PF_HP

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.

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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

Project Samples

Project Activity

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License

GNU General Public License version 2.0 (GPLv2)

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PF_HP Web Site

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Additional Project Details

Operating Systems

BSD, Linux

Languages

English

Intended Audience

Education, Healthcare Industry, Science/Research

User Interface

Console/Terminal

Programming Language

Eiffel

Related Categories

Eiffel Molecular Science Software, Eiffel Simulation Software, Eiffel Bio-Informatics Software, Eiffel Brute Force Tool

Registered

2014-02-14

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