PANNA: Properties from Artificial Neural Network Architectures. - Ruggero Lot; Franco Pellegrini; Yusuf Shaidu; Emine Küçükbenli (Comput. Phys. Commun., 2020)

PANNA 2.0: Efficient neural network interatomic potentials and new architectures. - Franco Pellegrini; Ruggero Lot; Yusuf Shaidu; Emine Küçükbenli (CoRR, 2023)

LATTE: an atomic environment descriptor based on Cartesian tensor contractions. - Franco Pellegrini; Stefano de Gironcoli; Emine Küçükbenli (CoRR, 2024)

EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants. - Allan dos Santos Costa; Ilan Mitnikov; Franco Pellegrini; Ameya Daigavane; Mario Geiger; Zhonglin Cao; Karsten Kreis; Tess E. Smidt; Emine Küçükbenli; Joseph Jacobson (CoRR, 2024)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - Peter St. John; Dejun Lin; Polina Binder; Malcolm Greaves; Vega Shah; John St. John; Adrian Lange; Patrick D. Hsu; Rajesh Illango; Arvind Ramanathan; Anima Anandkumar; David H. Brookes; et al. (CoRR, 2024)

Proteina: Scaling Flow-based Protein Structure Generative Models. - Tomas Geffner; Kieran Didi; Zuobai Zhang; Danny Reidenbach; Zhonglin Cao; Jason Yim; Mario Geiger; Christian Dallago; Emine Küçükbenli; Arash Vahdat; Karsten Kreis (ICLR, 2025)

Optimizing Data Distribution and Kernel Performance for Efficient Training of Chemistry Foundation Models: A Case Study with MACE. - Jesun Firoz; Franco Pellegrini; Mario Geiger; Darren Hsu; Jenna A. Bilbrey; Han-Yi Chou; Maximilian Stadler; Markus Hoehnerbach; Tingyu Wang; Dejun Lin; Emine Küçükbenli; Henry W. Sprueill; et al. (CoRR, 2025)

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials. - Cong Fu 003; Yuchao Lin; Zachary Krueger; Haiyang Yu 005; Maho Nakata; Jianwen Xie; Emine Küçükbenli; Xiaofeng Qian; Shuiwang Ji (CoRR, 2025)

Tensor Decomposition Networks for Fast Machine Learning Interatomic Potential Computations. - Yuchao Lin; Cong Fu 003; Zachary Krueger; Haiyang Yu 005; Maho Nakata; Jianwen Xie; Emine Küçükbenli; Xiaofeng Qian; Shuiwang Ji (CoRR, 2025)

ToxBench: A Binding Affinity Prediction Benchmark with AB-FEP-Calculated Labels for Human Estrogen Receptor Alpha. - Meng Liu 015; Karl Leswing; Simon K. S. Chu; Farhad Ramezanghorbani; Griffin Young; Gabriel Marques; Prerna Das; Anjali Panikar; Esther Jamir; Mohammed Sulaiman Shamsudeen; K. Shawn Watts; Ananya Sen; et al. (CoRR, 2025)

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching. - Tomas Geffner; Kieran Didi; Zhonglin Cao; Danny Reidenbach; Zuobai Zhang; Christian Dallago; Emine Küçükbenli; Karsten Kreis; Arash Vahdat (CoRR, 2025)

Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow. - Zhonglin Cao; Mario Geiger; Allan dos Santos Costa; Danny Reidenbach; Karsten Kreis; Tomas Geffner; Franco Pellegrini; Guoqing Zhou; Emine Küçükbenli (CoRR, 2025)