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Protein-ligand docking based on beta-shape. (English) Zbl 1310.92041
Gavrilova, Marina L. (ed.) et al., Transactions on Computational Science IX. Special issue on Voronoi diagrams in science and engineering. Berlin: Springer (ISBN 978-3-642-16006-6/pbk). Lecture Notes in Computer Science 6290. Journal Subline, 123-138 (2010).
Summary: Protein-ligand docking is to predict the location and orientation of a ligand with respect to a protein within its binding site, and has been known to be essential for the development of new drugs. The protein-ligand docking problem is usually formulated as an energy minimization problem to identify the docked conformation of the ligand. A ligand usually docks around a depressed region, called a pocket, on the surface of a protein. Presented in this paper is a docking method, called BetaDock, based on the newly developed geometric construct called the \(\beta \)-shape and the \(\beta \)-complex. To cope with the computational intractability, the global minimum of the potential energy function is searched using the genetic algorithm. The proposed algorithm first locates initial chromosomes at some locations within the pocket recognized according to the local shape of the \(\beta \)-shape. Then, the algorithm proceeds generations by taking advantage of powerful properties of the \(\beta \)-shape to achieve an extremely fast and good solution. We claim that the proposed method is much faster than other popular docking softwares including AutoDock.
For the entire collection see [Zbl 1198.68031].
MSC:
92D20 Protein sequences, DNA sequences
68U05 Computer graphics; computational geometry (digital and algorithmic aspects)
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