Applying SILCS to identify a novel binding site, develop pharmacophores for in silico screening and rank compounds we helped identify HIF inhibitors that are active against a variety of tumors.

Those timings include the presence of lone pairs and anisotropic polarizability on selected H-bond acceptors, LJ terms on selected Drudes and other features that maximize the accuracy of the CHARMM-Drude model. And it can be used for FEP, metadynamics etc. using CHARMM or OpenMM/PLUMED.

Considering joining us at the 2026 International Society of Quantum Biology and Pharmacology (ISQBP) meeting. June 15-16, 2026 in Cluj-Naoca, Romania. isqbp2026.com

We developed a simple theory and showed that Random Acceleration Molecular Dynamics (RAMD) is consistent with a Smoluchowski equation with an effective temperature and diffusion coefficient that depend quadratically on the magnitude of the random force. pubs.aip.org/aip/jcp/arti...

Congratulations Roland!

scientists: be honest, how often do you take a day off for the beach and call it pier review

Hey #chemsky - NMR people! At King's we're hiring an NMR technical manager! Come join a lovely department and get to work with some fantastic chemists! www.kcl.ac.uk/jobs/134186-...

Download our large database of postdoc fellowships in all fields of research. Database freely available to all; 281 fellowships. Download here: research.jhu.edu/rdt/funding-...

I can remember seeing Dick Allen at Connie Mack Stadium in Philly swing at a pitch over his head and drive into the outfield for a nice hit. He was incredible.

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...

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!

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.

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...

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....

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.

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....

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

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/...

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.

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

Silcsbio is hiring. Be the driving force behind our revenue growth, responsible for connecting researchers and pharmaceutical innovators with our advanced molecular modeling tools and services based on the SILCS technology. www.indeed.com/viewjob?jk=a...

We've worked collaboratively targeting protein translation. doi.org/10.1093/nar/...

Martin Karplus died on Saturday, Dec 28 at age 94. Martin was my freshman Chem 10 professor, my undergraduate research advisor, and my PhD advisor. I will always be grateful for his true kindness to me as a mentor through some difficult times in my life. cen.acs.org/people/obitu...

Yes, Martin died peacefully at home in his sleep Saturday evening. His impact was large and on many levels for those of us that had the opportunity to work with him.

SILCS-Water allows for inclusion of explicit waters during ligand docking offering improved binding affinities and poses for select systems in a computationally efficient approach. SilcsBio is hosting seminar on January 7, 2025. Please join us! events.teams.microsoft.com/event/713bec...

Jimmy Carter was a true public servant and peacemaker. Our country is a better place because of him. My thoughts are with his family.

Hey, haven't posted for a while but trying to transition over from the "ex"... We've recently published a few papers on the polarizable Drude FF as follows. doi.org/10.1063/5.02... doi.org/10.1021/acs.... doi.org/10.1021/acs.... doi.org/10.1021/acs....

I'd like to join. Thanks. mackerell.umaryland.edu

Join us at the ISQBP President's Meeting, 19-23 May 2024 in Athens Greece: isqbp2024.org A diverse collection of outstanding speakers in a great venue.

Another exciting preprint up, this one from Haley Michel on the dynamics of the LTR-III GQ, with a focus on the duplex:quadruplex junction. Conventional MD and GaMD and an amazing amount of effort and tenacity from Haley in making this one happen. www.biorxiv.org/content/10.1...

ADH fun fact: My Ph.D. advisor, Regina Pietruszko (now 94), was involved in the discovery of the isozyme of alcohol dehydrogenase. It was the second protein for which the presence of an isozyme was known. Check it out. febs.onlinelibrary.wiley.com/doi/10.1111/...

The #ISQBP2024 President's meeting will take place 19-23 May in Athens, Greece! We are now accepting abstract submissions for oral and poster presentations: isqbp2024.org Early-bird registration: 1 February 2023 Looking forward to welcoming all in Athens!

Reviving a paper about halogens acting as Hbond acceptors and forming favorable out of plane interactions with Hbond donors in proteins (not halogen bonds!). I think this type of interaction is not properly consider in CADD/Med. Chem. Take a look. PMCID: PMC5523114 DOI: 10.1021/acs.jpcb.7b04198