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Datasets:
alexchilton
/
nanobody-contact-maps

Tasks:
Text Generation
Modalities:
Text
Formats:
parquet
Size:
1K - 10K
Tags:
protein
contact-map
structure
nanobody
Libraries:
Datasets
pandas
License:
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amino_acid_sequence
sequencelengths
91
2.46k
length
int64
91
2.46k
c_alpha_coordinates
sequencelengths
91
2.46k
distance_matrix
sequencelengths
91
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YAML Metadata Warning: The task_categories "image-generation" is not in the official list: text-classification, token-classification, table-question-answering, question-answering, zero-shot-classification, translation, summarization, feature-extraction, text-generation, fill-mask, sentence-similarity, text-to-speech, text-to-audio, automatic-speech-recognition, audio-to-audio, audio-classification, audio-text-to-text, voice-activity-detection, depth-estimation, image-classification, object-detection, image-segmentation, text-to-image, image-to-text, image-to-image, image-to-video, unconditional-image-generation, video-classification, reinforcement-learning, robotics, tabular-classification, tabular-regression, tabular-to-text, table-to-text, multiple-choice, text-ranking, text-retrieval, time-series-forecasting, text-to-video, image-text-to-text, visual-question-answering, document-question-answering, zero-shot-image-classification, graph-ml, mask-generation, zero-shot-object-detection, text-to-3d, image-to-3d, image-feature-extraction, video-text-to-text, keypoint-detection, visual-document-retrieval, any-to-any, video-to-video, other

Protein Contact Map Dataset

Dataset Description

This dataset contains protein structures with contact maps and related information from nanobody sequences.

Dataset Summary

  • Number of proteins: 2992
  • Source: Nanobody protein structures (nanos_networkx_small)
  • Created by: alexchilton
  • Date: 2025-05-04

Dataset Structure

Each protein entry contains:

  • amino_acid_sequence: List of amino acid names
  • length: Number of residues
  • c_alpha_coordinates: List of [x,y,z] coordinates for C-alpha atoms
  • distance_matrix: Pairwise distance matrix between C-alpha atoms
  • contact_maps: List of binary contact maps with different distance thresholds
  • contact_map_configs: Configuration for each contact map (lower/upper bounds)

Usage 

from datasets import load_dataset
dataset = load_dataset("alexchilton/nanobody-contact-maps")

# Access a protein
protein = dataset['train'][0]
print(f"Length: {protein['length']}")
print(f"First 10 residues: {protein['amino_acid_sequence'][:10]}")

Citation

If you use this dataset, please cite:

@dataset{protein_contact_maps,
  title={Nanobody Protein Contact Map Dataset},
  author={Alex Chilton},
  year={2025},
  url={https://huggingface.co/datasets/alexchilton/nanobody-contact-maps}
}
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Size of downloaded dataset files:
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