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PF_HP

Free download PF_HP Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named PF_HP whose latest release can be downloaded as README.txt. It can be run online in the free hosting provider OnWorks for workstations.

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PF_HP


DESCRIPTION

Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings).

Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die Proteinfaltung.

Spende einen Cappuccino:
Bitcoin: 1HqrdnfQgi9B4LW8UEvLAwh7X5gXPCoQ5B
Litecoin: Lbo2jxD85ymyq5167r7yFVZkEr73F2h44B
Paypal: paypal.me/GerritLeder

Credits
======
Principle Investigator
--------------------------
Gerrit Leder: protein folding algorithm design and testing, and initial implementation in Eiffel.

Eiffel Consultant
---------------------
Finnian Reilly: Eiffel code optimization and parallel processing adaptation.
www.hex11software.com
finnian at eiffel hyphen loop dot com



Features

  • parallel computation with command line flag -pf2_mt
  • defaults to 4 threads can be customized with switch -threads ...
  • custom 0-1-bitstring with command line flag -sequence ...
  • serial algorithm with command line flag -pf2
  • To-Do: Bugfix pf3 and pf3_mt, Implementation w/ directions S, R and L
  • To-Do: make lib EL void-safe
  • To-Do: unit-tests on CLI and IDE


Audience

Healthcare Industry, Science/Research, Education


User interface

Console/Terminal


Programming Language

Eiffel


Categories

Molecular Science, Simulations, Bio-Informatics

This is an application that can also be fetched from https://sourceforge.net/projects/pfhp/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.


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