| DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking G Corso, H Stärk, B Jing, R Barzilay, T Jaakkola ICLR 2023: International Conference on Learning Representations (full paper)., 2023 | 899 | 2023 |
| EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction H Stärk, OE Ganea, L Pattanaik, R Barzilay, T Jaakkola ICML 2022: International Conference on Machine Learning (full paper). Also …, 2022 | 441 | 2022 |
| 3D Infomax improves GNNs for Molecular Property Prediction H Stärk, D Beaini, G Corso, P Tossou, C Dallago, S Günnemann, P Liò ICML 2022: International Conference on Machine Learning (full paper). Also …, 2022 | 362 | 2022 |
| Graph neural networks G Corso, H Stark, S Jegelka, T Jaakkola, R Barzilay Nature Reviews Methods Primers 4 (1), 17, 2024 | 341 | 2024 |
| Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design I Igashov, H Stärk, C Vignac, VG Satorras, P Frossard, M Welling, ... Nature Machine Intelligence 6 (4), 417-427, 2022 | 270 | 2022 |
| Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery F Wong, A Krishnan, EJ Zheng, H Stärk, AL Manson, AM Earl, T Jaakkola, ... Molecular systems biology 18 (9), e11081, 2022 | 266 | 2022 |
| Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction S Passaro, G Corso, J Wohlwend, M Reveiz, S Thaler, V Ram Somnath, ... BioRxiv, 2025.06. 14.659707, 2025 | 221 | 2025 |
| Light Attention Predicts Protein Location from the Language of Life H Stärk, C Dallago, M Heinzinger, B Rost Bioinformatics Advances. Also at 2 ICLR'21 Workshops, 1 ICML'21 Workshop …, 2021 | 147 | 2021 |
| Dirichlet Flow Matching with Applications to DNA Sequence Design H Stark, B Jing, C Wang, G Corso, B Berger, R Barzilay, T Jaakkola ICML 2024; also Spotlight at ICLR 2024 MLGenX workshop, 2024 | 90 | 2024 |
| DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models MA Ketata, C Laue, R Mammadov, H Stärk, M Wu, G Corso, C Marquet, ... arXiv preprint arXiv:2304.03889, 2023 | 85 | 2023 |
| Diffusion models in protein structure and docking J Yim, H Stärk, G Corso, B Jing, R Barzilay, TS Jaakkola Wiley Interdisciplinary Reviews: Computational Molecular Science 14 (2), e1711, 2024 | 72 | 2024 |
| PLINDER: The protein-ligand interactions dataset and evaluation resource J Durairaj, Y Adeshina, Z Cao, X Zhang, V Oleinikovas, T Duignan, ... bioRxiv, 2024.07. 17.603955, 2024 | 65 | 2024 |
| Generative Modeling of Molecular Dynamics Trajectories B Jing, H Stärk, T Jaakkola, B Berger NeurIPS 2024, 2024 | 52 | 2024 |
| ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation M Hassan, N Shenoy, J Lee, H Stärk, S Thaler, D Beaini Advances in Neural Information Processing Systems 37, 128798-128824, 2025 | 32 | 2025 |
| Think while you generate: Discrete diffusion with planned denoising S Liu, J Nam, A Campbell, H Stärk, Y Xu, T Jaakkola, ... ICLR 2025, 2024 | 31 | 2024 |
| PINDER: The protein interaction dataset and evaluation resource D Kovtun, M Akdel, A Goncearenco, G Zhou, G Holt, D Baugher, D Lin, ... bioRxiv, 2024.07. 17.603980, 2024 | 26 | 2024 |
| Generalized laplacian positional encoding for graph representation learning S Maskey, A Parviz, M Thiessen, H Stärk, Y Sadikaj, H Maron NeurIPS 2022 Workshop on Symmetry and Geometry in Neural Representations, 2022 | 26 | 2022 |
| Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design H Stärk, B Jing, R Barzilay, T Jaakkola ICML 2024; also Spotlight at NeurIPS 2023 AI4Science Workshop, 2023 | 25 | 2023 |
| DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility M Plainer, M Toth, S Dobers, H Stark, G Corso, C Marquet, R Barzilay | 20 | 2023 |
| Blind protein-ligand docking with diffusion-based deep generative models G Corso, B Jing, H Stark, R Barzilay, T Jaakkola Biophysical Journal 122 (3), 143a, 2023 | 12 | 2023 |
Tommi JaakkolaMITVerified email at csail.mit.edu
