemical environments from the chemical graph. In Stage 2, these atom embeddings are transformed into feature vectors that preserve appropriate symmetries for atom, bond, angle, and proper/improper torsion inference via Janossy pooling.54 In Stage 3, molecular mechanics parameters are directly predicted from these feature vectors using feed-forward neural networks. This parameter assignment process is performed once per molecular species, allowing the potential energy to be rapidly computed using standard molecular mechanics or molecular dynamics frameworks thereafter. The collection of parameters FNN describing the espaloma model can be considered as the equivalent complete specification of a traditional molecular mechanics force field such as GAFF38,39/AM1-BCC55,56 in that it encodes the equivalent of traditional typing rules, parameter assignment tables, and even partial charge models. Reproduced from ref. 49 with permission from the Royal Society of Chemistry.

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Christian Seitz @chemchristian.bsky.social · 17/02/2025

exciting times! Will definitely be trying this out

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Adrian Bunzel @bunzela.bsky.social · 12/02/2025

🚨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/🧵

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Bind Research @bindresearch.org · 11/02/2025

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.

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Melike @mberksoz.bsky.social · 11/02/2025

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

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Diego del Alamo @delalamo.xyz · 13/02/2025

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....

Nanobodies with extended CDR3 conformations are correctly predicted the majority of the time, whereas kinked CDR3 conformations are rarely correctly predicted

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Osvaldo Burastero @osvalb.bsky.social · 31/01/2025

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

mbdb-data.org

Molecular Biophysics Database

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John Chodera @jchodera.bsky.social · 31/01/2025

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...

linkedin.com

Memorial Sloan Kettering Cancer Center hiring AI Drug Discovery Lead in New York, NY | LinkedIn

Posted 4:46:37 PM. $118,800.00-$196,200.00Company Overview The people of Memorial Sloan Kettering Cancer Center (MSK)…See this and similar jobs on LinkedIn.

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Texas Advanced Computing Center at UT Austin @taccutexas.bsky.social · 31/01/2025

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

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livecomsjournal.bsky.social @livecomsjournal.bsky.social · 30/01/2025

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

livecomsjournal.org

Why LiveCoMS matters | Living Journal of Computational Molecular Science

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Ardem Patapoutian @ardemp.bskyverified.social · 26/01/2025

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.

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Rafael Najmanovich @rnajmanovich.bsky.social · 24/01/2025

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.

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Martin Vögele @martinvoegele.bsky.social · 07/01/2025

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

doi.org

Systematic analysis of biomolecular conformational ensembles with PENSA

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system

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Arne Elofsson @handle.invalid · 07/01/2025

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.

scilifelab.se

PULSE

SciLifeLab PULSE: Program for Future Leaders in Life Science SciLifeLab PULSE is a comprehensive postdoctoral program, that will train 48 future leaders in life sciences. PULSE focuses on innovative, ...

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Giacomo Bartolucci (he) @gbart.bsky.social · 04/01/2025

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

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Christian Seitz @chemchristian.bsky.social · 10/12/2024

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

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Bryan Dickinson @chembiobryan.bsky.social · 10/12/2024

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

docs.google.com

PPI Prediction Challenge #2

For this protein-protein interaction prediction challenge, we present three target proteins: KRAS, RAF (the KRAS binding domain), and Mdm2. For each target protein, we are providing you a list of 8 po...

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Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · 06/12/2024

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

arxiv.org

Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows

The diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, wi...

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Isabelle Rosenthal @neurosenthali.bsky.social · 26/11/2024

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 🧠🤖

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Radoslav Krivak @rdkbio.bsky.social · 22/11/2024

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

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Judith Behnsen @judith-behnsen.bsky.social · 25/11/2024

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...

uic.csod.com

Bridge to Faculty Postdoctoral Research Associate in Microbiology and Immunology

Bridge to Faculty Postdoctoral Research Associate in Microbiology and ImmunologyThe Department of Microbiology and Immunology (MI) at the University o...

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Arvind Ramanathan @ramanathanlab.bsky.social · 26/11/2024

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

youtu.be

NVIDIA SC24 Special Address

YouTube video by NVIDIA

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Christian Seitz @chemchristian.bsky.social · 25/11/2024

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!

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