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Alex MacKerell

@alexmackerell.bsky.social
687 followers 88 following 35 posts

Computational chemistry and biophysics. Empirical force fields, CADD, RNA, carbohydrates, and methods developments including SILCS (site identification by ligand competitive saturation, See SilcsBio LLC) and enhanced-sampling GCMC. And I surf....

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Alex MacKerell @alexmackerell.bsky.social · 18/09/2026
Check out our paper on identification of ligand binding sites starting from apo RNA using enhanced sampling with the Drude polarizable force field and the SILCS technology in conjunction with RNA specific collective variables and scoring functions. pubs.acs.org/jctcce/artic...
pubs.acs.org
Integrating Enhanced Molecular Sampling, RNA-Specific Scoring Functions, and SILCS Technology for Small-Molecule Targeting of RNA
Abstract. Increasing knowledge of the wide range of biological functions of ribonucleic acids (RNAs) has made them a critical target in drug development. A
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Mittal Group @ TAMU @mittalgrouptamu.bsky.social · 02/07/2026
(Part 1/2) Excited to share our recent work led by Dr. Shiv Rekhi, now out in JACS (pubs.acs.org/doi/full/10....). We show that biomolecular condensates act as distinct solvation environments that reshape amino acid pKₐ values, favoring protonated states within the dense phase.
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Eugene Serebryany @eserebry.bsky.social · 26/06/2026
Are you on the faculty job market? Interested in coming to work here at Stony Brook? (You should be!) Physiology & Biophysics (my home department) is looking to add faculty at the Asst/Assoc Prof level: apply.interfolio.com/148377
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Alex MacKerell @alexmackerell.bsky.social · 14/06/2026
We just arrived in Cluj-Napoca. Looking forward to seeing everyone.
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Alex MacKerell @alexmackerell.bsky.social · 22/05/2026
Nice. That reminds of a photo I took of the Boston skyline from Marblehead MA back around 1990. It was one of those chance moments when the sky, land, and sea all came together. I was using Ektachrome 400 ASA so the image is rather grainy.
Photo of the Boston skyline taken from Marblehead, MA. There is a wave breaking in the foreground.
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Alex MacKerell @alexmackerell.bsky.social · 13/04/2026
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.
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Alex MacKerell @alexmackerell.bsky.social · 19/03/2026
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.
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Alex MacKerell @alexmackerell.bsky.social · 19/03/2026
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
isqbp2026.com
2026 ISQBP President’s Meeting
breaking barriers with the computational microscope
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benoitroux.bsky.social @benoitroux.bsky.social · 10/02/2026
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...
pubs.aip.org
A theoretical framework for random acceleration molecular dynamics simulations
The dissociation of a ligand bound to a receptor is a rare event occurring on a timescale that is far longer than can be afforded by standard simulation methodo
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Alex MacKerell @alexmackerell.bsky.social · 13/01/2026
Congratulations Roland!
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Yell In a War @jelenawoehr.bsky.social · 19/12/2025
scientists: be honest, how often do you take a day off for the beach and call it pier review
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Matt de Vere @mattdv-t.bsky.social · 18/12/2025
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-...
kcl.ac.uk
Technical Manager (NMR) | King's College London
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Denis Wirtz @deniswirtz.bsky.social · 13/12/2025
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-...
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Alex MacKerell @alexmackerell.bsky.social · 09/12/2025
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.
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Dr. Fiona @fionachembot.bsky.social · 01/12/2025
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?
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
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 06/11/2025
Nope, we ain’t. It was a really enjoyable day. Thank you.
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Justin Lemkul @justinlemkulvt.bsky.social · 06/11/2025
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...
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Alex MacKerell @alexmackerell.bsky.social · 06/11/2025
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...
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Polly Fordyce @pollyfordyce.bsky.social · 17/09/2025
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...
chemh.stanford.edu
Faculty Recruitment
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Alex MacKerell @alexmackerell.bsky.social · 17/09/2025
We've been putting these tools to use. Worth checking out.
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Alex MacKerell @alexmackerell.bsky.social · 15/07/2025
Welcome!
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Jean-Philip Piquemal @jppiquem.bsky.social · 07/07/2025
Honored to join the Editorial Board of the Journal of Computational Chemistry #compchem #compchemsky #chemsky onlinelibrary.wiley.com/journal/1096...
onlinelibrary.wiley.com
Journal of Computational Chemistry
Click on the title to browse this journal
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Alex MacKerell @alexmackerell.bsky.social · 29/06/2025
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.
