Reconstructing protein structure from solvent exposure using tabu search |
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Authors: | Martin Paluszewski Thomas Hamelryck Pawel Winter |
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Institution: | (1) Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark;(2) Bioinformatics Center, Institute of Molecular Biology, University of Copenhagen, Universitetsparken 15 building 10, 2100 Copenhagen, Denmark |
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Abstract: | Background A new, promising solvent exposure measure, called half-sphere-exposure (HSE), has recently been proposed. Here, we study the reconstruction of a protein's C
α
trace solely from structure-derived HSE information. This problem is of relevance for de novo structure prediction using predicted HSE measure. For comparison, we also consider the well-established contact number (CN)
measure. We define energy functions based on the HSE- or CN-vectors and minimize them using two conformational search heuristics:
Monte Carlo simulation (MCS) and tabu search (TS). While MCS has been the dominant conformational search heuristic in literature, TS has been applied only a few times.
To discretize the conformational space, we use lattice models with various complexity. |
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