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esmfold_ppi

https://github.com/hengma1001/esmfold_ppi

Science Score: 44.0%

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    Low similarity (15.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: hengma1001
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 47.9 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created about 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme Contributing License Code of conduct Citation Security

README.md

esm_ppi

The package is built to fold single protein and protein-protein complexes using ESMFold.

Built on python template

Installation

Clone the repo to your local machine.

bash git clone https://github.com/hengma1001/esmfold_ppi.git cd esmfold_ppi

Create a conda environment for the folding applications.

bash conda create -n esmfold python=3.9 conda activate esmfold

Install PyTorch.

bash conda install pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 -c pytorch

Install other dependencies.

bash pip install -r envs/requirements.txt

Install the package.

bash pip install -e .

Run the folding

The esmfold run can be initiated with following commands.

bash cd examples python -m esmfold_ppi.run_fold -c fold.yml

For the input yaml format, the variables are defined as follow.

```yaml

input sequences in fasta format

seq_file: ./example.fa

output directory for the colmena workflow

outputdir: runtest/

esmfold: # the cache directory for the esmfold weight torchhubdir: ~/.cache

compute setting for parsl

computesettings: # use local machine name: workstation # number of GPUs to use, can also be a list of gpu ids availableaccelerators: 2 ```

...

Owner

  • Name: Heng Ma
  • Login: hengma1001
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it as below.
authors:
  - family-names: Pauloski
    given-names: Greg
    orcid: https://orcid.org/0000-0002-6547-6902
license: MIT
repository-code: https://github.com/foobar-author/foobar
title: FooBar
url: https://foobar.dev

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Dependencies

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envs/requirements.txt pypi
  • colmena *
  • fair-esm *
  • mdanalysis *
  • pandas *
  • parsl ==2023.11.20
  • pytorch-lightning ==1.8.4
pyproject.toml pypi
  • requests *