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---
dataset_info:
features:
- name: input_ids
sequence: int32
- name: coords
sequence:
sequence: float64
- name: labels
dtype: int64
- name: token_type_ids
sequence: int8
splits:
- name: train
num_bytes: 1419748993
num_examples: 2864
- name: val
num_bytes: 394945349
num_examples: 937
- name: test
num_bytes: 214263730
num_examples: 347
download_size: 774980058
dataset_size: 2028958072
configs:
- config_name: default
data_files:
- split: train
path: data/train-*
- split: val
path: data/val-*
- split: test
path: data/test-*
---
# Mutation Stability Prediction
## Overview
The Mutation Stability Prediction (MSP) task involves classifying whether
mutations in the SKEMPI 2.0 database (J. Jankauskaite, B. Jiménez-García et al., 2019) are stabilizing or not using the provided protein structures.
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.
A total of 4148 mutant structures accompanied by their 316 WT structures are provided.
Non-point mutations or mutants that caused non-binding of the complex were screened out from SKEMPI.
Additionally, mutations involving a disulfide bond and mutants from the PDBs 1KBH or 1JCK were ignored due to processing difficulties.
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.
If a mutant had multiple conflicting stability results in the original data, the first result seen when processing the SKEMPI dataset was used.
## Datasets
- splits:
- split-by-year:
## Format
Each item in the dataset contains the following keys:
- ['input_ids'] The set of atomic numbers for both the mutated and original atoms concatenated together.
- ['coords'] The 3D coordinates for both the mutated and original atoms concatenated together.
- ['label'] 1 for better binding, 0 for worse or equal.
- ['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)
## Citation Information
```
@article{townshend2020atom3d,
title={Atom3d: Tasks on molecules in three dimensions},
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},
journal={arXiv preprint arXiv:2012.04035},
year={2020}
}
```
```
@article{jankauskaite2019skempi,
title={SKEMPI 2.0: an updated benchmark of changes in protein--protein binding energy, kinetics and thermodynamics upon mutation},
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},
journal={Bioinformatics},
volume={35},
number={3},
pages={462--469},
year={2019},
publisher={Oxford University Press}
}
```
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