vector-institute/atom3d-msp

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}
}