Chia‐en A. Chang

Mechanistic Dissection of Conformational Transition of Bicyclic Peptide via Molecular Modeling and Deep Learning

This study introduces a deep learning model to analyze conformational transitions in cyclic peptides, revealing key residues and nonlinear torsional motions that govern structural changes.

Mechanistic Dissection of Entropic Penalty upon Ligand Binding and Molecular Flexibility via Molecular Dynamics Simulations and Machine Learning

This study quantifies molecular entropy and its changes during ligand binding using MD simulations and machine learning, revealing key motions and their thermodynamic impacts.

Revealing imatinib-kinase specificity via analyzing changes in protein dynamics and computing molecular binding affinity

This study uses molecular dynamics simulations to analyze imatinib-kinase interactions, identifying factors that predict binding specificity and guide drug repurposing.

CACNA1C as a Prognostic Biomarker and Therapeutic Target in High-Grade Serous Ovarian Cancer: Clinical Validation and Molecular Dynamics of Nifedipine Blockade

This paper identifies CACNA1C as a prognostic biomarker and therapeutic target in high-grade serous ovarian cancer, showing nifedipine suppresses tumor growth through calcium channel blockade.

Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning

This paper introduces a deep learning model to sample conformational ensembles of dynamic proteins, demonstrating its ability to generate novel conformations and rationalize experimental findings.

Pathway Specific Unbinding Free Energy Profiles of Ritonavir Dissociation From HIV-1 Protease

This study analyzes ritonavir dissociation from HIV-1 protease using molecular dynamics simulations to identify pathways and free energy landscapes, revealing the role of hydrogen bonding and residue correlations in unbinding mechanisms.

PROTAC-induced Protein Structural Dynamics in Targeted Protein Degradation

This study computationally models PROTAC-induced protein dynamics to explain variation in degradation potency despite identical warheads.

Discovery of New CDK8 ligands with a Novel Virtual Drug Screening Tool

This study develops a virtual drug screening tool to discover new CDK8 type II ligands, identifying a potent compound with a Kd value of 42.5 nM.