Xuhui Huang @xuhuihuangchem.bsky.social · 01/02/2026Our recent preprint shows that metastable, short-lived PPIs captured by MD and IGME define key design targets for PROTACs, enabling rational discovery of sub-nanomolar RIPK1 degraders. Great collab w/ Weiping Tang! Congrats to Yue & co-authors! chemrxiv.org/doi/full/10.... - 002 2
Xuhui Huang @xuhuihuangchem.bsky.social · 21/12/2025What a great #Pacifichem2025! @pacifichem.bsky.social Thanks to all the speakers and participants for an outstanding symposium on ML for biomolecular dynamics. Exciting science and wonderful conversations! See you at the next Pacifichem in 5 years! 041 4
Xuhui Huang @xuhuihuangchem.bsky.social · 14/12/2025If you’re attending #Pacifichem2025 ( @pacifichem.bsky.social ifichem.bsky.social) next week, please stop by our symposium on ML for Biomolecular Dynamics! Dates: December 17-18, 2025 Venue: Room317A, Hawaii Convention Center. pacifichem.org 031 3
Xuhui Huang @xuhuihuangchem.bsky.social · 14/12/2025Excited to see our IGME models applied to unravel the free energy landscape of the tetra-nucleosome. Wonderful collaboration with @binzmit.bsky.social! Congrats to all the authors! 021 2
Xuhui Huang @xuhuihuangchem.bsky.social · 14/12/2025Huge congratulations to Bojun Liu on an outstanding Ph.D. defense! Even more special: Bojun is our group’s 20th Ph.D. graduate and won the Boomer Award on the same day! Wishing you all the best in your postdoc journey with @binzmit.bsky.social 000 0
Xuhui Huang @xuhuihuangchem.bsky.social · 01/11/2025RPA, 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! 141 4
Xuhui Huang @xuhuihuangchem.bsky.social · 25/10/2025The 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! 030 3
Xuhui Huang @xuhuihuangchem.bsky.social · 16/10/2025I 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/... 074 7
Xuhui Huang @xuhuihuangchem.bsky.social · 25/09/2025Big congratulations to Frank on receiving this year’s Hirschfelder Prize! Excited to welcome Frank and Cecilia to Madison in late Oct! 042 4
Reposted by Xuhui HuangJeff Martell @jeffmartell.bsky.social · 28/08/2025We teamed up with @xuhuihuangchem.bsky.social to perform structural modeling and substrate docking to gain insights into the beneficial mutations. 7/n 111 1
Reposted by Xuhui HuangJeff Martell @jeffmartell.bsky.social · 28/08/2025Congrats 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 041 4
Xuhui Huang @xuhuihuangchem.bsky.social · 25/08/2025Check 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! 020 2
Xuhui Huang @xuhuihuangchem.bsky.social · 12/08/2025This 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! 061 6
Xuhui Huang @xuhuihuangchem.bsky.social · 19/07/2025Super 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! 153 5
Xuhui Huang @xuhuihuangchem.bsky.social · 14/07/2025Squeaks, 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... 0120 12
Xuhui Huang @xuhuihuangchem.bsky.social · 13/06/2025Congratulations 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 030 3
Xuhui Huang @xuhuihuangchem.bsky.social · 10/06/2025Excited 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 193 9
Xuhui Huang @xuhuihuangchem.bsky.social · 06/06/2025Congratulations 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. 020 2
Xuhui Huang @xuhuihuangchem.bsky.social · 06/06/2025Big 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 010 1
Xuhui Huang @xuhuihuangchem.bsky.social · 30/04/2025Dong 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.... 163 6
Xuhui Huang @xuhuihuangchem.bsky.social · 27/04/2025The 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! 040 4
Xuhui Huang @xuhuihuangchem.bsky.social · 21/04/2025Excited 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.orgAMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular DynamicsElucidating collective variables (CVs) for biomolecular dynamics is crucial for understanding numerous biological processes. By leveraging the tensor-train data structure, a multilinear version of the... 040 4
Xuhui Huang @xuhuihuangchem.bsky.social · 16/04/2025We 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/... 041 4
Xuhui Huang @xuhuihuangchem.bsky.social · 26/03/2025Just 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! 032 3
Xuhui Huang @xuhuihuangchem.bsky.social · 23/03/2025 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! 0102 10
Xuhui Huang @xuhuihuangchem.bsky.social · 13/03/2025A 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! 170 7
