Data
The data folder contains data files used in the manuscript. It is subdivided into the following folders:
| Section | Description |
|---|---|
| chkpts | Where model checkpoints are stored. |
| embeddings | Where protein embedding databases are stored. |
| kw | Where protein embedding databases are stored. |
| lengths | Where data for the length analysis. |
| mutation | Where data for the mutation analysis. |
| pllm | Where pLM datasets are stored. |
| ppi | Where PPI datasets are stored. |
| tokenizer | Where tokenizers are stored. |
chkpts
This folder contains model checkpoints for the SqueezeProt variants, RAPPPID, and ProSE.
| Folder | Description |
|---|---|
squeezeprot-sp.non-strict/checkpoint-1390896 |
Weights for SqueezeProt-SP (Non-strict). |
squeezeprot-sp.strict/checkpoint-1383824 |
Weights for SqueezeProt-SP (Strict). |
squeezeprot-sp.u50/checkpoint-2477920 |
Weights for SqueezeProt-U50. |
sars_cov2 |
Various weights for pLM-based PPI models used in the SARS-CoV-2 analysis. |
rapppid/1690837077.519848_red-dreamy.ckpt |
Weights for RAPPPID. These weights were previously published in Szymborski et al.. |
prose/prose_dlm_3x1024.sav |
Weights for ProSE. These weights were previously published in Bepler et al.. |
ppi |
Various weights for pLM-based PPI models. |
kw/logs/KeywordNet |
SqueezeProt-SP keyword annotation models. |
This folder also contains sub-folders ppi, sars_cov2 where checkpoints of the pLM-based PPI inference models are stored. Checkpoints are stored according to their model names, which are hashes of the model hyperparameters. You can see all the hyper-parameters in the hparams.json file within the model's folder.
Mappings from Model IDs to their Hyperparameters
| Model ID | pLM | Seed | Input Dimension |
|---|---|---|---|
iRcKUvufAzeh9CuJAtFMgjRq8Yo= |
ESM | 1 | 6165 |
aLK3NQAPP9uHfEDhrBCaFXTjE9I= |
ESM | 2 | 6165 |
x5i3FQ9dA3iI6IoHUyCzgydVWgM= |
ESM | 3 | 6165 |
DoetbgdKMxDuKdfRWOUHSGAXTf0= |
ProtBERT | 1 | 1024 |
jjvmU1efEjj1VWqJ8frthcAuiK4= |
ProtBERT | 2 | 1024 |
nHLZTP7wTAmtJSlpLtAYOH6gAj0= |
ProtBERT | 3 | 1024 |
Dvy3BYf00JQ18SHKOSdCu9zWojs= |
ProtT5 | 1 | 1024 |
XAnrmSjztabYNXRBbdrU2uV8XRM= |
ProtT5 | 2 | 1024 |
PUoe1MerYJArEl8h4d-P40V06zA= |
ProtT5 | 3 | 1024 |
xSIEaL28YQW14K0UhNoWmwX-_HU= |
ProSE | 1 | 6165 |
7KwnY62-2a7UBaKz3jplmvRqSWk= |
ProSE | 2 | 6165 |
3VHXtNHqEashvmxcWsXwCxgPqs0= |
ProSE | 3 | 6165 |
048O3lE7pCo4Y_qpQAZLfxYrz6Q= |
ProteinBERT | 1 | 1562 |
Ir_BXqrPDOutyG20qLfc2Sn4qoE= |
ProteinBERT | 2 | 1562 |
7x1W0IhBtFMoEdgUYTJCY6yuhoc= |
ProteinBERT | 3 | 1562 |
c-HcTcy0NwO7JY8U3lu8Nva7d7o= |
SqueezeProt-SP (Strict) | 1 | 768 |
hdhFlXCydBsLZrIicCM4LMrNWoE= |
SqueezeProt-SP (Strict) | 2 | 768 |
r8TQa4FnoUdDvr2LPGZqZk4z6y4= |
SqueezeProt-SP (Strict) | 3 | 768 |
vFjXUGbR0vMEu8Bu0j2C2445J2A= |
SqueezeProt-SP (Strict) | 4 | 768 |
5yEzfPl2E2eT54OJXLF0K75z_3I= |
SqueezeProt-SP (Strict) | 5 | 768 |
W9DvdTJ7bW1GaCV3TyJ7HZznwZw= |
SqueezeProt-SP (Strict) | 6 | 768 |
ngRDPuiaLHeCXQJvigyMuE1tsmw= |
SqueezeProt-SP (Strict) | 7 | 768 |
MFwIN5YJ_98AUYYGORMlCvgv8j4= |
SqueezeProt-SP (Strict) | 8 | 768 |
yGeHPlv6AviEUwC4jssZy-FuTBM= |
SqueezeProt-SP (Strict) | 9 | 768 |
s3SMyXYEAmNECJgqSfhKutisFLc= |
SqueezeProt-SP (Strict) | 10 | 768 |
0KCyeB_K-ZCIlNwpl3rRopZyM0I= |
SqueezeProt-SP (Non-strict) | 1 | 768 |
1c-2iUOfs3Ye_pV0WGtCApV1Rgg= |
SqueezeProt-SP (Non-strict) | 2 | 768 |
8F6cxSJIb1syPfiZDK04DgCaP90= |
SqueezeProt-SP (Non-strict) | 3 | 768 |
SsTLBBEPiGnpX91hunP9-E8w6jY= |
SqueezeProt-SP (Non-strict) | 4 | 768 |
EdJtO7pKkYBjeeGajJ33-hySWfE= |
SqueezeProt-SP (Non-strict) | 5 | 768 |
K51CpKE1he98de-DV7Pq67DE4ok= |
SqueezeProt-SP (Non-strict) | 6 | 768 |
6U8njyd40iXoaBCx4WdL57FOX9o= |
SqueezeProt-SP (Non-strict) | 7 | 768 |
7YxAquqSeLtB1I85ItoXQvtGsg8= |
SqueezeProt-SP (Non-strict) | 8 | 768 |
qI4P2gmDPMvY6epwa6cIgG9PQlE= |
SqueezeProt-SP (Non-strict) | 9 | 768 |
MmCcff1PHh0lOvl84LiytfrznMw= |
SqueezeProt-SP (Non-strict) | 10 | 768 |
uARWusUXomAV5qa0X9e2V4C5wwI= |
SqueezeProt-U50 | 1 | 768 |
cpns6_wtKs93e6ekMXxkBilEGv4= |
SqueezeProt-U50 | 2 | 768 |
OcZKrg-rYN5RsfC6TH9btqfdVV8= |
SqueezeProt-U50 | 3 | 768 |
embeddings
This folder holds pre-computed UniProt protein embeddings for each model. Embeddings are stored in LMDB databases.
