WISC_news

Congratulations to Bojun, Jordan, and Ilona on publishing the TS-DAR method in Nature Communications! Many thanks as well to our collaborators, Prof. Sharon Li and Xuefeng. The TS-DAR method simultaneously identifies transition states across multiple …

We’re excited to welcome 3 new graduate students: Chengwei Dong (Chemistry, B.S. from Peking U.), Peter Swanson (Chemistry, B.S. from UNE, jointly supervised with Arun Yethiraj), and Andres Lira (Biophysics, B.S. from UC Davis, jointly …

Our lab (PI) receive a Research Forward award for funding our development of a chemical feature-based Transformer platform to predict molecular glues! Excited to collaborate with Prof. Sharon Li (UW-Madison, CS) and Weiping Tang (UW-Madison, Pharmacy)!

Our tutorial on building non-Markovian models (qMSMs, IGME) from MD simulations for protein dynamics was published as a featured and cover article at JCP.  Please try it out on GitHub: https://github.com/xuhuihuang/GME_tutorials!

Our 2nd collaborative NIH R01 grant with Prof. Jiaoyang Jiang (PI, UW-Madison Pharmacy) and Prof. Lingjun Li (co-I) was funded. We’ll study the enzyme removing O-GlcNAc post-translational modifications. 

We welcome three new group members: Yichong Lao (1st year graduate student from Biophysics Program), Longbang Liu (1st year graduate student from Chemistry), and Kazuya Okita (a visiting student from Osaka University, Japan)!

Our IGME paper is selected as a Featured Article by JCP! It efficiently models biomolecular dynamics by employing time integrations of memory kernels and avoiding numerical instability in time-dependent memory kernels.

Our GraphVAMPnets provides an efficient way to find CVs for self-assembly. Graph embeddings ensure structures invariant to permutations and rotations, and the VAMP theory (no detailed-balance requirement) handles insufficient sampling of dissociation transitions.  This article …

Our Latent space Path Clustering (LPC) method can efficiently group parallel kinetic pathways into distinct metastable path channels. It utilizes the variational autoencoder (VAE) to learn the spatial distributions of kinetic pathways and perform path …

Our collaborative research with Prof. Jiaoyang Jiang and Prof. Lingjun Li in School of Pharmacy at UW-Madison has been funded by a new $1.65 million NIH R01 grant (PI: Jiang)! Congratulations! We look forward to …