datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
Proteinscasp14-casp15-cameo-test-proteinsprotein_stability_single_mutation
Protein Data Stability - Single Mutation
This repository contains data on the change in protein stability with a single mutation.
Attribution of Data Sources
Primary Source: Tsuboyama, K., Dauparas, J., Chen, J. et al. Mega-scale experimental analysis of protein folding stability in biology and design. Nature 620, 434–444 (2023). Link to the paper
Dataset Link: Zenodo Record
As to where the dataset comes from in this broader work, the relevant dataset (#3) is shown in… See the full description on the dataset page: https://huggingface.co/datasets/Trelis/protein_stability_single_mutation.Dataset-Structure_Class-ProteinShake
Description
Structural Class Prediction is a multi-class classification task to predict the correct structural class of given protein. This task is is built on the SCOP database.
Protein Format: SA sequence (PDB)
Splits
The dataset is from ProteinShake Building datasets and benchmarks for deep learning on protein structures. We use the splits based on 70% structure similarity, with the number of training, validation and test set shown below:
Train: 7990
Valid: 955
Test:… See the full description on the dataset page: https://huggingface.co/datasets/SaProtHub/Dataset-Structure_Class-ProteinShake.pyaptamer-proteins-shin2023greenbeing-proteins
GreenBeing Proteins dataset
Proteins from UniProtKB (knowledge base), from select food crops and related species.
Amino acid sequences use IUPAC-IUB codes where letters A-Z map to amino acids.
Usage (due to different schema on splits):
load_dataset("monsoon-nlp/greenbeing-proteins", "pretraining", split="pretraining")
XML source from https://www.uniprot.org/help/downloads
CoLab notebook: https://colab.research.google.com/drive/1M6sO0Ws6i5z9VUXIXopiOqo1OkQ7K-1g?usp=sharing… See the full description on the dataset page: https://huggingface.co/datasets/monsoon-nlp/greenbeing-proteins.Dataset-Structural_Similarity-ProteinShake
Description
Structure Similarity Prediction predicts the (aligned) Local Distance Difference Test (LDDT) of the structures given an unaligned pair of proteins. Target values are computed after alignment with TM-align for all pairs of 1000 randomly sampled single-chain proteins.
Protein Format: SA sequence(PDB)
Splits
The dataset is from ProteinShake Building datasets and benchmarks for deep learning on protein structures. We use the splits based on 70% structure… See the full description on the dataset page: https://huggingface.co/datasets/SaProtHub/Dataset-Structural_Similarity-ProteinShake.aging_proteins
Description of the Dataset
This is (part of) the dataset used in
Prediction and characterization of human ageing-related proteins by using machine learning.
This can be used to train a binary sequence classifier using protein language models such as ESM-2.
Please also see the github for the paper for more information.
protein_solubility_classDataset-Binding_Site_Detection-ProteinShake
Description
Binding Site Detection predicts , predict whether a protein residue belongs to a small molecule binding cavity. Binding site residues are those within the binding pocket provided by PDBBind. Default metric is Matthew's Correlation.
Splits
Protein Format: SA sequence (PDB)
The dataset is from ProteinShake Building datasets and benchmarks for deep learning on protein structures. We use the splits based on 70% structure similarity, with the number of training… See the full description on the dataset page: https://huggingface.co/datasets/SaProtHub/Dataset-Binding_Site_Detection-ProteinShake.primate-proteinsAll primate proteins in UniProtKB (knowledge base) which have been reviewed (Swiss-Prot), including but not limited to humans.
Each row contains a gene name, species or subspecies, an amino acid sequence, and comments / annotations available in UniProt.
A gene name may match multiple entries / IDs on UniProt from different accessions.
Annotations may be empty, or may include information such as:
likely function, written in English
location inside of cell (e.g. "Subcellular locations:… See the full description on the dataset page: https://huggingface.co/datasets/monsoon-nlp/primate-proteins.protein-secondary-structure-predictprotein-secondary-structure-nppe2
Protein Secondary Structure Prediction Dataset (NPPE-2)
Dataset Description
This dataset is used for the Protein Secondary Structure Prediction competition from the Deep Learning and Generative AI course at IIT Madras.
Task
Predict the secondary structure of proteins at the residue level using:
Q8 (sst8): Eight-state secondary structure classification (DSSP notation)
Q3 (sst3): Three-state secondary structure classification
Evaluation Metric… See the full description on the dataset page: https://huggingface.co/datasets/neuralninja110/protein-secondary-structure-nppe2.protein_structure_uncertainty_auditor_v01Protein Structure Uncertainty Auditor v0.1
This dataset tests whether language models can correctly recognize uncertainty and epistemic limits when talking about protein structure and AlphaFold style predictions.
Each row contains
claim
grounding_status
rationale_hint
correct_action
grounding_status values
groundedthe claim is a reasonable interpretation of structure and confidence
speculativethe claim is plausible but needs more context or experiment
unfoundedthe claim overreaches what… See the full description on the dataset page: https://huggingface.co/datasets/ClarusC64/protein_structure_uncertainty_auditor_v01.llps-proteinsprotein_structure_uncertainty_auditor_v0.2Protein Structure Uncertainty Auditor
GoalDetect when predicted protein structures are too uncertain for downstream use.
Model must output
uncertainty_flag (yes/no)
uncertainty_type
recommendation
This dataset tests whether models can audit structural confidence before use in:
drug design
docking
mutation mapping
function inference
Run scorer
python scorer.py --predictions predictions.jsonl --test_csv data/test.csv
protein-secondary-structure-nppeUniRef90-GPCR-ProteinsAll UniRef90 sequences of G-protein coupled receptors (GPCR) class proteins across all species. G-protein coupled receptors are evolutionarily related proteins and cell surface receptors that detect molecules outside the cell in Eukariotes.
Contains both confirmed and putative proteins.
Proteinswildtype_proteinsProteins-NOVAproteinsThis dataset contains protein structures used for the evaluation of AlphaFold2, ESMFold, and OmegaFold in the bachelor thesis "Comparative Analysis of Protein Structure Prediction Tools".
All protein structures in the dataset were selected from PDB and comply with the following criteria:
The structure was deposited into PDB between 22 July 2022 and 22 July 2024. This condition ensures that the data could not have been used during the training of prediction tools compared in the thesis.
The… See the full description on the dataset page: https://huggingface.co/datasets/hyskova-anna/proteins.Protein_Secondary_Structure_Prediction