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