GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber

Julie A. Harris, Ruibin Liu, Vinicius Martins de Oliveira, Erik Antonio Vázquez-Montelongo, Jack A. Henderson and Jana Shen

J. Chem. Theory Comput., 2022, 18, 7510
DOI: 10.1021/acs.jctc.2c00586

Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors

Vijayakumar Gosu, Santanu Sasidharan, Prakash Saudagar, Kamalakannan Radhakrishnan, Hak-Kyo Lee and Donghyun Shin

Computers in Biology and Medicine, 2023, 160, 106978
DOI: 10.1016/j.compbiomed.2023.106978

Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53

Theresa Klett, Martin Schwer, Larissa Ernst, Marc Engelhardt, Simon Jaag, Benedikt Masberg, Cornelius Knappe, Michael Lämmerhofer, Matthias Gehringer and Frank Boeckler

DDDT, 2024, Volume 18, 2653
DOI: 10.2147/DDDT.S466829

Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads

Ruibin Liu, Erik A. Vázquez-Montelongo, Shuhua Ma and Jana Shen

J. Chem. Inf. Model., 2023, 63, 4912
DOI: 10.1021/acs.jcim.3c00720

Electrostatics in Computational Biophysics and Its Implications for Disease Effects

Shengjie Sun, Pitambar Poudel, Emil Alexov and Lin Li

IJMS, 2022, 23, 10347
DOI: 10.3390/ijms231810347

QM/MM Simulations of Afatinib-EGFR Addition: The Role of β-Dimethylaminomethyl Substitution

Shuhua Ma, Heeral Patel, Craig A. Peeples and Jana Shen

J. Chem. Theory Comput., 2024, 20, 5528
DOI: 10.1021/acs.jctc.4c00290

Structure-based rational design of covalent probes

Matthew Holcomb, Manuel Llanos, Althea Hansel-Harris and Stefano Forli

Commun Chem, 2025, 8
DOI: 10.1038/s42004-025-01606-y

One-Shot Rational Design of Covalent Drugs with CovalentLab

Xi Xue, Xiangying Liu, Xue Liu, Hanyu Sun, Shize Li, Kai Chen, Hanmiao Xu, Liangning Li, Chengxia Mao, Jingjie Yan, Peilan Yang, Baolian Wang, Tingjun Hou, Tingting Du and Xiaojian Wang

JACS Au, 2025, 5, 5676
DOI: 10.1021/jacsau.5c01161

Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases

Aarion Romany, Ruibin Liu, Shaoqi Zhan, Joseph Clayton and Jana Shen

J. Chem. Inf. Model., 2023, 63, 2483
DOI: 10.1021/acs.jcim.3c00014

Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines

Ruibin Liu, Joseph Clayton, Mingzhe Shen, Shubham Bhatnagar and Jana Shen

JACS Au, 2024, 4, 1374
DOI: 10.1021/jacsau.3c00749

Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation

Wenbo Yu, David J. Weber and Alexander D. MacKerell

J. Chem. Theory Comput., 2023, 19, 3007
DOI: 10.1021/acs.jctc.3c00232