deepdirect 0.2.5

In silico approach to generate mutations for protein complexes towards a specified direction (increase/decrease) in binding affinity.

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# deepdirect

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Deepdirect is an in silico approach to generate mutations for protein
complexes towards a specified direction (increase/decrease) in binding
affinity.

## System requirements and dependencies

### Hardware Requirements

`deepdirect` model is able to be trained and perform its operations on a
standard computer.

### OS Requirements

The `deepdirect` model should be compatible with Windows, Mac, and Linux
operating systems. The package has been tested on the following systems:

- Linux 3.10.0
- Windows 10

### Dependencies

`deepdirect` framework is built and trained on the `Tensorflow 2.4.0`
and `Keras 2.4.0`.

## Framework construction

The python file including all required deepdirect framework built
function is able to be downloaded from GitHub:
`deepdirect_framework/model_function.py`

## Data structure

- `data` folder contains the original datasets used for building the
  training datasets.
- `deepdirect_framework` folder contains the trained model weights and
  the model constructing functions.
- `deepdirect_paper` folder contains codes for building and training
  models, and performing analysis in the deepdirect manuscript. The file
  `ab_bind_data_extract.py` and `skempi_data_extract.py` contains code
  for constructing training datasets for Deepdirect framework.
  `train_step_1.py` contains code for training step 1 for the mutation
  mutator. `final_model.py` contains code for training step 2 (final)
  for the mutation mutator. `model_function.py` contains code for
  constructing the Deepdirect framework.
  `model_evaluation_application.py` contains code for model evaluation,
  and teh application on Novavax-vaccine. `evolution_analysis.py`
  contains code for performing evolution analysis.

## File source

For files that are required as input in the code but not generated from
other codes, please refer to the data availability section in the
original paper.

## Installation

Clone repository:

    git clone https://github.com/tianlt/deepdirect.git

Create virtual environment:

    conda create --name deepdirect python=3.6.8

Activate virtual environment:

    conda activate deepdirect

Install dependencies:

    pip install tensorflow==2.4.0
    pip install keras==2.4.0

## Running deepdirect

### data processing

Data to be input to deepdirect include sequence to be mutated `pre`, RBD
site `rbd`, ligand-receptor index `same`, protein tertiary structure
information `x`, `y` and `z`, and random noise `input_noi`. All input
has to be `tf.float32` type.

### Build deepdirect mutator with trained weights

    aa_mutator = build_aa_mutator()

    aa_mutator.load_weights(
        'deepdirect_framework/model_i_weights.h5')

### Binding affinity-guided mutation

    aa_mutator.predict([pre, rbd, same, x, y, z, input_noi])

### Additional information

Expected outputs: mutated amino acid sequence

Expected runtime for mutation: ~1 mintue

## Issues and bug reports

Please use <https://github.com/tianlt/deepdirect/issues> to submit
issues, bug reports, and comments.

## License

deepdirect is distributed under the [GNU General Public License version
2 (GPLv2)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html).