Alex MacKerell

picture of a TV screen hanging in a hallway, the TV screen shows slide which reads "Herzlich willkommen im Chemischen Laboratorium, Inaugural Lecture (GDCH), Fiona Kearns University of Freiburg 'Emerging opportunities in Biophysics: Glycoprotein Characterization by Simulation'" with a picture of a woman, The slide also indicates the date (Dec 15, 2025), time (5:15) and location (Horsaal Chemie) for the lecture

Are you from @uni-freiburg.de? wanna come see me talk about my research on Dec 15 at 5:15 in the main Chemie Horsaal?

Nope, we ain’t. It was a really enjoyable day. Thank you.

Excited to share a new update to the Drude polarizable force field - phosphorylated amino acids! A long-term project that took quite a bit of effort. Great work with PhD student Laura Gil Pineda, former undergrad Candace Miller, and @alexmackerell.bsky.social

authors.elsevier.com/a/1m2md1SPTB...

We enjoyed your visit to Univ Maryland Baltimore and great to spend time with a colleague with whom I shared an office 35 years ago! Ain't dead yet...

And certainly don't ask generative AI to create a Z-matrix for your molecule. The outcomes are not pretty!

Faculty Recruitment

Please apply to our tenure-track faculty position at
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...

We've been putting these tools to use. Worth checking out.

Welcome!

Journal of Computational Chemistry Click on the title to browse this journal

Honored to join the Editorial Board of the Journal of Computational Chemistry #compchem #compchemsky #chemsky onlinelibrary.wiley.com/journal/1096...

Take a look. The perspective includes examples of how MD simulations and the SILCS technology can be used to facilitate antibody-drug conjugate (ADC) development including regions of the mAb that have potential interactions with the drug warhead.

Väldigt bra! I hope all is well!

Representative images on a journal cover of the different types of molecular movement pathways.

Nice to get a JCIM cover! Check out the SILCS-based method for dissociation pathway identification, 10.1021/acs.jcim.4c01814, and the SILCS-Kinetics physics/ML method for rapid estimation (really fast...) of small molecule koff values was just accepted in JCTC.
@silcsbio

While I've seen a bad FF or two, the system volume could be so far off that the water can't condense properly.

I have heard from a reliable source that the NIGMS council is rescheduled for sometime In April even though it isn’t posted yet. Not sure about other councils

We are excited to have @alexmackerell.bsky.social this month for our Integrative Modeling in Biophysics e-series!! It’s all about polarizable force field next week. #drude

Tues March 11, 5:30 PM IST (2:00 CEST, 7:00 AM USET) For details about this series, visit: sites.google.com/view/mbu-inf...

Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set Small molecule empirical force fields (FFs), including the CHARMM General Force Field (CGenFF), are designed to have wide coverage of organic molecules and to rapidly assign parameters to molecules no...

For all the CGenFF fans out there, we've undertaken a significant expansion of the training set and extended the coverage to 4-membered rings.

pubs.acs.org/doi/10.1021/...

Access CGenFF at cgenff.com

What they are doing is known to the art. Though the method may be more successful than previous attempts, people have been trying this for a long time with and range of methods and varying levels of success. Harold Scheraga would tell you all about it if he was still around!

Get to a physical therapist. I've had good outcomes and I continue to do regular exercises focused on my many issues. Getting old....

Postdoc position in computational structural biology Join our team and contribute to the development of HADDOCK, our integrative modelling software, as part of an exciting EU-India research collaboration.

I have two open postdoctoral researcher positions in my group. I am looking for applicants with interest and expertise in computational structural biology and research software development. These positions are part of GANANA, a collaborative European/Indian project Check www.uu.nl/en/organisat...

🤓Our new article investigates how refined parameters for the Drude polarizable force field perform in capturing complex biomolecular interactions with ions. Congratulations to the team! 👏 #iamcals #hokies #utprosim #virginiatech #whyvt pubs.acs.org/doi/full/10....

It's like they were just faking support for our communities all along.

Microsoft Virtual Events Powered by Teams Microsoft Virtual Events Powered by Teams

Check out the SILCS v2025 Release Webinar

Key Highlights being covered:
- Precise docking w/ water inclusion
- Improved ML-based hotspot ranking
- Streamlined multi-cofactor simulations

📅 Feb 13, 2025, 12 PM ET
Register: events.teams.microsoft.com/event/214c66...

Sounds like the decision making process we use during force field optimization....

Queer Voices in Computational Biology: The 1st ISCB LGBTQI+ Symposium Abstract. The 1st ISCB LGBTQI+ Symposium, held during Pride month in 2024, marked a significant milestone by the International Society for Computational Bi

The article on the 1st Int'l Society for Computational Biology LGBTQI+ Symposium is out. Many thanks to @gonzaparra.bsky.social for organizing & putting the article together & to @iscb.bsky.social for sponsoring & hosting the online symposium. We won't give in to the hate. tinyurl.com/2v7mn6j5

FDA Approves Novel Non-Opioid Treatment for Moderate to Severe Acute Pain The FDA approved Journavx (suzetrigine) 50 mg oral tablets, a first-in-class non-opioid analgesic to treat moderate to severe acute pain in adults.

The FDA approved a non-opioid painkiller for the first time in what seems like forever. What do I find COOL and what COOLS my expectations? A thread.
www.fda.gov/news-events/...

a man with glasses and a black shirt says " it 's a small step that really goes a long way " ALT: a man with glasses and a black shirt says " it 's a small step that really goes a long way "

SOME GOOD NEWS ABOUT NIH FUNDING

Closed sessions of institute and center Advisory Counsel meetings are now permitted. This is where grant applications are discussed and approved for potential funding.

Open sessions where there are public presentations and discussions are still not allowed.

The Eagles people are winning.

I am not in the mood for MDPI today.

It was an honor to put the obituary together for Martin with the help of Charlie Brooks, Carol Post, Lennart Nilsson and Benoit Roux as well as the Nature staff writer. Nature only allows a single author on these articles.

Martin Karplus, Chemist Who Made Early Computers a Tool, Dies at 94 (Gift Article) Proving skeptics wrong, he shared a Nobel Prize in 2013 for using computers to better understand chemical reactions and biological processes.

Obituary for computational chemistry pioneer Martin Karplus in the New York Times (gift link).
#CompChem #ChemSky 🧪
www.nytimes.com/2025/01/13/s...