lamm-mit/protein-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

Harmonic mean of macro F1 scores: $$\text{score}=\frac{2\cdot F{1}_{Q8}\cdot F{1}_{Q3}}{F{1}_{Q8}+F{1}_{Q3}}\backslash text\{score\}\; =\; \backslash frac\{2\; \backslash cdot\; F1\_\{Q8\}\; \backslash cdot\; F1\_\{Q3\}\}\{F1\_\{Q8\}\; +\; F1\_\{Q3\}\}$$

Dataset Statistics

Split	Sequences	Total Residues
Train	7,262	1,763,921
Test	1,816	-

Sequence Length Statistics

• Minimum: 20 residues
• Maximum: 1,632 residues
• Mean: 242.9 residues

Label Distribution

Q8 (Eight-State) Labels

Label	Description	Percentage
H	Alpha helix	31.6%
C	Coil/Loop	24.2%
E	Beta strand	21.0%
T	Turn	10.6%
S	Bend	7.7%
G	3-10 helix	3.8%
B	Beta bridge	1.1%
I	Pi helix	<0.1%

Q3 (Three-State) Labels

Label	Description	Percentage
C	Coil (C, T, S from Q8)	42.6%
H	Helix (H, G, I from Q8)	35.4%
E	Strand (E, B from Q8)	22.1%

File Structure

├── train.csv      # Training data with sequences and labels
├── test.csv       # Test sequences (no labels)
└── sample_submission.csv  # Submission format

Column Descriptions

train.csv:

• id: Unique sequence identifier
• seq: Amino acid sequence (20 standard amino acids)
• sst8: Q8 secondary structure labels
• sst3: Q3 secondary structure labels

test.csv:

• id: Unique sequence identifier
• seq: Amino acid sequence

Usage

from datasets import load_dataset

dataset = load_dataset("neuralninja110/protein-secondary-structure-nppe2")

# Access training data
train_data = dataset['train']
print(train_data[0])

Citation

If you use this dataset, please cite:

@misc{nppe2_2025,
  author = {Rahul Ashok},
  title = {Protein Secondary Structure Prediction Dataset (NPPE-2)},
  year = {2025},
  publisher = {HuggingFace},
  howpublished = {\url{https://huggingface.co/datasets/neuralninja110/protein-secondary-structure-nppe2}}
}

Author

Rahul Ashok
Indian Institute of Technology Madras
23f1001177@ds.study.iitm.ac.in