| Diffdock: Diffusion steps, twists, and turns for molecular docking G Corso, H Stärk, B Jing, R Barzilay, T Jaakkola Eleventh International Conference on Learning Representations (ICLR 2023), 2023 | 572 | 2023 |
| Learning from protein structure with geometric vector perceptrons B Jing, S Eismann, P Suriana, RJL Townshend, R Dror Ninth International Conference on Learning Representations (ICLR 2021), 2021 | 543 | 2021 |
| Torsional Diffusion for Molecular Conformer Generation B Jing, G Corso, J Chang, R Barzilay, T Jaakkola Neural Information Processing Systems 2022, 2022 | 309 | 2022 |
| ATOM3D: Tasks On Molecules in Three Dimensions RJL Townshend, M Vögele, P Suriana, A Derry, A Powers, Y Laloudakis, ... NeurIPS 2021 Track on Datasets and Benchmarks, 2021 | 138 | 2021 |
| AlphaFold meets flow matching for generating protein ensembles B Jing, B Berger, T Jaakkola Forty-first International Conference on Machine Learning (ICML 2024), 2024 | 95 | 2024 |
| Equivariant Graph Neural Networks for 3D Macromolecular Structure B Jing, S Eismann, PN Soni, RO Dror ICML 2021 Workshop on Computational Biology, 2021 | 95 | 2021 |
| Subspace diffusion generative models B Jing, G Corso, R Berlinghieri, T Jaakkola European Conference on Computer Vision 2022, 2022 | 86 | 2022 |
| EigenFold: Generative Protein Structure Prediction with Diffusion Models B Jing, E Erives, P Pao-Huang, G Corso, B Berger, T Jaakkola ICLR Machine Learning for Drug Discovery Workshop 2023, 2023 | 77 | 2023 |
| Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes S Eismann, RJL Townshend, N Thomas, M Jagota, B Jing, RO Dror Proteins: Structure, Function, and Bioinformatics 89 (5), 493-501, 2021 | 76* | 2021 |
| Dirichlet flow matching with applications to dna sequence design H Stark, B Jing, C Wang, G Corso, B Berger, R Barzilay, T Jaakkola Forty-first International Conference on Machine Learning (ICML 2024), 2024 | 41 | 2024 |
| Harmonic Self-Conditioned Flow Matching for joint Multi-Ligand Docking and Binding Site Design H Stark, B Jing, R Barzilay, T Jaakkola Forty-first International Conference on Machine Learning (ICML 2024), 2024 | 33* | 2024 |
| 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 | 27 | 2024 |
| Protein model quality assessment using rotation‐equivariant transformations on point clouds S Eismann, P Suriana, B Jing, RJL Townshend, RO Dror Proteins: Structure, Function, and Bioinformatics 91 (8), 1089-1096, 2023 | 14* | 2023 |
| Generative modeling of molecular dynamics trajectories B Jing, H Stärk, T Jaakkola, B Berger Neural Information Processing Systems 2024, 2024 | 10 | 2024 |
| Scalable multimer structure prediction using diffusion models P Pao-Huang, B Jing, B Berger NeurIPS 2023 AI for Science Workshop, 2023 | 3 | 2023 |
| Rotation-invariant gait identification with quaternion convolutional neural networks (student abstract) B Jing, V Prabhu, A Gu, J Whaley Proceedings of the AAAI conference on artificial intelligence 35 (18), 15805 …, 2021 | 3 | 2021 |
| Sgvae: Sequential graph variational autoencoder B Jing, EA Chi, J Tang arXiv preprint arXiv:1912.07800, 2019 | 3 | 2019 |
| Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms B Jing, T Jaakkola, B Berger Twelvth International Conference on Learning Representations (ICLR 2024), 2024 | 1 | 2024 |
| ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids H Stark, B Jing, T Geffner, J Yim, T Jaakkola, A Vahdat, K Kreis Thirteenth International Conference on Learning Representations (ICLR 2025), 2025 | | 2025 |
| Learning the language of protein–protein interactions V Ullanat, B Jing, S Sledzieski, B Berger bioRxiv, 2025.03. 09.642188, 2025 | | 2025 |
