Xuhui Huang
@xuhuihuangchem.bsky.social
Hirschfelder Chair, Professor of Chemistry, University of Wisconsin-Madison, Director, Theoretical Chemistry Institute, Theoretical chemistry and Biophysics, previously at HKUST, https://huang.chem.wisc.edu/
Pinned
Xuhui Huang
@xuhuihuangchem.bsky.social
· Jun 10
Excited to share our latest paper on @natcomputsci.nature.com! We present MEMnets, a deep learning framework for coarse-graining protein dynamics, driven by an analytical statistical mechanics theory to minimize memory kernels. Congratulations to all the authors! @uwmadisonchem.bsky.social
RPA, long known for its role in DNA replication and repair, is now shown to boost telomerase activity!
Big congrats to @cijilim.bsky.social's lab for this milestone achievement!
Glad our lab (via Michael O’Connor) could contribute to this collaboration!
Big congrats to @cijilim.bsky.social's lab for this milestone achievement!
Glad our lab (via Michael O’Connor) could contribute to this collaboration!
Our paper in Science is out! @souravagrawal.bsky.social, @rlynn.bsky.social, @susvirkar.bsky.social, and the rest of the team show human RPA is a telomerase processivity factor essential for telomere maintenance. This reshapes our thinking about telomerase regulation. www.science.org/doi/10.1126/...
Human RPA is an essential telomerase processivity factor for maintaining telomeres
Telomerase counteracts telomere shortening by repeatedly adding DNA repeats to chromosome ends. We identified the replication protein A (RPA) heterotrimer as a telomerase processivity factor critical ...
www.science.org
November 1, 2025 at 7:15 PM
RPA, long known for its role in DNA replication and repair, is now shown to boost telomerase activity!
Big congrats to @cijilim.bsky.social's lab for this milestone achievement!
Glad our lab (via Michael O’Connor) could contribute to this collaboration!
Big congrats to @cijilim.bsky.social's lab for this milestone achievement!
Glad our lab (via Michael O’Connor) could contribute to this collaboration!
The 2nd Nat. Chem. Bio. paper led by Sasha is out! @nyumedpostdocs.bsky.social
While our Aug study revealed how ApaH decaps Np4A-capped RNAs, this work uncovers how RNAP adds the Np4As during transcription initiation.
Happy our group could contribute in a small way. Congs!
While our Aug study revealed how ApaH decaps Np4A-capped RNAs, this work uncovers how RNAP adds the Np4As during transcription initiation.
Happy our group could contribute in a small way. Congs!
A new paper reveals the structural basis of how E. coli and T. thermophilus RNA polymerases initiate transcription from Np4 alarmones producing Np4-capped transcripts
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Molecular basis for noncanonical transcription initiation from Np4A alarmones - Nature Chemical Biology
Duan and Kaushik et al. reveal the structural basis of how Escherichia coli and Thermus thermophilus RNA polymerases initiate transcription from Np4A alarmones producing Np4-capped transcripts. The ca...
www.nature.com
October 25, 2025 at 6:17 PM
The 2nd Nat. Chem. Bio. paper led by Sasha is out! @nyumedpostdocs.bsky.social
While our Aug study revealed how ApaH decaps Np4A-capped RNAs, this work uncovers how RNAP adds the Np4As during transcription initiation.
Happy our group could contribute in a small way. Congs!
While our Aug study revealed how ApaH decaps Np4A-capped RNAs, this work uncovers how RNAP adds the Np4As during transcription initiation.
Happy our group could contribute in a small way. Congs!
I received many requests to share materials from our undergraduate course “Machine Learning in Chemistry”
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
October 16, 2025 at 1:27 AM
I received many requests to share materials from our undergraduate course “Machine Learning in Chemistry”
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
Big congratulations to Frank on receiving this year’s Hirschfelder Prize! Excited to welcome Frank and Cecilia to Madison in late Oct!
Thank you UW–Madison for this great honor! In 2016 I changed my group to AI4Science and went all-in on deep learning solutions for the molecular sciences. Best decision of my career in hindsight. Amazing what's become of that field - now AI for Science is a @msftresearch.bsky.social lab.
Congratulations to Frank Noé, Partner Research Manager at Microsoft Research AI for Science, who received the 2025–2026 Joseph O. Hirschfelder Prize in Theoretical Chemistry for pioneering contributions at the interface of AI and chemistry. msft.it/6015sqq4R
September 25, 2025 at 9:40 PM
Big congratulations to Frank on receiving this year’s Hirschfelder Prize! Excited to welcome Frank and Cecilia to Madison in late Oct!
