PSICO: Solving Protein Structures with Constraint Programming and Optimization

Authors:
Ludwig Krippahl;Pedro Barahona
Affiliations:
Dep. de Informática, Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal ludi@dq.fct.unl.pt;Dep. de Informática, Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal pb@di.fct.unl.pt
Venue:
Constraints
Year:
2002

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Abstract

In this paper we propose PSICO (Processing Structural Information with Constraint programming and Optimisation) as a constraint-based approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA (“Dynamics algorithm for NMR applications”) an existing commercial application based on simulated annealing. On a test case with experimental data on the dimeric protein Desulforedoxin, the method proposed here supplied similar results in less than 10 minutes compared to approximately 10 hours of computation time for DYANA. Although the quality of results can still be improved, this shows that CP technology can greatly reduce computation time, a major advantage because structural NMR technique generally demands multiple runs of structural computation.