Molecular docking using shape descriptors
Journal of Computational Chemistry
Journal of Computational Chemistry
Approximating the diameter, width, smallest enclosing cylinder, and minimum-width annulus
Proceedings of the sixteenth annual symposium on Computational geometry
Maintaining approximate extent measures of moving points
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Faster core-set constructions and data stream algorithms in fixed dimensions
SCG '04 Proceedings of the twentieth annual symposium on Computational geometry
Molecular docking with opposition-based differential evolution
Proceedings of the 27th Annual ACM Symposium on Applied Computing
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Predicting the binding mode(s) of a drug molecule to a target receptor is pivotal in structure-based rational drug design. In contrast to most approaches to solve this problem, the idea in this paper is to analyze the search problem from a computational perspective. By building on top of an existing docking tool, new methods are proposed and relevant computational results are proven. These methods and results are applicable for other place-and-join frameworks as well. A fast approximation scheme for the docking of rigid fragments is described that guarantees certain geometric approximation factors. It is also demonstrated that this can be translated into an energy approximation for simple scoring functions. A polynomial time algorithm is developed for the matching phase of the docked rigid fragments. It is demonstrated that the generic matching problem is NP-hard. At the same time, the optimality of the proposed algorithm is proven under certain scoring function conditions. The matching results are also applicable for some of the fragment-based de novo design methods. On the practical side, the proposed method is tested on 829 complexes from the PDB. The results show that the closest predicted pose to the native structure has the average RMS deviation of 1.06 Å.