https://github.com/nyxflower/upsr

Predicting the enzymatic functions of protein structures
https://github.com/nyxflower/upsr

Last synced: 26 days ago
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Predicting the enzymatic functions of protein structures

• Host: GitHub
• URL: https://github.com/nyxflower/upsr
• Owner: NYXFLOWER
• License: mit
• Created: 2019-11-11T18:54:27.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2022-06-16T01:45:19.000Z (over 2 years ago)
• Last Synced: 2024-03-20T00:20:23.815Z (8 months ago)
• Language: Python
• Homepage:
• Size: 54 MB
• Stars: 2
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        


(under development...)

## Datasets

Protein Data Bank (RCSB-PDB):

- file format content v-3.3 [[doc]](http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)

- Programmatic access [[doc]](https://www.rcsb.org/pages/webservices)

Basic Local Alignment Search Tool (BLAST):

- Using the Common URL API [[doc]](https://ncbi.github.io/blast-cloud/dev/using-url-api.html)

UniProt

- Access programmatically [[doc]](https://www.uniprot.org/help/api)

## Papers

### Review

A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli

[[paper]](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-134)

### Methods

#### Protein Solubility Prediction

DeepSol: A Deep Learning Framework for Sequence-Based Protein Solubility Prediction 

[[paper]](https://sameerkhurana10.github.io/papers/pre_print.pdf)

[[source]](https://zenodo.org/record/1162886#.XdLx8ZJKhMY)

Structural Learning of Proteins Using Graph ConvolutionalNeural Networks

[[paper]](https://www.biorxiv.org/content/biorxiv/early/2019/04/16/610444.full.pdf)

SolXplain: An Explainable Sequence-Based Protein Solubility Predictor

[[paper]](https://www.biorxiv.org/content/early/2019/05/27/651067.full.pdf)

Solart: A Structure-Based Method To Predict Protein Solubility And Aggregation

[[paper]](https://www.biorxiv.org/content/early/2019/04/07/600734.full.pdf)

[[Webserver]](http://babylone.ulb.ac.be/SOLART/)

#### Protein Function Prediction

deepNF: deep network fusion for protein function prediction (*Bioinformatics* 2018) [[paper]](https://academic.oup.com/bioinformatics/article/34/22/3873/5026651)

#### ps model

- graph construction: k-nearest neighbours according to relative distance

## Tools

Biopython - freely available tools for biological computation

[[doc]](http://biopython.org/DIST/docs/tutorial/Tutorial.html)

[[doc_cn]](https://biopython-cn.readthedocs.io/zh_CN/latest/index.html)

ssbio - python package for structural systems biology

[[doc]](https://ssbio.readthedocs.io/en/latest/)

PyMOL - a user-sponsored molecular visualization system

[[web]](https://pymol.org/2/)

Pyecharts - open source visualization tools for Jupyter

[[Github]](https://github.com/pyecharts/pyecharts)