Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms
Authors: Bowen Jing, Tommi S. Jaakkola, Bonnie Berger
ICLR 2024 | Conference PDF | Archive PDF | Plain Text | LLM Run Details
| Reproducibility Variable | Result | LLM Response |
|---|---|---|
| Research Type | Experimental | We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields. |
| Researcher Affiliation | Academia | Bowen Jing1, Tommi Jaakkola1, Bonnie Berger1 2 1CSAIL, Massachusetts Institute of Technology 2Dept. of Mathematics, Massachusetts Institute of Technology |
| Pseudocode | Yes | Algorithm 1: TRANSLATIONAL FFT (...) Algorithm 2: ROTATIONAL FFT (...) Algorithm 3: TRANSLATIONAL SCORING (...) Algorithm 4: ROTATIONAL SCORING |
| Open Source Code | Yes | Code is available at https://github.com/bjing2016/scalar-fields. |
| Open Datasets | Yes | We train and test our model on the PDBBind dataset (Liu et al., 2017) with splits as defined by St ark et al. (2022). |
| Dataset Splits | Yes | As noted previously, we use train, validation, and test splits from St ark et al. (2022). |
| Hardware Specification | Yes | All runtime measurements were performed on a machine with 64 Intel Xeon Gold 6130 CPUs and 8 Nvidia Tesla V100 GPUs. |
| Software Dependencies | No | The paper mentions software like 'RDKit', 'Gnina', 'Vina', 'TANKBind', and 'Diff Dock', but it does not specify version numbers for these or any other ancillary software components, nor does it list specific library versions (e.g., Python, PyTorch versions). |
| Experiment Setup | Yes | All other model and inference-time hyperparameters are discussed in Appendix E. (...) These hyperparameters and their search spaces are detailed in Table 4 (...) The search space for these resolution hyperpameters is detailed in Table 5. |