Marc van der Kamp

As always, accuracy is critical. What I said was:
"In some respects this government under Keir Starmer looks more Tory than the Tories".
I had just spelt out exactly which respects I meant: its anti-protest laws and the Planning and Infrastructure Bill.

MRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York on FindAPhD.com PhD Project - MRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York, listed on FindAPhD.com

Would you like to fight against antimicrobial resistance (AMR) developing antibiotics? Apply to the PhD opportunity below and come to York. Collaboration with colegroupncl.bsky.social, @dghilarov.bsky.social and Inspiralis Ltd.
Fully funded via DiMeN DTP 💡
www.findaphd.com/phds/project...

On my way to a first academic visit to beautiful St Andrews! 🚝💺
Plenty of time on the train (I hope) to finish my slides for tomorrow’s seminar…
“Multi-scale simulation of enzymes: Insights into biocatalysts and antibiotic resistance” 🖥️🧪

On 15th Sept, billionaire & Royal Society fellow Elon Musk called for political & interethnic violence, to pre-empt (ie, begin) a civil war. ("Whether you choose violence or not, violence is coming to you. You either fight back or you die."). A fortnight later, the Society expresses its disapproval

Other 3.  G. Gryn’ova , T. Bereau, C. Müller, P. Friederich, R. C. Wade, A. Nunes-Alves, T. A. Soares, K. Merz Jr.,  EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput...

Due to popular demand, I am sharing my slide deck on #environmental costs of #ML in #compchem & #materials_science www.grynova-ccc.org/other.html - incl. work by @skepteis.bsky.social @pschwllr.bsky.social and others.
Please send any other relevant resources my way, I’ll be maintaining this deck.

If you’d like to focus on ligand binding sites (e.g. enzyme-substrate), you can get students to use enlighten2.github.io - directly in PyMOL.

Screenshot with BBC in depth headline from Laura Kuenssberg reading: “How much trouble is Labour in-and is the PM the right man for the job?”

I’d like to give the BBC the benefit of the doubt, but I can’t remember push notifications on “How much trouble is the Conservative Party in and is Sunak* the right man for the job”… 🤔
(* or Truss, Johnson etc)

Discover the pilot call for assignment of HPC resources to African-based researchers opened by CECAM in collaboration with ICTP and the support of CSCS and CINECA. Deadline for submission Oct. 31 2025. www.cecam.org/compaf

PhD project with @gw4biomeddtp.bsky.social available (Sept '26)!
Use #compchem multiscale reaction simulations & experiment to understand and combat antimicrobial resistance by Class C beta-lactamase #enzymes.

More info: gw4biomed.ac.uk/overcoming-%...

Deadline Oct 20th, but contact me by Oct 5th.

A concrete thing every UK person who cares about trans rights can do right now:

1. Email a link of this report to your MP, with highlights from the executive summary in your email. Ask them what it means for your constituency and their party - highlight trans people's legally mandated human rights

www.researchprofessional.com/0/rr/news/uk...

A reminder that the mRNA vaccine technology saved millions of lives during the Covid pandemic and received the 2023 Nobel Prize for Medicine

Federal mRNA funding cut is 'most dangerous public health decision' ever, expert says Many public health experts and scientists say they are stunned by Health Secretary Robert F. Kennedy Jr’s decision to cancel nearly half a billion dollars in federal funding for future vaccine develop...

It’s mind boggling how many additional people this administration is killing.

“I have been in this business for over 50 years on the front lines of public health…And I can say unequivocally that this was the most dangerous public health decision I have ever seen made by a government body.”

Happy Birthday, Rosalind Franklin. She captured an X-ray diffraction image of DNA and stated that a helical structure was probable. Watson and Crick then created a detailed model based on her results. They initially received credit for the discovery and were awarded the Nobel Prize after her death.🧪

HITS Journalist in Residence 2️⃣0️⃣2️⃣6️⃣

Call for experienced science journalists: Explore new research areas and learn about #ML and data-driven science in Germany. The program offers a stay of 3-6 months (€ 6,000/mo.). Apply until 5 October 2025: ow.ly/8lew50Wt6yS

#HITSJIR2025

Photo © Christin Hume

#compchem #enzymes #catalysis

Simulating enzyme catalysis with electrostatically embedded machine learning potentials To simulate enzyme reactions, multiscale quantum mechanics/molecular mechanics (QM/MM) approaches are well established and popular. However, accurately and efficiently estimating enzyme activity is a ...

🚨 Preprint! 🚨
We show that enzyme catalysis can be accurately simulated with ML/MM, >1000x faster than with DFT/MM!

Combining gasphase MLPs with our EMLE approach, we show ML(EMLE)/MM fully captures catalysis in two enzyme reactions.

See also:
github.com/chemle/

doi.org/10.26434/che...

🚨 Check out the updated version of our latest preprint with @adrianmulholla1.bsky.social, @marcvanderkamp.bsky.social, and many others!
📄 Read it here 👉https://chemrxiv.org/engage/chemrxiv/article-details/685d6114c1cb1ecda080add6

Journalists keep asking me, baffled, “What’s the Trump administration really trying to do to the science agencies?”

