Emine Kucukbenli

Senior Research Scientist, NVIDIA

Joined

June 2021

Names

Emine Kucukbenli (Preferred)

Emails

****@gmail.com (Confirmed)

****@nvidia.com (Confirmed)

Personal Links

Google Scholar

Career & Education History

Senior Research Scientist

NVIDIA (nvidia.com)

2022 – Present

Clinical Assistant Professor

Boston University (bu.edu)

2020 – 2022

Postdoc

Harvard University (harvard.edu)

2019 – 2020

Advisors, Relations & Conflicts

Coauthor

Shuiwang Ji

2024 – 2025

Postdoc Advisor

Efthimios Kaxiras

2019 – 2020

Expertise

atomistic modelling

material science

neural potentials

MLIP

Present

drug discovery

docking

protein design

Present

Publications

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials
Cong Fu, Yuchao Lin, Zachary Krueger, Haiyang Yu, Maho Nakata, Jianwen Xie, Emine Kucukbenli, Xiaofeng Qian, Shuiwang Ji
- Accepted by TMLR
- Readers: Everyone
Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute
Kieran Didi, Zuobai Zhang, Guoqing Zhou, Danny Reidenbach, Zhonglin Cao, Sooyoung Cha, Tomas Geffner, Christian Dallago, Jian Tang, Michael M. Bronstein, Martin Steinegger, Emine Kucukbenli, Arash Vahdat, Karsten Kreis
- ICLR 2026 Oral
- Readers: Everyone
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
Tomas Geffner, Kieran Didi, Zhonglin Cao, Danny Reidenbach, Zuobai Zhang, Christian Dallago, Emine Kucukbenli, Karsten Kreis, Arash Vahdat
- ICLR 2026 Poster
- Readers: Everyone
Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design
Danny Reidenbach, Zhonglin Cao, Zuobai Zhang, Kieran Didi, Tomas Geffner, Guoqing Zhou, Jian Tang, Christian Dallago, Arash Vahdat, Emine Kucukbenli, Karsten Kreis
- NeurIPS2025-AI4Science Poster
- Readers: Everyone
ToxBench: A Binding Affinity Prediction Benchmark with AB-FEP-Calculated Labels for Human Estrogen Receptor Alpha
Meng Liu, 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, Hari Priya Devannagari, Edward B. Miller, Muyun Lihan, Howook Hwang, Janet Paulsen, Xin Yu, Kyle Gion, Timur Rvachov et al. (2 additional authors not shown)
- GenBio 2025 Poster
- Readers: Everyone
Tensor Decomposition Networks for Fast Machine Learning Interatomic Potential Computations
Yuchao Lin, Cong Fu, Zachary Krueger, Haiyang Yu, Maho Nakata, Jianwen Xie, Emine Kucukbenli, Xiaofeng Qian, Shuiwang Ji
- NeurIPS 2025 poster
- Readers: Everyone
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 Smidt, Emine Kucukbenli, JOSEPH JACOBSON
- GEM
- Readers: Everyone
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 Kucukbenli
- ICLR 2025 DeLTa Workshop Poster
- Readers: Everyone
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 Kucukbenli
- GEM
- Readers: Everyone
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 Kucukbenli
- ICML 2025 poster
- Readers: Everyone

View all 14 publications

Co-Authors

View all 68 co-authors