Reposted by Xuhui Huang
We teamed up with @xuhuihuangchem.bsky.social to perform structural modeling and substrate docking to gain insights into the beneficial mutations.
7/n
7/n
August 28, 2025 at 7:10 PM
We teamed up with @xuhuihuangchem.bsky.social to perform structural modeling and substrate docking to gain insights into the beneficial mutations.
7/n
7/n
Reposted by Xuhui Huang
Congrats to Ashley Ogorek and @shubha-pani.bsky.social, who co-led this study, as well as the entire team: Eli, Jelena, Yichong, Fernando, Rachel, @xuhuihuangchem.bsky.social. This was a really fun collaboration with @chembiobryan.bsky.social - stay tuned for more to come!
/end
/end
August 28, 2025 at 7:11 PM
Congrats to Ashley Ogorek and @shubha-pani.bsky.social, who co-led this study, as well as the entire team: Eli, Jelena, Yichong, Fernando, Rachel, @xuhuihuangchem.bsky.social. This was a really fun collaboration with @chembiobryan.bsky.social - stay tuned for more to come!
/end
/end
Check out our new Python package, EPIPY!
It streamlines 3DRISM calculations—great for studying RNA/DNA solvation, predicting dewetting, and placing water molecules, etc.
Github: github.com/EPISOLreleas...
Preprint for a tutorial: chemrxiv.org/engage/chemr...
Congs to Peter and Siqin!
It streamlines 3DRISM calculations—great for studying RNA/DNA solvation, predicting dewetting, and placing water molecules, etc.
Github: github.com/EPISOLreleas...
Preprint for a tutorial: chemrxiv.org/engage/chemr...
Congs to Peter and Siqin!
August 25, 2025 at 10:53 PM
Check out our new Python package, EPIPY!
It streamlines 3DRISM calculations—great for studying RNA/DNA solvation, predicting dewetting, and placing water molecules, etc.
Github: github.com/EPISOLreleas...
Preprint for a tutorial: chemrxiv.org/engage/chemr...
Congs to Peter and Siqin!
It streamlines 3DRISM calculations—great for studying RNA/DNA solvation, predicting dewetting, and placing water molecules, etc.
Github: github.com/EPISOLreleas...
Preprint for a tutorial: chemrxiv.org/engage/chemr...
Congs to Peter and Siqin!
This study led by Sasha’s group
@nyumedpostdocs.bsky.social reveals the mechanisms of de-capping Np4N, a noncanonical initiating nucleotide for RNAP. It binds substrates in two orientations, so target-mimic drugs might fail if one still works! Glad we contributed to this work! Congs to team!
@nyumedpostdocs.bsky.social reveals the mechanisms of de-capping Np4N, a noncanonical initiating nucleotide for RNAP. It binds substrates in two orientations, so target-mimic drugs might fail if one still works! Glad we contributed to this work! Congs to team!
A new paper reports how E. coli ApaH hydrolyzes enigmatic Np4N alarmones and decaps Np4-capped RNA, thereby impacting their lifetimes
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ApaH decaps Np4N-capped RNAs in two alternative orientations - Nature Chemical Biology
This study shows how Escherichia coli ApaH hydrolyzes enigmatic Np4N alarmones and decaps Np4-capped RNAs, thereby impacting their lifetimes. Key features enable ApaH to bind RNA substrates in two ori...
www.nature.com
August 12, 2025 at 4:01 AM
This study led by Sasha’s group
@nyumedpostdocs.bsky.social reveals the mechanisms of de-capping Np4N, a noncanonical initiating nucleotide for RNAP. It binds substrates in two orientations, so target-mimic drugs might fail if one still works! Glad we contributed to this work! Congs to team!
@nyumedpostdocs.bsky.social reveals the mechanisms of de-capping Np4N, a noncanonical initiating nucleotide for RNAP. It binds substrates in two orientations, so target-mimic drugs might fail if one still works! Glad we contributed to this work! Congs to team!
Super excited 3 days at the CECAM workshop co-organized with @drgregbowman.bsky.social @bettinagkeller.bsky.social! Protein dynamics is definitely shaping up to be the next big topic in AI for Science! Huge thanks to @cecamevents.bsky.social, @uwdsi.bsky.social, TCI, Chem, Emma and the DSI staff!
July 19, 2025 at 5:05 PM
Super excited 3 days at the CECAM workshop co-organized with @drgregbowman.bsky.social @bettinagkeller.bsky.social! Protein dynamics is definitely shaping up to be the next big topic in AI for Science! Huge thanks to @cecamevents.bsky.social, @uwdsi.bsky.social, TCI, Chem, Emma and the DSI staff!