| Database | pLM |
|---|---|
esm.lmdb |
ESM |
prose.lmdb |
ProSE |
proteinbert.lmdb |
ProteinBERT |
prottrans_bert.lmdb |
ProtBERT |
prottrans_t5.lmdb |
ProtT5 |
rapppid.lmdb |
RAPPPID |
squeezeprot-sp.nonstrict.lmdb |
SqueezeProt-SP (Non-strict) |
squeezeprot_sp_strict.lmdb |
SqueezeProt-SP (Strict) |
squeezeprot_u50.lmdb |
SqueezeProt-U50 |
Sub-folders mutation and sars-cov-2 include embeddings for mutated proteins from ELASPIC and SARS-CoV-2 proteins, respectively.
kw
This folder contains data for the UniProt Keyword annotations.
| Folder | Description |
|---|---|
hparams |
Log of hyperparameters for the keyword models trains. |
out |
Inferred probabilities on a testing dataset. Filename corresponds to model number. |
kw.json.gz |
List of UniProt Keywords. |
kw_ids.json |
Matching UniProt Keywords to their categories. |
kw_meta.json |
Number of instances for each UniProt Keyword. |
kw_train.csv |
Contains UniProt accession numbers and the associated keywords and sequences for training the annotation model. |
kw_test.csv |
Contains UniProt accession numbers and the associated keywords and sequences for testing the annotation model. |
kw_train_vecs.csv |
Contains UniProt accession numbers and the associated keywords, sequences, and embeddings for training the annotation model. |
kw_test_vecs.csv |
Contains UniProt accession numbers and the associated keywords, sequences, and embeddings for testing the annotation model. |
lengths
This folder contains data for the protein length analyses.
| Folder | Description |
|---|---|
length_histogram.csv.gz |
Data for the length histogram. |
mutation
This folder contains data for the mutation analyses.
| Folder | Description |
|---|---|
elaspic-trainin-set-interface-ids.csv |
Data from the ELASPIC2 manuscript. |
pllm
This folder contains data used to train the SqueezeProt-SP pLMs.
| Folder | Description |
|---|---|
uniprot_sprot.nonstrict.eval.fasta |
FASTA file containing sequences of proteins which are assigned to the evaluation split of the non-strict SqueezeProt-SP model. |
uniprot_sprot.nonstrict.eval.txt |
Text file containing sequences of proteins which are assigned to the evaluation split of the non-strict SqueezeProt-SP model. |
uniprot_sprot.nonstrict.train.fasta |
FASTA file containing sequences of proteins which are assigned to the training split of the non-strict SqueezeProt-SP model. |
uniprot_sprot.nonstrict.train.txt |
Text file containing sequences of proteins which are assigned to the training split of the non-strict SqueezeProt-SP model. |
ppi
The PPI datasets used in the manuscript are present in this folder. They are:
| File | Description |
|---|---|
rapppid_[common_string_9606.protein.links.detailed.v12.0_upkb.csv]_Mz70T9t-4Y-i6jWD9sEtcjOr0X8=.h5 |
Human PPI dataset from Szymborski et al.. |
sars-cov-2/baits.fasta |
Sequences of bait proteins from Gordon et al.. |
sars-cov-2/preys.fasta |
Sequences of prey proteins from Gordon et al.. |
sars-cov-2/covid_ppi.csv |
Human/SARS-CoV-2 PPI pairs from Gordon et al.. |
tokenizer
This folder contains the tokenizer used for the SqueezeProt variants.
| Folder | Description |
|---|---|
tokenizer/bert-based-cased |
A tokenizer for the SqueezeProt variants. |
tokenizer/rapppid |
A tokenizer for the RAPPPID model. |