https://github.com/danlooo/cpfp

Comparative protein function prediction - a Java toolkit to deal with DSSP data
https://github.com/danlooo/cpfp

Last synced: about 2 months ago
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Comparative protein function prediction - a Java toolkit to deal with DSSP data

• Host: GitHub
• URL: https://github.com/danlooo/cpfp
• Owner: danlooo
• License: gpl-3.0
• Created: 2015-01-15T18:08:03.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2015-01-23T21:47:56.000Z (almost 10 years ago)
• Last Synced: 2023-02-27T18:51:19.783Z (almost 2 years ago)
• Language: Java
• Homepage:
• Size: 1.06 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# CPFP

Comparative protein function prediction - a java toolkit to deal with [DSSP](http://swift.cmbi.ru.nl/gv/dssp/) data

There are thousands of protein structures in the [Protein Data Bank](http://www.rcsb.org/pdb/home/home.do). The [DSSP-Server](http://swift.cmbi.ru.nl/gv/dssp/) provides secondary structure information about the protein backbone of each chain in the PDB. This algorithm assigns one of the seven structure elements to each amino acid.

These structure elements are:

* H = α-helix

* B = residue in isolated β-bridge

* E = extended strand, participates in β ladder

* G = 3-helix (310 helix)

* I = 5 helix (π-helix)

* T = hydrogen bonded turn

* S = bend

This project aims to access these structure information via a java toolkit.

# Tutorial

[Sample Code](https://github.com/Eubel/cpfp/wiki/Samples)

# External code

We used these third party classes in our project:

* [lambdaj](https://code.google.com/p/lambdaj/) for selecting items in lists

* [DoubleFormatUtil](http://svn.apache.org/viewvc/xmlgraphics/commons/trunk/src/java/org/apache/xmlgraphics/util/DoubleFormatUtil.java?revision=1346428&view=co) for rapid double to string conversion

# Authors

* Loos D

* Vogt F