Datasets:

yk0
/

litscrape

pretty_name: LitScrape Protein Binder Interactions
license: mit
language:
  - en
tags:
  - protein
  - protein-protein-interaction
  - binder-design
  - biology
  - literature-curation
size_categories:
  - 1K<n<10K
configs:
  - config_name: default
    data_files:
      - split: train
        path: data.csv

LitScrape

This is a protein binder interaction dataset built from multiple design papers and supplementary information source files.

Each row is a target-binder pair with:

the target name and target sequence
the binder identifier and binder sequence
a binary interaction label
the paper/source of origin

Columns

source_publication: paper or source string associated with the interaction
target: target name
target_sequence: target amino-acid sequence
binder_id: binder identifier from the source dataset
binder_sequence: binder amino-acid sequence
label: binary interaction label (1 = positive, 0 = negative)
binding_affinity_nm: binding affinity in nanomolar units when reported; blank otherwise

Construction

We did not use a threshold to determine whether an interaction is binding or non-binding. Instead, we used the author-designated labels. Some methods only include binder sequences for positives, while others include the binder sequences for negatives in the supplementary information. We include the author reported binding affinities whe possible, noting that each method may use a different technology to measure this affinity.

Sources

[Overath et al.](Predicting experimental success in de novo binder design: a meta-analysis of 3,766 experimentally characterised binders)
Latent-X
Dickinson PPI Challenge
Bindcraft Supplementary Information
AlphaProteo Supplementary Information
PPIFlow
RFDiffusion Supplementary Information