Reconstructing protein structure from solvent exposure using tabu search.

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 Calpha 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.

Results

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SUBMITTER: Paluszewski M 

PROVIDER: S-EPMC1635054 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature