A PyTorch implementation of NodeCoder pipeline, a Graph Convolutional Network (GCN) framework for protein residue characterization.
Project description
A PyTorch implementation of NodeCoder Pipeline, a Graph Convolutional Network (GCN) - based framework for protein residue characterization. This work was presented at NeurIPS MLSB 2021: Residue characterization on AlphaFold2 protein structures using graph neural networks. link to paper
Abstract:
Three-dimensional structure prediction tools offer a rapid means to approximate the topology of a protein structure for any
protein sequence. Recent progress in deep learning-based structure prediction has led to highly accurate predictions that have
recently been used to systematically predict 20 whole proteomes by DeepMindโs AlphaFold and the EMBL-EBI. While highly convenient,
structure prediction tools lack much of the functional context presented by experimental studies, such as binding sites or
post-translational modifications. Here, we introduce a machine learning framework to rapidly model any residue-based
classification using AlphaFold2 structure-augmented protein representations. Specifically, graphs describing the 3D structure of
each protein in the AlphaFold2 human proteome are generated and used as input representations to a Graph Convolutional Network
(GCN), which annotates specific regions of interest based on the structural attributes of the amino acid residues, including their
local neighbors. We demonstrate the approach using six varied amino acid classification tasks.
Table of Contents
๐งฌ What does NodeCoder Pipeline do?
โ๏ธ Installing NodeCoder
๐ NodeCoder Usage
๐๏ธ Graph data files
๐ Output files
๐ค Collaborators
๐ License
๐ Citing this work
๐งฌ What does the NodeCoder Pipeline do?
The NodeCoder is a generalized framework that annotates 3D protein structures with predicted tasks such as
binding sites. The NodeCoder model is based on Graph Convolutional Network. NodeCoder generates proteins' graphs from
ALphaFold2 augmented proteins' structures where the nodes are the amino acid residues and edges are inter-residue
contacts within a preset distance. The NodeCoder model is then trained with generated graph data for users task of
interest like: Task = ['y_Ligand']
.
When running inference, NodeCoder takes the Protein ID like EGFR_HUMAN and for the proteins that are already in
the database, input graph data files are created from the AlphaFold2 protein structure in addition to calculating some
structure-based and sequence-based residue features. The input graph data will then be given to the trained model for
prediction of multiple tasks of interest such as binding sites or post-translational modifications.
โ๏ธ Installing NodeCoder
Required dependencies
The codebase is implemented in Python 3.8 and package versions used for development are:
numpy 1.19.2
pandas 1.2.4
scipy 1.6.3
torch 0.4.1
torchvision 0.9.1
torchaudio 0.8.1
torch_scatter 2.0.6
torch_sparse 0.6.9
torch_cluster 1.5.9
torch_spline_conv 1.2.0
torch-geometric 1.7.0
scikit-learn 0.24.2
matplotlib 3.3.3
biopython 1.77
freesasa 2.0.5.post2
loguru 0.6.0
Installation steps
Here is the step-by-step NodeCoder installation process:
Method 1 - install test.pypi package
- Before installing NodeCoder, we highly recommend to create a virutal Python 3.8 environment using venv command, or Anaconda. Assuming you have anaconda3 installed on your computer, on your Terminal run the following command line:
$ conda create -n <your_python_env> python=3.8
- Make sure your virtual environment is active. For conda environment you can use this command line:
$ conda activate <your_python_env>
- Now you can install NodeCoder with this command line:
$ pip install --extra-index-url https://test.pypi.org/simple/ NodeCoder
Method 2 - install from GitHub repository
Follow above-mentioned steps 1-2, and continue with the following steps:
3. Clone the repository:
$ git clone https://github.com/NasimAbdollahi/NodeCoder.git
- Make sure you are in the root directory of the NodeCoder package
~/NodeCoder/
(where setup.py is). Now install NodeCoder package with following command line, which will install all dependencies in the python environment you created in step 1:
$ pip install .
๐ NodeCoder Usage
NodeCoder package can be employed for train and inference. Here we describe how to use it:
๐๏ธ Preprocessing raw data
link to paper NodeCoder uses AlphaFold2 modeled protein structures as input. AlphaFold protein structure database provides open access to protein structure predictions of human proteome and other key proteins of interest. Prediction labels can be obtained from BioLip database and Uniprot database.
Once you downloaded the protein databases, first step is to run the NodeCoder's featurizer module to process these raw
data sets and extract node features and labels.
When using NodeCoder's featurizer module, preprocess_raw_data
, you will need to specify the directories you have the
datasets saved:
alphafold_data_path
uniprot_data_path
biolip_data_path
biolip_data_skip_path
The featurizer module will create two files for every protein in the selected proteome:
*.features.csv
and *.tasks.csv
. These files are saved in
NodeCoder/data/input_data/featurized_data/TAX_ID/
directory in separate folders of
features
and tasks
.
For example if user choose human proteome, 9606
, then the following tree structure will be generated:
data/input_data/featurized_data/
โโโ 9606
โโโ features
โโโ tasks
The command line to run the featurizer module is:
$ python NodeCoder/preprocess_raw_data.py
To use NodeCoder as python package, import preprocessing module as:
>>> from NodeCoder import preprocess_raw_data
>>> preprocess_raw_data.main(alphafold_data_path='.', uniprot_data_path='.', biolip_data_path='.', biolip_data_skip_path='.')
The default species/proteome is HUMAN, but user can change it with the following parameters:
>>> preprocess_raw_data.main(alphafold_data_path='.', uniprot_data_path='.', biolip_data_path='.', biolip_data_skip_path='.',
TAX_ID='9606', PROTEOME_ID='UP000005640')
๐๏ธ Generate graph data
The next step after running the featurizer is to generate graph data from the features and tasks files. NodeCoder has a
graph-generator module that generate protein graph data by taking a threshold for distance between amino acid residues.
The threshold distance is required to be defined by user in Angstrom unit to create the graph contact network, threshold_dist = 5
.
Graph data files are saved in this directory ./data/input_data/graph_data_*A/
with the
following tree structure (the example here is for 8A cut-off distance and 5 folds for cross-validation):
data/input_data/graph_data_8A/
โโโ 9606
โโโ 5FoldCV
The command line to run the graph generator module is:
$ python NodeCoder/generate_graph_data.py
To use NodeCoder as python package, import generate_graph_data module as:
>>> from NodeCoder import generate_graph_data
>>> generate_graph_data.main()
Where, user can specify the following parameters
>>> generate_graph_data.main(TAX_ID='9606', PROTEOME_ID='UP000005640', threshold_dist=5, cross_validation_fold_number=5)
Note that for cross-validation setting, separate graphs are created for each fold.
๐ง Train NodeCoder
To train NodeCoder's graph-based model, user can use train.py
module.
Script parser.py
has the model parameters used for training the model.
User would need to use the following parameters in train.py
script to specify the task/tasks of interest and the
cutoff distance for defining the protein contact network:
Task = ['y_Ligand']
threshold_dist = 5
Command line to train NodeCoder:
$ python NodeCoder/train.py
To use NodeCoder as python package, import train module as:
>>> from NodeCoder import train
>>> train.main()
Where, user can specify the following parameters
>>> train.main(threshold_dist=5, multi_task_learning=False, Task=['y_Ligand'], centrality_feature=True,
cross_validation_fold_number=5, epochs=1000)
Here is a list of available training tasks (residue labels/annotations) :
'y_CHAIN', 'y_TRANSMEM', 'y_MOD_RES', 'y_ACT_SITE', 'y_NP_BIND',
'y_LIPID', 'y_CARBOHYD', 'y_DISULFID', 'y_VARIANT', 'y_Artifact',
'y_Peptide', 'y_Nucleic', 'y_Inorganic', 'y_Cofactor', 'y_Ligand'
๐ค Inference with NodeCoder
To use trained NodeCoder for protein functions prediction, user needs to run predict.py
script.
User would need to use the following parameters in predict.py
script to specify the protein of interest, functions
of interest and the cutoff distance for defining the protein contact network:
Task = ['y_Ligand']
threshold_dist = 5
Command line to run inference with NodeCoder:
$ python NodeCoder/main_predict.py
To use NodeCoder as python package, import train module as:
>>> from NodeCoder import predict
>>> predict.main()
Where, user can specify the following parameters
>>> predict.main(protein_ID='KI3L1_HUMAN', threshold_dist=5, trained_model_fold_number=1, multi_task_learning=False,
Task=['y_Ligand'], centrality_feature=True, cross_validation_fold_number=5, epochs=1000)
The user shall make sure the model with the desired parameters should have been trained already, otherwise the user would need to first train the model then use this pipeline for prediction.
๐๏ธ Graph data files
When graph data is generated from featurized data, files are saved in this directory ./data/input_data/graph_data_*A/
.
Specific sub-directories are created depends on user choice of cutoff distance for protein contact network, proteom, and
number of cross-validation folds. This helps user to keep track of different test cases.
For every fold, following data files are created for train and validation sets:
data/input_data/graph_data_5A/9606/
โโโ *FoldCV
โโโ train_1_ProteinFileNames.csv
โโโ train_1_ProteinFiles.csv
โโโ train_1_edge_features.csv
โโโ train_1_edges.csv
โโโ train_1_features.csv
โโโ train_1_nodes_ProteinID.csv
โโโ train_1_target.csv
โโโ ....
โโโ validation_1_ProteinFileNames.csv
โโโ validation_1_ProteinFiles.csv
โโโ validation_1_edge_features.csv
โโโ validation_1_edges.csv
โโโ validation_1_features.csv
โโโ validation_1_nodes_ProteinID.csv
โโโ validation_1_target.csv
โโโ ...
Generated graph data files includes:
*_features.csv
Nodes' feature vectors are concatenated to create a long list of features for all nodes in the graph. The first row is a header:
node_id | feature_id | value |
---|---|---|
node number in the graph | one int. value of 0-45 | ... |
*_edges.csv
It contains the list node-pairs for all edges in the graph:
id1 | id2 |
---|---|
index of node 1 | index of node 2 |
*_edge_features.csv
It contains the edge features for all edges in the graph. Currently, three different features are calculated for the edges; however, the current model only uses the squared reciprocal of edge length as weight.
id1 | id2 | edge_length | edge_cosine_angle | edge_sequence_distance |
---|---|---|---|---|
index of node 1 | index of node 2 | Euclidean distance between the node pair | Cosine distance between the node pair | Sequence distance between the node pair |
*_target.csv
It the target labels for all nodes in the graph. The number of columns depends on the number of targets that user specify for prediction.
y_task1 | y_task2 | y_task3 | y_task4 | y_task5 | y_task6 |
---|---|---|---|---|---|
0/1 | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 |
*_ProteinFiles.csv
Protein File | Node Num | Removed NaNs |
---|---|---|
EGFR_HUMAN | 1207 | 0 |
PTC1_HUMAN | 1444 | 0 |
DDX10_HUMAN | 872 | 0 |
... | ... | ... |
RBL1_HUMAN | 1065 | 0 |
*_nodes_ProteinID.csv
If more than one protein is given to the model, this file keeps track of the residues that belong to each protein.
node_id | protein_id_flag | protein_id |
---|---|---|
0 | 0 | EGFR_HUMAN |
1 | 0 | EGFR_HUMAN |
2 | 0 | EGFR_HUMAN |
3 | 0 | EGFR_HUMAN |
4 | 0 | EGFR_HUMAN |
... | ... | ... |
1207 | 1 | E2F8_HUMAN |
1208 | 1 | E2F8_HUMAN |
1209 | 1 | E2F8_HUMAN |
... | ... | ... |
Amino Acid Residue (AA) feature vector:
feature ID | feature name | feature Description |
---|---|---|
0-19 | feat_A, feat_B, ..., feat_Y | primary structure - one-hot-encoding binary vector of the 20 natural amino acid names |
20-23 | feat_PHI, feat_PSI, feat_TAU, feat_THETA | Dihedral angles, ฯ, ฯ, ฯ, ฮธ |
24 | feat_BBSASA | Back Bone Solvent Accessibility |
25 | feat_SCSASA | Side Chain Solvent Accessibility |
26 | feat_pLDDT | Show file differences that haven't been staged |
27-41 | feat_DSSP_* | Secondary structure features, e.g. ฮฑ-helix and ฮฒ-sheet |
42 | feat_CentricDist | Euclidean distance of AA residue from the center of protein |
43 | feat_CentricCosineDist | Cosine distance of AA residue from the center of protein |
44 | feat_iPlus | AA info of a node before node i in protein sequence |
45 | feat_iMinus | AA info of a node after node i in protein sequence |
๐ Output files
All output files are saved in this directory ./results/graph_*A/
. Specific sub-directories are created
according to model parameters, so that user can keep track of different test cases.