Squeaks, brats, and Spotted Cows! Warmed up for the CECAM Flagship Workshop “Biomolecular Dynamics in the Age of Machine Learning” starting tomorrow — the first CECAM workshop in Wisconsin! @bettinagkeller.bsky.social @drgregbowman.bsky.social @cecamevents.bsky.social
www.cecam.org/workshop-det...
www.cecam.org/workshop-det...
July 14, 2025 at 4:11 AM
Squeaks, brats, and Spotted Cows! Warmed up for the CECAM Flagship Workshop “Biomolecular Dynamics in the Age of Machine Learning” starting tomorrow — the first CECAM workshop in Wisconsin! @bettinagkeller.bsky.social @drgregbowman.bsky.social @cecamevents.bsky.social
www.cecam.org/workshop-det...
www.cecam.org/workshop-det...
Congratulations to Mingyi on an outstanding PhD defense—our lab’s 19th PhD! Wishing you all the best as you begin your next chapter in the Bay Area biotech industry! @uwmadisonchem.bsky.social
June 13, 2025 at 10:44 PM
Congratulations to Mingyi on an outstanding PhD defense—our lab’s 19th PhD! Wishing you all the best as you begin your next chapter in the Bay Area biotech industry! @uwmadisonchem.bsky.social
Excited to share our latest paper on @natcomputsci.nature.com! We present MEMnets, a deep learning framework for coarse-graining protein dynamics, driven by an analytical statistical mechanics theory to minimize memory kernels. Congratulations to all the authors! @uwmadisonchem.bsky.social
June 10, 2025 at 8:42 PM
Excited to share our latest paper on @natcomputsci.nature.com! We present MEMnets, a deep learning framework for coarse-graining protein dynamics, driven by an analytical statistical mechanics theory to minimize memory kernels. Congratulations to all the authors! @uwmadisonchem.bsky.social
Congratulations to Jordan Boysen on winning the 2025 ACS Division of Physical Chemistry Undergraduate Award!
Jordan has been with our group since Jan 2023 and is an exceptionally talented student. Best wishes as he begins grad school at U. Chicago Chem.
Jordan has been with our group since Jan 2023 and is an exceptionally talented student. Best wishes as he begins grad school at U. Chicago Chem.
June 6, 2025 at 4:53 AM
Congratulations to Jordan Boysen on winning the 2025 ACS Division of Physical Chemistry Undergraduate Award!
Jordan has been with our group since Jan 2023 and is an exceptionally talented student. Best wishes as he begins grad school at U. Chicago Chem.
Jordan has been with our group since Jan 2023 and is an exceptionally talented student. Best wishes as he begins grad school at U. Chicago Chem.
Big congratulations to Bojun Lin from our group on winning the APL Computational Physics Best Poster Award at 55th Midwest Theoretical Chemistry Conference (MWTCC55)! Great job, Bojun! @uwmadisonchem.bsky.social @waynestatechem.bsky.social
June 6, 2025 at 3:50 AM
Big congratulations to Bojun Lin from our group on winning the APL Computational Physics Best Poster Award at 55th Midwest Theoretical Chemistry Conference (MWTCC55)! Great job, Bojun! @uwmadisonchem.bsky.social @waynestatechem.bsky.social
Dong Wang @ucsdpharmacy.bsky.social and our group @uwmadscience.bsky.social used time-resolved X-ray and metadynamics simulations to uncover how 8-oxoguanine (8OG) flips conformation to help RNA Pol II bypass oxidative DNA damage. @jacs.acspublications.org
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
April 30, 2025 at 7:24 PM
Dong Wang @ucsdpharmacy.bsky.social and our group @uwmadscience.bsky.social used time-resolved X-ray and metadynamics simulations to uncover how 8-oxoguanine (8OG) flips conformation to help RNA Pol II bypass oxidative DNA damage. @jacs.acspublications.org
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
The semester is wrapping up! I gave my final Chem361 lecture last Thur. Looking forward to next week's final project presentations - every student who passes will receive a custom 3D-printed keychain I designed as a souvenir for the inaugural ML in Chemistry class!
April 26, 2025 at 11:18 PM
The semester is wrapping up! I gave my final Chem361 lecture last Thur. Looking forward to next week's final project presentations - every student who passes will receive a custom 3D-printed keychain I designed as a souvenir for the inaugural ML in Chemistry class!
Excited to share that our AMUSET-TICA, a tensor-based approach for identifying CVs, is now published in JCTC’s MSM special issue (guest-edited by @drgregbowman.bsky.social, @cecclementi.bsky.social, and me)! Big congrats to all the authors!
