Jana Shen

Structural basis of ultraviolet sensitivity and gating in an anion-conducting apusomonad rhodopsin

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.

Activation pathway of the human voltage-gated proton channel

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.

Slow Dissociation of Nitazenes from the μ-Opioid Receptor Underlies the Challenge of Overdose Reversal

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.

Illuminating the Ligandable Proteome with AI Protein Profiling

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.

Membrane Permeability Drives the Extreme Potency of Fentanyl but not Isotonitazene

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.

How Electric Field Remodels the Nanofibril Structure of Chitosan Hydrogels: the Role of Dewetting During Electro-Assembly

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.

Predicting Protein Electrostatics with Protein Language Models

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

A Putative Binding Model of Nitazene Derivatives at the mu-Opioid Receptor

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

KaMLs for Predicting Protein pKa Values and Ionization States: Are Trees All You Need?

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.

Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics

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.

Machine Learned Classification of Ligand Intrinsic Activities at Human mu-Opioid Receptor

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.

QM/MM simulations of EFGR with afatinib reveal the role of the beta-dimethylaminomethyl substitution

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.

Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K

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.

Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines

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.