protein_net

  • Description:

ProteinNet is a standardized data set for machine learning of protein structure. It provides protein sequences, structures (secondary and tertiary), multiple sequence alignments (MSAs), position-specific scoring matrices (PSSMs), and standardized training / validation / test splits. ProteinNet builds on the biennial CASP assessments, which carry out blind predictions of recently solved but publicly unavailable protein structures, to provide test sets that push the frontiers of computational methodology. It is organized as a series of data sets, spanning CASP 7 through 12 (covering a ten-year period), to provide a range of data set sizes that enable assessment of new methods in relatively data poor and data rich regimes.

FeaturesDict({
    'evolutionary': Tensor(shape=(None, 21), dtype=float32),
    'id': Text(shape=(), dtype=string),
    'length': int32,
    'mask': Tensor(shape=(None,), dtype=bool),
    'primary': Sequence(ClassLabel(shape=(), dtype=int64, num_classes=20)),
    'tertiary': Tensor(shape=(None, 3), dtype=float32),
})
  • Feature documentation:
Feature Class Shape Dtype Description
FeaturesDict
evolutionary Tensor (None, 21) float32
id Text string
length Tensor int32
mask Tensor (None,) bool
primary Sequence(ClassLabel) (None,) int64
tertiary Tensor (None, 3) float32 
@article{ProteinNet19,
title = { {ProteinNet}: a standardized data set for machine learning of protein structure},
author = {AlQuraishi, Mohammed},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {1--10},
year = {2019},
publisher = {BioMed Central}
}

protein_net/casp7 (default config)

  • Download size: 3.18 GiB

  • Dataset size: 2.53 GiB

  • Splits:

Split Examples
'test' 93
'train_100' 34,557
'train_30' 10,333
'train_50' 13,024
'train_70' 15,207
'train_90' 17,611
'train_95' 17,938
'validation' 224

protein_net/casp8

  • Download size: 4.96 GiB

  • Dataset size: 3.55 GiB

  • Splits:

Split Examples
'test' 120
'train_100' 48,087
'train_30' 13,881
'train_50' 17,970
'train_70' 21,191
'train_90' 24,556
'train_95' 25,035
'validation' 224

protein_net/casp9

  • Download size: 6.65 GiB

  • Dataset size: 4.54 GiB

  • Splits:

Split Examples
'test' 116
'train_100' 60,350
'train_30' 16,973
'train_50' 22,172
'train_70' 26,263
'train_90' 30,513
'train_95' 31,128
'validation' 224

protein_net/casp10

  • Download size: 8.65 GiB

  • Dataset size: 5.57 GiB

  • Splits:

Split Examples
'test' 95
'train_100' 73,116
'train_30' 19,495
'train_50' 25,897
'train_70' 31,001
'train_90' 36,258
'train_95' 37,033
'validation' 224

protein_net/casp11

  • Download size: 10.81 GiB

  • Dataset size: 6.72 GiB

  • Splits:

Split Examples
'test' 81
'train_100' 87,573
'train_30' 22,344
'train_50' 29,936
'train_70' 36,005
'train_90' 42,507
'train_95' 43,544
'validation' 224

protein_net/casp12

  • Download size: 13.18 GiB

  • Dataset size: 8.05 GiB

  • Splits:

Split Examples
'test' 40
'train_100' 104,059
'train_30' 25,299
'train_50' 34,039
'train_70' 41,522
'train_90' 49,600
'train_95' 50,914
'validation' 224