T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles. - Rizi Ai; M. Qaiser Fatmi; Chia-en A. Chang (J. Comput. Aided Mol. Des., 2010)

The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase. - M. Qaiser Fatmi; Chia-en A. Chang (PLoS Comput. Biol., 2010)

Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design. - Wanli You; Yu-ming M. Huang; Smitha Kizhake; Amarnath Natarajan; Chia-en A. Chang (PLoS Comput. Biol., 2016)

A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery. - Timothy Cholko; Wei Chen; Zhiye Tang; Chia-en A. Chang (J. Comput. Aided Mol. Des., 2018)

Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. - Wanli You; Chia-en A. Chang (J. Chem. Inf. Model., 2018)

GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems. - Timothy Cholko; Shivansh Kaushik; Kingsley Y. Wu; Ruben Montes; Chia-en A. Chang (J. Chem. Inf. Model., 2022)

Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning. - Talant Ruzmetov; Ta I Hung; Saisri Padmaja Jonnalagedda; Si-Han Chen; Parisa Fasihianifard; Zhefeng Guo; Bir Bhanu; Chia-en A. Chang (J. Chem. Inf. Model., 2025)