Classical force field parameters for the heme prosthetic group of cytochrome c. - Felix Autenrieth; Emad Tajkhorshid; Jérôme Baudry; Zaida Luthey-Schulten (J. Comput. Chem., 2004)

Scalable molecular dynamics with NAMD. - James C. Phillips; Rosemary Braun; Wei Wang 342; James C. Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant V. Kalé; Klaus Schulten (J. Comput. Chem., 2005)

Modeling and Dynamics of the Inward-Facing State of a Na+/Cl- Dependent Neurotransmitter Transporter Homologue. - Saher Afshan Shaikh; Emad Tajkhorshid (PLoS Comput. Biol., 2010)

Rapid parameterization of small molecules using the force field toolkit. - Christopher G. Mayne; Jan Saam; Klaus Schulten; Emad Tajkhorshid; James C. Gumbart (J. Comput. Chem., 2013)

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. - Josh Vincent Vermaas; David J. Hardy; John E. Stone; Emad Tajkhorshid; Axel Kohlmeyer (J. Chem. Inf. Model., 2016)

Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. - Shashank Pant; Emad Tajkhorshid (J. Comput. Chem., 2020)

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. - Haochuan Chen; Julio D. C. Maia; Brian K. Radak; David J. Hardy; Wensheng Cai; Christophe Chipot; Emad Tajkhorshid (J. Chem. Inf. Model., 2020)

Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus. - David J. Hardy; John E. Stone; Barry Isralewitz; Emad Tajkhorshid (UrgentHPC@SC, 2021)

Experiences Porting NAMD to the Data Parallel C++ Programming Model. - David J. Hardy; Jaemin Choi; Wei Jiang; Emad Tajkhorshid (IWOCL, 2022)

End-to-end AI Framework for Hyperparameter Optimization, Model Training, and Interpretable Inference for Molecules and Crystals. - Hyun Park; Ruijie Zhu 004; Eliu A. Huerta; Santanu Chaudhuri; Emad Tajkhorshid; Donny Cooper (CoRR, 2022)

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. - Anda Trifan; Defne Gorgun; Michael Salim; Zongyi Li; Alexander Brace; Maxim Zvyagin; Heng Ma; Austin Clyde; David Clark; David J. Hardy; Tom Burnley; Lei Huang 019; et al. (Int. J. High Perform. Comput. Appl., 2022)

Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes. - Giuseppe Licari; Sepehr Dehghani-Ghahnaviyeh; Emad Tajkhorshid (J. Chem. Inf. Model., 2022)

Assembly and Analysis of Cell-Scale Membrane Envelopes. - Josh Vincent Vermaas; Christopher G. Mayne; Eric Shinn; Emad Tajkhorshid (J. Chem. Inf. Model., 2022)

Cybershuttle: An End-to-End Cyberinfrastructure Continuum to Accelerate Discovery in Science and Engineering. - Suresh Marru; Marlon E. Pierce; Beth Plale; Sudhakar Pamidighantam; Dimuthu Wannipurage; Marcus Christie; Isuru Ranawaka; Eroma Abeysinghe; Rob Quick; Emad Tajkhorshid; Seid Koric; Jim Basney; et al. (PEARC, 2023)

GHP-MOFassemble: Diffusion modeling, high throughput screening, and molecular dynamics for rational discovery of novel metal-organic frameworks for carbon capture at scale. - Hyun Park; Xiaoli Yan; Ruijie Zhu 004; Eliu A. Huerta; Santanu Chaudhuri; Donny Cooper; Ian T. Foster; Emad Tajkhorshid (CoRR, 2023)

Prediction of Diblock Copolymer Morphology via Machine Learning. - Hyun Park; Boyuan Yu; Juhae Park; Ge Sun; Emad Tajkhorshid; Juan J. de Pablo; Ludwig Schneider (CoRR, 2023)

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. - Mariano Spivak; John E. Stone; João Ribeiro 003; Jan Saam; Peter L. Freddolino; Rafael C. Bernardi; Emad Tajkhorshid (J. Chem. Inf. Model., 2023)

Topological Learning Approach to Characterizing Biological Membranes. - Andres S. Arango; Hyun Park; Emad Tajkhorshid (J. Chem. Inf. Model., 2024)

Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. - Muyun Lihan; Emad Tajkhorshid (J. Chem. Inf. Model., 2024)

GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules. - Zhiyu Zhao; Emad Tajkhorshid (J. Chem. Inf. Model., 2024)

MOFA: Discovering Materials for Carbon Capture with a GenAI- and Simulation-Based Workflow. - Xiaoli Yan; Nathaniel Hudson 001; Hyun Park; Daniel Grzenda; J. Gregory Pauloski; Marcus Schwarting; Haochen Pan; Hassan Harb; Sam Foreman; Chris Knight 001; Tom Gibbs; Kyle Chard; et al. (CoRR, 2025)