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app-prometry

A library to calculate geometric parameters of protein structures and perform criteria search

https://github.com/rae-gh/app-prometry

Science Score: 67.0%

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    Low similarity (12.6%) to scientific vocabulary

Keywords

protein-geoemtry protein-structure protein-validation
Last synced: 10 months ago · JSON representation ·

Repository

A library to calculate geometric parameters of protein structures and perform criteria search

Basic Info
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  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 17
  • Releases: 1
Topics
protein-geoemtry protein-structure protein-validation
Created about 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

DOI

plot

PROMETRY

Documentation by pydoctor

A library to calculate geometric parameters of protein structures and perform criteria search.

Prometry has a defined geoemtric-search language described in the help pages. It can find distances, angles or dihedrals by describing 2,3 or 4 atoms respectively using the standard atom names for proteins. The 20 standard amino acids and their atoms can be viewed here.

Additionally criteria can be described to expand or decrease the search space such as distance criteria and amino acid restrictions. This means the library can create dataframes for uses as diverse as contact maps, nearest neighbours, possible hydrogen bonds or a simple correlation such as the Ramachandran plot.

The application is freely hosted by streamlit: PROMETRY

This website gives a brief demonstration of some of the ways that prometry can be used.

You can also make use of this website directly to create all your data - all the plots and dataframes are downloadable. Please cite appropriately.

All the source code for the library and this application is made freely available in the spirit of open science.

If you make use of anything from this application (dataframe data, plots, python code, scientific ideas...) please follow the guidance on the Citing page.

Please raise any requests or problems as a github issue

This site is distributed by continuous deployment from the main branch of the github repo

This application has been developed by Rachel Alcraft as an offshoot of a PhD at Birkbeck, University of London © Rachel Alcraft (2023). Supervisor Dr. Mark A. Williams.

Owner

  • Name: Rae PhD projects
  • Login: rae-gh
  • Kind: organization

Citation (citation.cff) 

cff-version: 0.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Alcraft"
  given-names: "Rachel"
  orcid: "https://orcid.org/0000-0003-2674-6321"
- family-names: "Williams"
  given-names: "Mark Antony"
  orcid: "https://orcid.org/0000-0002-1645-2189"
title: "PROMETRY: A library to calculate geometric parameters of protein structures and perform criteria search."
version: 0.1.0
doi: 10.5281/zenodo.10251232
date-released: 02-Dec-2023
url: "https://github.com/rae-gh/app-prometry"

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