Do you have a master in computer science, computational chemistry or computational biology ? We have a fully funded PhD position opening to develop ML-based pKa prediction methods ! Science Twitter (X?), could you please help us spread the word ?

📣 WE ARE HIRING (TT assist. or assoc. prof) Come be my colleague at the University of Copenhagen 🇩🇰! Copenhagen is a great city to live in 🚲🌤️ 👪 and you will have lots of great colleagues 🧑‍🔬🧑‍💼 working on diverse topics🧪🧫🧶🍝🧬🖥️ Deadline Sept 22: employment.ku.dk/faculty/?show=…

Excited to share our research with Bartłomiej Surpeta,PhD and Jan Brezovsky, recently published in JCIM JCIM & JCTC Journals! We explored rare protein tunnels using GaMD simulations, unlocking insights for drug development and protein engineering. 🧬#compchem doi.org/10.1021/acs.jc…

Interested in molecular dynamics simulations, free energy calculations, enzymes and evolution? My colleague Johan Åqvist is recruiting postdoctoral researchers, apply here: uu.varbi.com/en/what:job/jo…

AlphaFold3 reproduced and params/code released. 🤩

Length of the simulation and assessment of convergence are CRUCIAL. Just because a tutorial does 100 ns does NOT mean that is enough time for your application. Maybe it is, maybe not. You have to prove it. You also have to run replicates. Full stop.

Decently "randomized" ones pls

A lot of work still to do, but indeed seems that CG MD simulations can be quite a good substitute for demanding all-atom ones when dealing with finding even quite rare transient tunnels in protein structures. Thanks for great input form Adolfo Poma & Siewert-Jan Marrink labs!!

Academic ironies

Join us at Freie Universität as Post-Doc in molecular simulation of chemical reactions. Dive into rare events, machine-learned force fields & dynamical reweighting. 4 years, 100% TV-L. More details: bcp.fu-berlin.de/en/chemie/chem… #CompChem #machinelearning #postdoc

doi.org/10.1016/j.csbj…

Our ARTEM tool for #RNA #3D #motif search does not rely on annotated interactions. It could identify a D-loop/T-loop-like motif with two non-interacting pyrimidines (U206/U233, right) instead of the canonical long-range base pair (left). Find out more: doi.org/10.1093/nar/gk…

We are still searching for a postdoc to work on applying and developing computational structural biology tools to understabd protein-nucleic acids recognition in different contexts

1/5 🧵 Thrilled to share our latest research with Jan Brezovsky & Tunneling Group! We investigated how different water models (TIP3P, OPC, TIP4P-Ew) affect water migration and transport kinetics through enzyme tunnels. Read here -> pubs.acs.org/doi/full/10.10…

Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model #MolecularDynamics pubs.acs.org/doi/10.1021/ac… aravind_ram_ Igor Marchlewski Artur Góra Jan Brezovsky Tunneling Group IMBB AMU Poznań #JCIM Vol65 Issue1 #compchem

Gregor’s #Journal_Club on mitigating the basis set superposition error with the counterpoise correction opens the “Good practices” theme we will be exploring in the coming journal clubs - stay tuned! #compchem grynova-ccc.org/journal-club.h…

I have 3 PhD and 3 postdoc positions available at Utrecht University, all in the context of ‘solid-state #NMR & drug discovery (#antibiotics: small molecules & peptides)’ Starting date is flexible. Please see here: weingarth-group.net/student-projec… #Postdoc #PhD

With this review in Plant Physiology, we look at ABCG transporters, from in silico modeling and the recent advancements in the structural biology perspective. doi.org/10.1093/plphys… Image credit to Ola Bigos 😎

🚀 Excited to release a major update to the Boltz-1 model: Boltz-1x! Boltz-1x introduces inference-time steering for much higher physical quality, CUDA kernels for faster, more memory-efficient inference and training, and more! 🔥🧵

Please RT! I have 2 postdoctoral positions in my lab Biomedical Research Foundation Academy of Athens to work on MD sims for protein allostery, cryptic pocket identification, CADD/FEP. Knowledge in coarse-grained MD is a plus. More info: linkedin.com/hiring/jobs/42…. Send me an email with your CV if interested!