Marc van der Kamp

Marc van der Kamp

@marcvanderkamp.bsky.social

Computational biochemist (he/him), PI of the http://vanderkampgroup.com. Likes #enzymes & #compchem, #diversity #inclusion

1.3K followers458 following101 posts

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Marc van der Kamp
@marcvanderkamp.bsky.social

New paper out @chemicalscience.rsc.org! 🚀 Simulating enzyme catalysis with electrostatically embedded machine learning potentials Paper: pubs.rsc.org/en/content/a... Code & data: github.com/chemle/emle-... #CompChem #Enzymes 1/7

github.comGitHub - chemle/emle-enzymes-paper: Supporting data for "Simulating enzyme catalysis with electrostatically embedded machine learning potentials"Supporting data for "Simulating enzyme catalysis with electrostatically embedded machine learning potentials" - chemle/emle-enzymes-paper

Marc van der Kamp reposted

YesCymru
@yes.cymru

“You can tell the economic character of a nation by the way its infrastructure works.” Powerful words from George Monbiot on BBC Question Time explaining how Wales’s economy was built to extract wealth rather than enrich its own people, and why we need the powers to put that right. 🏴󠁧󠁢󠁷󠁬󠁳󠁿 #Annibyniaeth

Marc van der Kamp reposted

Stand Up for Science!
@standupforscience.net

Replying to @standupforscience.net

We scraped through the data and found that 50% of all clinical trials are at risk of being cancelled. 1,026 cancer trials 273 pediatric trials 115 heart disease trials 184 diabetes trials This is unacceptable and inhumane.

Marc van der Kamp reposted

Carl T. Bergstrom
@carlbergstrom.com

Nature did a short piece on our preprint about how LLMs will affect the practice of science; my more detailed thread is below.

nature.comScientists using LLMs will ‘do more, less well’, modelling study predictsResearch suggests that the combination of incentives to publish and the use of large language models will lead to more papers, but they will be less refined.
Carl T. Bergstrom@carlbergstrom.com

1. We—@eduede.bsky.social, @mjcrockett.bsky.social, Kevin Gross, and I—have a new preprint on the arXiv today, based on ideas that emerged during an @sfiscience.bsky.social workshop in November 2024: The unintended consequences of large language models as a labor-augmenting technology in science.

arxiv.orgThe unintended consequences of large language models as a labor-augmenting technology in scienceAs a labor-augmenting technology, large language models (LLMs) have the potential to accelerate scientific activity across the research pipeline. But even if LLMs perform on par with human experts at ...
Marc van der Kamp
@marcvanderkamp.bsky.social

This work moves us closer to routine computational screening of enzyme variants and AI‑designed enzymes. It also opens the door to fast ML-based evaluation of covalent drug reactivity in complex biological environments. 6/7

Marc van der Kamp
@marcvanderkamp.bsky.social

Applied to two very different enzymatic reactions, including one with a highly polarized transition state. In the Diels-Alderase AbyU, differential catalysis is captured: EMLE correctly distinguishes reactive vs. unreactive substrate poses. 4/n

Marc van der Kamp
@marcvanderkamp.bsky.social

We show that electrostatic ML embedding (EMLE) lets gas‑phase ML potentials accurately model enzyme catalysis — capturing pose‑dependent reactivity, highly polarized transition states, and even transferring across different enzyme families. 2/n

Marc van der Kamp
@marcvanderkamp.bsky.social

Predicting enzyme catalysis with high accuracy usually requires expensive QM/MM simulations—far too slow for modern biocatalyst or drug-design workflows. Our ML(EMLE)/MM approach is at least ~1000x faster than DFT QM/MM, and captures catalysis accurately, using MLPs trained in gas phase! 3/n

Marc van der Kamp
@marcvanderkamp.bsky.social

Not been active here (or other social media) for a while, but the group has not been standing still! I will try to post some updates over the coming days/weeks. Starting with a just accepted paper that I'm really excited about....

Marc van der Kamp
@marcvanderkamp.bsky.social

I happened to listen for a bit to the main Dutch news&sports radio station, on a Champions League night. Between updates, a ~5 min interview with a professional female footballer about (her) #Endometriosis! Great to hear this getting attention! #EndometriosisAwarenessMonth

Marc van der Kamp reposted

George Monbiot
@georgemonbiot.bsky.social

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.