Images of the Fab and Fc regions of the NIST monoclonal antibody showing the site identification by ligand competitive saturation (SILCS) FragMaps along with where the drug conjugate warhead can bind as predicted by the SILCS and how those regions correspond with residues predicted by MD simulations to interact with the warhead.
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Alex MacKerell @alexmackerell.bsky.social · 15/04/2025
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
Representative images on a journal cover of the different types of molecular movement pathways.
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Alex MacKerell @alexmackerell.bsky.social · 31/03/2025
While I've seen a bad FF or two, the system volume could be so far off that the water can't condense properly.
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Brenton Graveley @graveley.bsky.social · 14/03/2025
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
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Anand Srivastava @mbuanand.bsky.social · 08/03/2025
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...
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Alex MacKerell @alexmackerell.bsky.social · 04/03/2025
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
pubs.acs.org
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...
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Alex MacKerell @alexmackerell.bsky.social · 03/03/2025
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!
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Alex MacKerell @alexmackerell.bsky.social · 18/02/2025
Get to a physical therapist. I've had good outcomes and I continue to do regular exercises focused on my many issues. Getting old....
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Alexandre Bonvin @amjjbonvin.bsky.social · 14/02/2025
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...
uu.nl
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.
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Virginia Tech Biochemistry Department @vtbiochemistry.bsky.social · 11/02/2025
🤓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....
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 11/02/2025
It's like they were just faking support for our communities all along.
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Alex MacKerell @alexmackerell.bsky.social · 10/02/2025
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...
events.teams.microsoft.com
Microsoft Virtual Events Powered by Teams
Microsoft Virtual Events Powered by Teams
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Alex MacKerell @alexmackerell.bsky.social · 06/02/2025
Sounds like the decision making process we use during force field optimization....
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 06/02/2025
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
academic.oup.com
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
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chris cunningham @doctor-cunningham.bsky.social · 04/02/2025
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/...
fda.gov
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.
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Jeremy Berg @jeremymberg.bsky.social · 03/02/2025
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.
media.tenor.com
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 "
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 26/01/2025
The Eagles people are winning.
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 24/01/2025
I am not in the mood for MDPI today.
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Alex MacKerell @alexmackerell.bsky.social · 25/01/2025
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.
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Martin Vögele @martinvoegele.bsky.social · 14/01/2025
Obituary for computational chemistry pioneer Martin Karplus in the New York Times (gift link). #CompChem #ChemSky 🧪 www.nytimes.com/2025/01/13/s...
nytimes.com
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.
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Alex MacKerell @alexmackerell.bsky.social · 13/01/2025
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...
indeed.com
Sales Manager - SilcsBio - Baltimore, MD 21230 - Indeed.com
Early Charm, LLC
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Alex MacKerell @alexmackerell.bsky.social · 11/01/2025
We've worked collaboratively targeting protein translation. doi.org/10.1093/nar/...
doi.org
Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint
Abstract. We have identified chemical probes that simultaneously inhibit cancer cell progression and an immune checkpoint. Using the computational Site Ide
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 03/01/2025
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...
Speaking with Martin Karplus on the occasion of an award to him from the Government of Austria, August 15, 2024.Martin Karplus portraitMartin Karplus receiving the Nobel Prize in Chemistry, December 2013
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Alex MacKerell @alexmackerell.bsky.social · 31/12/2024
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.
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Alex MacKerell @alexmackerell.bsky.social · 30/12/2024
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...
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Elizabeth Warren @warren.senate.gov · 29/12/2024
Jimmy Carter was a true public servant and peacemaker. Our country is a better place because of him. My thoughts are with his family.
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Alex MacKerell @alexmackerell.bsky.social · 14/12/2024
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....
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Alex MacKerell @alexmackerell.bsky.social · 10/02/2024
I'd like to join. Thanks. mackerell.umaryland.edu
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