So I say “They are trying to destroy them. Cut off their funding, ruin their facilities, harass their staff into leaving.”

It’s not reform, and it never was. It’s destruction.

Insights into the Enhanced Ceftazidime Hydrolysis by Ent385 AmpC β-Lactamase from Multiscale Simulations The emergence of multidrug-resistant bacteria poses a significant threat to public health. Particularly, they are becoming increasingly resistant to β-lactam antibiotics, which are one of the most important drug classes for the treatment of bacterial infections. Ceftazidime-avibactam has shown promising activity against highly drug-resistant bacteria, including carbapenem-resistant Enterobacterales. However, an Ala294-Pro295 deletion in the Class CE. cloacaeAmpC β-lactamase can confer reduced susceptibility to these agents. In this study, we investigated the molecular mechanisms underlying the enhanced hydrolysis of ceftazidime by E. cloacae Ent385 AmpC β-lactamase with the deletion using quantum mechanics/molecular mechanics (QM/MM) simulations. We used constant pH molecular dynamics simulations of the β-lactamase-ceftazidime acyl-enzyme complex to verify the likely protonation states, confirming Tyr150 primarily exists as a tyrosinate. We then used QM/MM (DFTB2/ff14SB) umbrella sampling to calculate the reaction-free energy barriers (Δ‡G) for the deacylation step of cephalosporin hydrolysis. This reveals that Tyr150 (rather than the substrate) acts as the base. Importantly, the difference in Δ‡G between the canonical E. cloacae AmpC (P99) and the Ent385 variant with Ala294-Pro295 reinserted, on the one hand, and the Ent385 variant, on the other, was in very good agreement with the difference deduced from experimental kinetic data. Detailed analysis of the transition state ensembles, alongside additional simulations, shows that the Ala294-Pro295 deletion allows the entrance of an additional water molecule that helps stabilize the tetrahedral intermediate. Overall, our QM/MM simulations provide valuable insights into the reaction mechanism and reasons for enhanced ceftazidime breakdown. The protocol used in this study successfully captures the kinetic differences observed among the studied variants. This approach can be employed to investigate other Class C β-lactamase variants with similar features, providing insights into their mechanisms and potential contributions to reduced susceptibility to antibiotic treatments.

Our first foray into Class C beta-lactamases - explaining how #antibiotic ceftazidime is broken down more easily by AmpC variants.
#AMR
#enzymes
#compchem

Great work by @andersonlimaaa.bsky.social, as @royalsociety.org fellow

ACS Catalysis (Open Access): pubs.acs.org/doi/10.1021/...

Springer Nature Discovers MDPI – The Strain on Scientific Publishing Home page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro

Springer-Nature launched a series of "Discover" journals that closely mimic MDPI titles -- sharing *identical* journal names, and likely similar business model.

What is going on, and why researcher will - as always - fall for it?

A 🧵

the-strain-on-scientific-publishing.github.io/website/post...

Last year my wife had breast cancer and a double mastectomy.

This morning, for the first time ever, she was challenged in the changing rooms at the swimming pool. Her breasts were not what make her a woman - but, breasts or not, she is entitled to dignity and protection from vigilantes.

QBIC VII in Berlin. Registration is open: slots for oral presentations are available. @humboldtuni.bsky.social #chemsky #compchem

UK plummets down rankings for LGBTQ+ rights Last month’s Supreme Court ruling has seen the UK fall six places to 22nd. It’s time to fight back

“Only ten years ago we were the best in the world in the annual LGBTI Rights Ranking. We’re now 22nd... This is not just an embarrassment abroad – it’s also a tragedy at home for tens of thousands of people struggling to live lives of quiet dignity.” goodlaw.social/5mgp

The #CCPBioSim Biomolecular Simulation Annual Conference will be in Southampton, UK, 14-16 July 2025.
Registration is open!
Early-bird deadline: May 19
Details and the registration link can be found at www.ccpbiosim.ac.uk/events/upcom...

#compchem #biophysics

Being a first generation university graduate, the impact on a career in science Being in the first generation to access Higher Education (First Gen) is a barrier to academic success. First Gens face difficulties transitioning into, completing, and attaining competitive grades in ...

Very interesting study! I’m also a first generation PhD and graduate, but I fortunately had the parents support and the ability to build networks and connections. Raising awareness about the existing barriers is a great start. #chemsky #education #firstgen

“White Americans - white men especially - who didn’t need to compete against a broad-based pool... who continue to enjoy the presumption of expertise even when they are far outside their depth - have long been the original beneficiaries of race and gender-based affirmative action” 🔥

I’ll be there 🏳️‍⚧️🏳️‍🌈

A Comment from leaders in the field of biomolecular simulations brings attention to a need to establish FAIR principles for trajectory storage and sharing to favor reuse under an open science paradigm.

www.nature.com/articles/s41...