https://github.com/dillondaudert/proteindatasets

Creating and manipulating various protein sequence-structure datasets using Python, Julia, and other tools.
https://github.com/dillondaudert/proteindatasets

bioinformatics biopython blast dataset dssp fasta julia jupyter jupyter-notebook pandas protein psiblast python3 secondary structure tensorflow uniref50

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Creating and manipulating various protein sequence-structure datasets using Python, Julia, and other tools.

• Host: GitHub
• URL: https://github.com/dillondaudert/proteindatasets
• Owner: dillondaudert
• License: mit
• Created: 2018-03-20T17:23:31.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-09-01T22:54:17.000Z (about 6 years ago)
• Last Synced: 2024-04-17T14:14:11.621Z (7 months ago)
• Topics: bioinformatics, biopython, blast, dataset, dssp, fasta, julia, jupyter, jupyter-notebook, pandas, protein, psiblast, python3, secondary, structure, tensorflow, uniref50
• Language: Jupyter Notebook
• Homepage:
• Size: 138 KB
• Stars: 6
• Watchers: 3
• Forks: 5
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Protein sequence and structure datasets

This repo contains scripts for creating various protein sequence and structure

datasets, as well as some guides for how to use them. 

## Contents

### proteinfeatures

Protein amino acid features.

### cpdb

Working with the cullPDB dataset created in [Zhou & Troyanskaya, 

2014](https://arxiv.org/abs/1403.1347).

### cpdb2

Creating a new protein sequence-structure dataset following the methods used for

the cullPDB dataset, referred to as cpdb2.

### psiblast

Scripts for calling NCBI+ psiblast on large fasta files from BioPython and

handling the results using multiprocessing.