Hybrid MPI-thread parallelization of adaptive mesh operations. - Dan Ibanez; Ian Dunn; Mark S. Shephard (Parallel Comput., 2016)

Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure. - Ian Dunn; David Ryan Koes (CoRR, 2023)

Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation. - Ian Dunn; David Ryan Koes (CoRR, 2024)

Exploring Discrete Flow Matching for 3D De Novo Molecule Generation. - Ian Dunn; David Ryan Koes (CoRR, 2024)

CACHE Challenge #1: Docking with GNINA Is All You Need. - Ian Dunn; Somayeh Pirhadi; Yao Wang; Smmrithi Ravindran; Carter Concepcion; David Ryan Koes (J. Chem. Inf. Model., 2024)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. - Oleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz A. Abu-Saleh; Ayaz Ahmad; Jesus Alvarado-Huayhuaz; Oscar Emilio Arrúa Arce; Roly J. Armstrong; Cheryl H. Arrowsmith; Kelly E. Bachta; Hartmut Beck; Dénes Berta; Mateusz K. Bieniek; et al. (J. Chem. Inf. Model., 2025)

GEOM-Drugs Revisited: Toward More Chemically Accurate Benchmarks for 3D Molecule Generation. - Filipp Nikitin; Ian Dunn; David Ryan Koes; Olexandr Isayev (CoRR, 2025)

FlowMol3: Flow Matching for 3D De Novo Small-Molecule Generation. - Ian Dunn; David Ryan Koes (CoRR, 2025)