PF_HP Proteinfaltung 2D HP-model

PF_HP Prediction of proteinfolding in 2D HP-model (English)

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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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.
finnian at eiffel hyphen loop dot com

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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Impressum: Gerrit Leder