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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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

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Additional Project Details

Languages

English

Intended Audience

Healthcare Industry, Science/Research, Education

User Interface

Console/Terminal

Programming Language

Eiffel

Registered

2014-02-14