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--- |
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dataset_info: |
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features: |
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- name: input_ids |
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sequence: int32 |
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- name: coords |
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sequence: |
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sequence: float64 |
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- name: labels |
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dtype: int64 |
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- name: token_type_ids |
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sequence: int8 |
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splits: |
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- name: train |
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num_bytes: 1419748993 |
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num_examples: 2864 |
|
- name: val |
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num_bytes: 394945349 |
|
num_examples: 937 |
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- name: test |
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num_bytes: 214263730 |
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num_examples: 347 |
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download_size: 774980058 |
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dataset_size: 2028958072 |
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configs: |
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- config_name: default |
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data_files: |
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- split: train |
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path: data/train-* |
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- split: val |
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path: data/val-* |
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- split: test |
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path: data/test-* |
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--- |
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# Mutation Stability Prediction |
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## Overview |
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The Mutation Stability Prediction (MSP) task involves classifying whether |
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mutations in the SKEMPI 2.0 database (J. Jankauskaite, B. Jiménez-García et al., 2019) are stabilizing or not using the provided protein structures. |
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Each mutation in the MSP task includes a PDB file with the residue of interest transformed to the specified mutant amino acid as well as the native PDB file. |
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A total of 4148 mutant structures accompanied by their 316 WT structures are provided. |
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Non-point mutations or mutants that caused non-binding of the complex were screened out from SKEMPI. |
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Additionally, mutations involving a disulfide bond and mutants from the PDBs 1KBH or 1JCK were ignored due to processing difficulties. |
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A label of 1 was assigned to a mutant if the Kd of the mutant protein was less than that of the wild-type protein, indicating better binding, and 0 otherwise. |
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If a mutant had multiple conflicting stability results in the original data, the first result seen when processing the SKEMPI dataset was used. |
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## Datasets |
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- splits: |
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- split-by-year: |
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## Format |
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Each item in the dataset contains the following keys: |
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- ['input_ids'] The set of atomic numbers for both the mutated and original atoms concatenated together. |
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- ['coords'] The 3D coordinates for both the mutated and original atoms concatenated together. |
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- ['label'] 1 for better binding, 0 for worse or equal. |
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- ['token_type_ids'] A mask that corresponds to which `inputs_ids`/`coords` belong to the mutated or original atoms (0 for mutated , 1 for original) |
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## Citation Information |
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|
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``` |
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@article{townshend2020atom3d, |
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title={Atom3d: Tasks on molecules in three dimensions}, |
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author={Townshend, Raphael JL and V{\"o}gele, Martin and Suriana, Patricia and Derry, Alexander and Powers, Alexander and Laloudakis, Yianni and Balachandar, Sidhika and Jing, Bowen and Anderson, Brandon and Eismann, Stephan and others}, |
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journal={arXiv preprint arXiv:2012.04035}, |
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year={2020} |
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} |
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``` |
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|
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``` |
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@article{jankauskaite2019skempi, |
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title={SKEMPI 2.0: an updated benchmark of changes in protein--protein binding energy, kinetics and thermodynamics upon mutation}, |
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author={Jankauskait{\.e}, Justina and Jim{\'e}nez-Garc{\'\i}a, Brian and Dapk{\=u}nas, Justas and Fern{\'a}ndez-Recio, Juan and Moal, Iain H}, |
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journal={Bioinformatics}, |
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volume={35}, |
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number={3}, |
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pages={462--469}, |
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year={2019}, |
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publisher={Oxford University Press} |
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} |
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``` |
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