Alex MacKerell
@alexmackerell.bsky.social
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....
Reposted by Alex MacKerell
Nope, we ain’t. It was a really enjoyable day. Thank you.
November 6, 2025 at 5:07 AM
Nope, we ain’t. It was a really enjoyable day. Thank you.
Reposted by Alex MacKerell
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...
authors.elsevier.com/a/1m2md1SPTB...
November 6, 2025 at 1:27 PM
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...
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...
November 6, 2025 at 3:04 AM
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...
Reposted by Alex MacKerell
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...
@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...
Faculty Recruitment
chemh.stanford.edu
September 17, 2025 at 5:54 PM
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...
@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.
Clustering hundreds of millions of molecules in a single workstation is now a possibility!
Check the new code: github.com/mqcomplab/bb...
Check the new code: github.com/mqcomplab/bb...
GitHub - mqcomplab/bblean
Contribute to mqcomplab/bblean development by creating an account on GitHub.
github.com
September 17, 2025 at 2:48 AM
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...
Journal of Computational Chemistry
Click on the title to browse this journal
onlinelibrary.wiley.com
July 15, 2025 at 9:55 PM
Welcome!
Reposted by Alex MacKerell
Honored to join the Editorial Board of the Journal of Computational Chemistry #compchem #compchemsky #chemsky onlinelibrary.wiley.com/journal/1096...
Journal of Computational Chemistry
Click on the title to browse this journal
onlinelibrary.wiley.com
July 7, 2025 at 8:02 AM
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.
June 29, 2025 at 7:46 PM
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
@silcsbio
April 15, 2025 at 8:25 PM
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
@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.
When you're training a force field and step 2 of the simulation looks like this.
March 31, 2025 at 9:05 PM
While I've seen a bad FF or two, the system volume could be so far off that the water can't condense properly.
Reposted by Alex MacKerell
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
March 14, 2025 at 8:05 PM
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
Reposted by Alex MacKerell
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...
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...
March 8, 2025 at 10:04 AM
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...
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
pubs.acs.org/doi/10.1021/...
Access CGenFF at cgenff.com
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...
pubs.acs.org
March 4, 2025 at 8:11 PM
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/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!
DeepMind patents structure prediction. www.freepatentsonline.com/y2025/006970...
www.freepatentsonline.com
March 3, 2025 at 9:30 PM
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....
Anybody ever had a pinched nerve in their neck? It's killing me.
MRI shows protruding disks at C5,C6,C7. Pain down my arm. Pain "management" doctor tomorrow.
MRI shows protruding disks at C5,C6,C7. Pain down my arm. Pain "management" doctor tomorrow.
February 18, 2025 at 12:36 AM
Get to a physical therapist. I've had good outcomes and I continue to do regular exercises focused on my many issues. Getting old....
Reposted by Alex MacKerell
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...
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.
www.uu.nl
February 14, 2025 at 6:01 PM
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...
Reposted by Alex MacKerell
🤓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....
February 11, 2025 at 9:52 PM
🤓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....
Reposted by Alex MacKerell
It's like they were just faking support for our communities all along.
Google Calendar has removed key cultural events from their site including:
• Pride Month
• Black History Month
• Holocaust Remembrance Day
• Jewish Heritage
• Hispanic Heritage
• Indigenous People Month
• Pride Month
• Black History Month
• Holocaust Remembrance Day
• Jewish Heritage
• Hispanic Heritage
• Indigenous People Month
February 11, 2025 at 5:11 AM
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...
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...
Microsoft Virtual Events Powered by Teams
Microsoft Virtual Events Powered by Teams
events.teams.microsoft.com
February 10, 2025 at 8:28 PM
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...
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....
There are lots of hydrophobicity scales and perhaps the most well known and used is that from Kyte & Doolittle
If you ever use that scale, I recommend reading the original paper and noting the authors' pragmatism and honesty about manual adjustments and using intuition
doi.org/10.1016/0022...
If you ever use that scale, I recommend reading the original paper and noting the authors' pragmatism and honesty about manual adjustments and using intuition
doi.org/10.1016/0022...
February 6, 2025 at 11:15 PM
Sounds like the decision making process we use during force field optimization....
Reposted by Alex MacKerell
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
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
academic.oup.com
February 6, 2025 at 8:34 PM
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
Reposted by Alex MacKerell
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/...
www.fda.gov/news-events/...
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.
www.fda.gov
February 4, 2025 at 4:57 PM
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/...
www.fda.gov/news-events/...
Reposted by Alex MacKerell
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.
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.
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 "
media.tenor.com
February 3, 2025 at 6:35 PM
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.
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.
Reposted by Alex MacKerell
The Eagles people are winning.
January 26, 2025 at 10:49 PM
The Eagles people are winning.
Reposted by Alex MacKerell
I am not in the mood for MDPI today.
January 24, 2025 at 6:39 PM
I am not in the mood for MDPI today.