When training NodeCoder
In a cross-validation setting, the performance scores are saved in a .csv
file like
Model_Performance_Metrics_Fold1.csv
, for all folds. In addition to this, model state is also saved
in CheckPoints
sub-directory at certain epochs. The default checkpoint epoch is 50
, as well as the epoch
to save model performance, but user can change these with checkpoint_step
and performance_step
. At the end of training on each fold, the inference is performed by finding the optimum epoch and loading corresponding
trained model at the optimum epoch. At the end of inference, an output file is saved in Prediction
sub-directory that includes the predicted labels for all proteins in validation set. This can be useful for ranking proteins.
Once training NodeCoder is completed, the results are all saved in results
folder with the following tree structure
(the example here is for 8A cut-off distance, 5 folds for cross-validation and Ligand as prediction task):
results
โโโ graph_8A
โโโ 9606
โโโ 5FoldCV
โโโ y_Ligand_HiddenLayers_38_28_18_8_50Epochs_LR0.01
โโโ CheckPoints
โโโ Model_Performance_Curves.jpg
โโโ Model_Performance_Metrics_Fold1.csv
โโโ Prediction
Model parameters such as network structure, number of epochs and learning rate (LR) are reflected in the created subdirectory.
When predicting with NodeCoder
When running inference with trained NodeCoder, the prediction results are saved in a sub-directory with protein name.
The prediction result is a csv file like KI3L1_HUMAN_prediction_3Tasks_results.csv
, which is a dataframe
that contains the target labels, predicted labels and prediction probability of the labels per node (AA residue) for all
tasks of interest, {y1, y2, ..., yn}.
node_id | protein_id_flag | protein_id | Task 1 Target | Task 1 Prediction | Task 1 PredictionProb | ... | Task n Target | Task n Prediction | Task n PredictionProb |
---|---|---|---|---|---|---|---|---|---|
0 | 0 | E2F8_HUMAN | 0/1 | 0/1 | float | 0/1 | 0/1 | float | |
1 | 0 | E2F8_HUMAN | 0/1 | 0/1 | float | 0/1 | 0/1 | float |
Once inference is completed, the results are all saved in results
folder, with protein ID as the name of the subdirectory.
The following tree structure is an example for KI3L1_HUMAN
as the protein of interest, 8A cut-off distance and 5 folds
for cross-validation):
results
โโโ graph_8A
โโโ 9606
โโโ 5FoldCV
โโโ KI3L1_HUMAN
โ โโโ KI3L1_HUMAN_ProteinFiles.csv
โ โโโ KI3L1_HUMAN_edge_features.csv
โ โโโ KI3L1_HUMAN_edges.csv
โ โโโ KI3L1_HUMAN_features.csv
โ โโโ KI3L1_HUMAN_nodes_ProteinID.csv
โ โโโ KI3L1_HUMAN_prediction_1Tasks_results.csv
โ โโโ KI3L1_HUMAN_target.csv
โโโ ...
๐ค Collaborators
This project has been sponsored by Mitacs and Cyclica Inc..
The main contributors are:
Nasim Abdollahi, Ph.D., Post-doctoral Fellow at University of Toronto, Cyclica Inc.
Ali Madani, Ph.D., Machine Learning Director at Cyclica Inc.
Bo Wang, Ph.D., Canada CIFAR AI Chair at the Vector Institute, Professor at University of Toronto
Stephen MacKinnon, Ph.D., Chief Platform Officer at Cyclica Inc.
๐ License
MIT Licence
๐ Citing this work
@article {2021,
author = {Abdollahi, Nasim and Madani, Ali and Wang, Bo and MacKinnon,
Stephen},
title = {Residue characterization on AlphaFold2 protein structures using graph neural networks},
year = {2021},
doi = {},
publisher = {NeurIPS},
URL = {https://www.mlsb.io/papers_2021/MLSB2021_Residue_characterization_on_AlphaFold2.pdf},
journal = {NeurIPS, MLSB}
}
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