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
April 21, 2025 at 5:21 PM
Excited to share that our AMUSET-TICA, a tensor-based approach for identifying CVs, is now published in JCTC’s MSM special issue (guest-edited by @drgregbowman.bsky.social, @cecclementi.bsky.social, and me)! Big congrats to all the authors!
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
We developed an unsupervised ML model @pnas.org to relate structure of supercooled liquid to its long-term dynamics. It uncovers a a surprising role of medium- & long-range structure on long-time behavior. First collab with Arun, led by @yunruiqiu.bsky.social!
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
April 16, 2025 at 7:37 PM
We developed an unsupervised ML model @pnas.org to relate structure of supercooled liquid to its long-term dynamics. It uncovers a a surprising role of medium- & long-range structure on long-time behavior. First collab with Arun, led by @yunruiqiu.bsky.social!
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Just one week left! Please consider submitting an abstract to our Pacifichem 2025 @pacifichem.bsky.social symposium on machine learning for biomolecular dynamics. Deadline: April 2!
March 26, 2025 at 5:48 PM
Just one week left! Please consider submitting an abstract to our Pacifichem 2025 @pacifichem.bsky.social symposium on machine learning for biomolecular dynamics. Deadline: April 2!
Hello San Diego! I’m giving two talks #ACSSpring2025: one this afternoon on transition states in protein conformational changes in enhanced sampling symposium @barakhirshberg.bsky.social and another tomorrow on memory kernels in the reaction coordinate symposium. Stop by if you're interested!
March 23, 2025 at 5:34 PM
Hello San Diego! I’m giving two talks #ACSSpring2025: one this afternoon on transition states in protein conformational changes in enhanced sampling symposium @barakhirshberg.bsky.social and another tomorrow on memory kernels in the reaction coordinate symposium. Stop by if you're interested!
A much-needed escape from a hectic semester—insightful scientific discussions, inspiration, and fun! Mesilla is a hidden gem in New Mexico. Thanks to the organizers Rui Sun & Greg Voth!
March 13, 2025 at 9:05 PM
A much-needed escape from a hectic semester—insightful scientific discussions, inspiration, and fun! Mesilla is a hidden gem in New Mexico. Thanks to the organizers Rui Sun & Greg Voth!
Yeah, please consider nominating candidates for these awards! The deadline is March 21!
sites.google.com/site/acscomp...
@acscomp.bsky.social
sites.google.com/site/acscomp...
@acscomp.bsky.social
March 13, 2025 at 1:03 AM
Yeah, please consider nominating candidates for these awards! The deadline is March 21!
sites.google.com/site/acscomp...
@acscomp.bsky.social
sites.google.com/site/acscomp...
@acscomp.bsky.social
FeatureDock - a transformer-based docking software leveraging local chemical features - is now published in @Nature_NPJ! Congrats to Mingyi, Bojun, and Siqin!
Paper:
www.nature.com/articles/s44...
Software:
github.com/xuhuihuang/f...
Paper:
www.nature.com/articles/s44...
Software:
github.com/xuhuihuang/f...
FeatureDock for protein-ligand docking guided by physicochemical feature-based local environment learning using transformer - npj Drug Discovery
npj Drug Discovery - FeatureDock for protein-ligand docking guided by physicochemical feature-based local environment learning using transformer
www.nature.com
March 4, 2025 at 3:08 PM
FeatureDock - a transformer-based docking software leveraging local chemical features - is now published in @Nature_NPJ! Congrats to Mingyi, Bojun, and Siqin!
Paper:
www.nature.com/articles/s44...
Software:
github.com/xuhuihuang/f...
Paper:
www.nature.com/articles/s44...
Software:
github.com/xuhuihuang/f...
Our perspective on using computational tools to design bacterial RNA polymerase inhibitors is out in the "Computational Biochemistry" special issue of ACS Biochemistry. Congratulations to Eshani!
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens
The increase in antimicrobial resistance presents a major challenge in treating bacterial infections, underscoring the need for innovative drug discovery approaches and novel inhibitors. Bacterial RNA...
pubs.acs.org
February 27, 2025 at 5:37 PM
Our perspective on using computational tools to design bacterial RNA polymerase inhibitors is out in the "Computational Biochemistry" special issue of ACS Biochemistry. Congratulations to Eshani!
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Tomorrow marks the first day of the Year of the Snake! Happy Lunar New Year! Wishing everyone endless good fortune - we’re going to need it!
January 29, 2025 at 5:51 AM
Tomorrow marks the first day of the Year of the Snake! Happy Lunar New Year! Wishing everyone endless good fortune - we’re going to need it!