Alex Andreou@sturdyalex.bsky.social

George Monbiot: "This government is more Tory than the Tories." Bernard Jenkin: "This is the most left-wing government we have ever seen." Labour MP: 🤷🏽‍♂️ #PoliticsLive

Marc van der Kamp reposted

Agnes Noy
@agnesnoy.bsky.social

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...

findaphd.comMRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York on FindAPhD.comPhD Project - MRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York, listed on FindAPhD.com
Marc van der Kamp
@marcvanderkamp.bsky.social

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” 🖥️🧪

Marc van der Kamp reposted

Sunder Katwala (sundersays)
@sundersays.bsky.social

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

The Royal Society@royalsociety.org

"I am increasingly concerned over threats to the values that allow science to flourish." Read the full statement from the President of the Royal Society Sir Adrian Smith: royalsociety.org/news/2025/10...

royalsociety.orgA statement from the President of the Royal Society | Royal SocietyA statement from the President of the Royal Society regarding threats to the values that allow science to flourish.

Marc van der Kamp reposted

Ganna (Anya) Gryn’ova 🇺🇦
@grynova.bsky.social

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.

grynova-ccc.orgOther3.  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...

Marc van der Kamp reposted

CN Lester 🏳️‍⚧️
@cnlester.bsky.social

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

Trans Legal Project@translegalproject.bsky.social

TW. Needs to be widely shared with cisgender people, especially politicians. Utterly horrifying that Britain has come to this- that most of Britain is just looking the other way while a whole community is being eliminated from society because of lies and hatred. transactual.org.uk/wp-content/u...

Marc van der Kamp reposted

David Ho
@davidho.bsky.social

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.”

pbs.orgFederal mRNA funding cut is 'most dangerous public health decision' ever, expert saysMany 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...

Marc van der Kamp reposted

The Feminist Scientist
@feministscientist.bsky.social

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.🧪

Marc van der Kamp
@marcvanderkamp.bsky.social

#compchem #enzymes #catalysis

Marc van der Kamp@marcvanderkamp.bsky.social

🚨 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...

doi.orgSimulating enzyme catalysis with electrostatically embedded machine learning potentialsTo 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 ...
Marc van der Kamp
@marcvanderkamp.bsky.social

🚨 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...

doi.orgSimulating enzyme catalysis with electrostatically embedded machine learning potentialsTo 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 ...

Marc van der Kamp reposted

Derek Lowe
@dereklowe.bsky.social

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.

Dan Garisto@dangaristo.bsky.social

NEW: NSF will be kicked out of their building. Announcement will be made tomorrow by HUD Sec. and Governor of VA. HUD will take over the NSF building over the next two years. NSF staffer: "There is no planning for NSF, no identified future location, appropriation for a new building or a move."

Marc van der Kamp
@marcvanderkamp.bsky.social

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/...

pubs.acs.orgInsights into the Enhanced Ceftazidime Hydrolysis by Ent385 AmpC β-Lactamase from Multiscale SimulationsThe 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.

Marc van der Kamp reposted

Paolo Crosetto
@paolocrosetto.bsky.social

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...

the-strain-on-scientific-publishing.github.ioSpringer Nature Discovers MDPI – The Strain on Scientific PublishingHome page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro

Marc van der Kamp reposted

Juan Carlos Sancho-García
@quantumalicante.bsky.social

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

pubs.rsc.orgBeing a first generation university graduate, the impact on a career in scienceBeing 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 ...

Marc van der Kamp reposted

Amanda Weinstein
@profweinstein.bsky.social

“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” 🔥

Hakeem Jefferson@hakeemjefferson.bsky.social

A colleague at Stanford’s business school used The Stanford Daily to argue—poorly—against DEI. The piece was riddled with historical errors and left one searching for fact, so I broke my public writing hiatus to respond. I hope you’ll read and share the piece. stanforddaily.com/2025/04/22/w...

stanforddaily.comWhat DEI threatens isn’t merit. It’s monopoly.Political science professor Hakeem Jefferson argues for DEI's importance to de-monopolizing universities.