Jana Shen

This study determines the cryo-EM structure of SfApuR2, an ultraviolet-sensitive anion-conducting rhodopsin, and identifies structural features that explain its UV sensitivity and gating mechanism.

This study determines the activation pathway of the human voltage-gated proton channel hHV1 using computational methods, revealing voltage-driven structural changes and lipid effects validated by experiments.

The paper investigates the slow dissociation of nitazenes from the μ-opioid receptor, showing it contributes to overdose reversal challenges and provides structural insights into the mechanism.

This paper introduces AiPP, an AI-based platform for predicting ligandable sites in the human proteome, and demonstrates its application in discovering covalent inhibitors for PTPN6.

This study investigates how membrane permeability affects the potency of fentanyl and isotonitazene, finding that fentanyl's extreme potency may be due to its ability to accumulate in membranes and repartition to bind receptors.

This paper uses molecular dynamics simulations to show how an electric field remodels chitosan hydrogel nanofibril structure through active dewetting, leading to vertical contraction and compaction.

This paper introduces KaML-ESM2 and KaML-ESMC models to predict protein pKa values, outperforming existing methods but facing challenges with engineered residues.

This paper uses computational methods to model how nitazene derivatives bind to the mu-opioid receptor, identifying key binding modes and interactions.

This paper develops KaML models using decision trees and graph attention networks to predict protein pKa values and ionization states, outperforming existing methods and introducing a new pKa database.

This study evaluates force field limitations in constant pH molecular dynamics simulations of a mini-protein, showing significant pKa errors due to force field and water model choices.

The paper develops machine learning models to classify intrinsic activities of ligands at the human mu-opioid receptor using molecular descriptors and SMILES strings, achieving high accuracy even with limited data.

The paper uses QM/MM simulations to study the reaction mechanism of afatinib with Cys797 in EGFR, revealing a Michael addition mechanism involving deprotonation and stabilization by Asp800.

This study investigates why the Omicron variant's main protease is less stable than the wild-type by analyzing its structure, enzymatic activity, and biophysical properties.

The paper develops ML models to predict covalent ligandable cysteines using a curated database, achieving high accuracy and providing a web tool for drug discovery.

This study uses molecular dynamics simulations to uncover the mechanism of dimer selectivity and binding cooperativity of BRAF inhibitors, revealing structural changes and hydrogen bonding that influence inhibitor binding preferences.