Xuhui Huang @xuhuihuangchem.bsky.social · 13/03/2025Yeah, please consider nominating candidates for these awards! The deadline is March 21! sites.google.com/site/acscomp... @acscomp.bsky.socialsites.google.comACS Award for Computers in Chemical and Pharmaceutical ResearchSince 1984, The ACS Award for Computers in Chemical and Pharmaceutical Research has annually recognized outstanding individual achievement for the use of computers in education, product development, o... 021 2
Xuhui Huang @xuhuihuangchem.bsky.social · 04/03/2025FeatureDock - 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...nature.comFeatureDock for protein-ligand docking guided by physicochemical feature-based local environment learning using transformer - npj Drug Discoverynpj Drug Discovery - FeatureDock for protein-ligand docking guided by physicochemical feature-based local environment learning using transformer 051 5
Xuhui Huang @xuhuihuangchem.bsky.social · 27/02/2025Our 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.orgTargeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant PathogensThe 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... 021 2
Xuhui Huang @xuhuihuangchem.bsky.social · 29/01/2025Tomorrow 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! 190 9
Xuhui Huang @xuhuihuangchem.bsky.social · 18/01/2025Our group’s 1st preprint in 2025: a tensor-based approach for CV identification, led by Siqin Cao in collaboration with Micheliene Soley and Feliks Nuske! Thanks to all co-authors! chemrxiv.org/engage/chemr...chemrxiv.orgAMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular DynamicsElucidating Collective Variables (CVs) for biomolecular dynamics is crucial for understanding numerous biological processes. By leveraging the tensor-train data structure, a multilinear version of the... 040 4
Xuhui Huang @xuhuihuangchem.bsky.social · 11/01/2025My focus for Spring 2025: launching an undergraduate course developed from scratch - "Chem361: Machine Learning in Chemistry"! @UW-Madison Chemistry Here's a glimpse of what we'll explore: 040 4
Xuhui Huang @xuhuihuangchem.bsky.social · 04/01/2025The @cecamevents.bsky.social Flagship Workshop is coming to Madison! Hosted at @datascience_uw(thanks!), organized by @drgregbowman.bsky.social, @bettinagkeller.bsky.social, and me (CECAM-US-CENTRAL). We have slots for contributed talks - apply here (deadline: June 11): www.cecam.org/workshop-det... 3266 26
Xuhui Huang @xuhuihuangchem.bsky.social · 03/01/2025Exciting news! Our TS-DAR method is now published in @naturecomms.bsky.social! 🎉 TS-DAR identifies transition states across multiple free energy barriers in biomolecular dynamics—all at once! Paper: www.nature.com/articles/s41... Code: github.com/xuhuihuang/t... 1111 11
Xuhui Huang @xuhuihuangchem.bsky.social · 12/12/2024Yijing was my faculty mentor at HKUST - a brilliant mind in open system quantum dynamics and one of the most rigorous theoretical chemists I’ve ever met! Grateful to J Chem Phys @aip.bsky.social for this special issue in his honor - proud to be a guest editor. Please consider submitting your work! 041 4
Xuhui Huang @xuhuihuangchem.bsky.social · 05/12/2024Benoît Roux gave two fantastic lectures this week as part of our department's John Ferry Lectureship series in Macromolecular Science. I thoroughly enjoyed the exciting discussions on many topics in Stat Mech! 081 8
Xuhui Huang @xuhuihuangchem.bsky.social · 04/12/2024Whew! Finally finished all the tenure letters and grad school recommendation letters this year! Time to prep the final exam for my physical chemistry class! 280 8
Reposted by Xuhui HuangFolding@home @foldingathome.org · 25/11/2024To keep up with individual Folding@home researchers (past and present), check our FAH Researcher starter pack! We'll do our best to keep it up to date, so check back every so often. Link: go.bsky.app/AMkfpEq 12410 24
Xuhui Huang @xuhuihuangchem.bsky.social · 28/11/2024First-year grad students at UW-Madison Chemistry Dept have just completed their group selection process. We’re excited to welcome Chengwei Dong (B.S. from Peking U.) and Peter Swanson (B.S. from UNE, jointly supervised with Arun Yethiraj) to our group! Thrilled to have you both on board! 050 5
Xuhui Huang @xuhuihuangchem.bsky.social · 19/11/2024Our new preprint, led by @yunruiqiu.bsky.social and Shuming Liu (MIT), explores the use of IGME non-Markovian model to study chromatin folding in collaboration with Bin Zhang’s group at MIT. One interesting finding: memory kernels decay more slowly in nucleosome condensates than in free solution. 071 7