https://github.com/cvigilv/simspread
De novo target prediction by chemical similarity-guided network-based inference
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (8.0%) to scientific vocabulary
Keywords
cheminformatics
drug-discovery
drug-target-interactions
target-prediction
Last synced: 6 months ago
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Repository
De novo target prediction by chemical similarity-guided network-based inference
Basic Info
- Host: GitHub
- Owner: cvigilv
- License: mit
- Language: Julia
- Default Branch: main
- Homepage: https://doi.org/10.3390/ijms23179666
- Size: 263 MB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
cheminformatics
drug-discovery
drug-target-interactions
target-prediction
Created over 3 years ago
· Last pushed about 3 years ago
https://github.com/cvigilv/simspread/blob/main/
# *De novo* prediction of drug targets and candidates by chemical similarity-guided network-based inference
[](https://doi.org/10.3390/ijms23179666)
This repo contains the scripts for reproducing the results showcased in Vigil, Schuller (2022) "_De novo_ prediction of drug targets and candidates by chemical similarity-guided network-based inference".
## Table of Contents
- Requirements
- Repository description
- Usage
- Contact
## Requirements
Python requirements:
- `python` >= 3.9
- `matplotlib` >= 3.5.1
- `seaborn`>= 0.11.2
- `scikit-learn`>= 1.0.2
- `pandas`>= 1.4.1
- `tqdm` >= 4.62.3
Julia requirements:
- `julia` >= 1.7.2
- `CUDA.jl` >= 3.8.5
- `ArgParse.jl` >= 1.1.4
- `NamedArrays.jl` >= 0.9.6
Other:
- `bash`
- `jupyter-notebook`
## Repository description
This repository has the following organization:
```
.
bin # Scripts to run predictions
predict
10fold
loo
timesplit
data # Datasets used in study
chembl
wu2017
yamanishi2008
results # Results obtained
10fold
10fold_dti
loo
timesplit
src # Scripts needed to run predictions
evaluate
modules
predict
10fold
loo
timesplit
```
For each directory, a corresponding README is available for further information
## Usage
1. Clone this repo (for help see this [tutorial](https://help.github.com/articles/cloning-a-repository/)).
2. Scripts used to generate predictions are kept [here](bin/).
3. Scripts needed for predictions are kept [here](src/).
4. Datasets used in study are kept [here](data/).
## Contact
Any question, suggestion, advice and/or help needed to reproduce results, please contact Carlos Vigil Vsquez @ cvigil2@uc.cl.
Owner
- Name: Carlos Vigil-Vásquez
- Login: cvigilv
- Kind: user
- Location: Santiago, Chile
- Twitter: BioWASD
- Repositories: 5
- Profile: https://github.com/cvigilv
Chilean biochemist, Neovim plugin developer, and JuliaLanguage enthusiast. Photographer from time to time.
GitHub Events
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