Fast and robust computation of molecular surfaces
Proceedings of the eleventh annual symposium on Computational geometry
Geometric Hashing: An Overview
IEEE Computational Science & Engineering
Efficient Unbound Docking of Rigid Molecules
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Diffusion Distance for Histogram Comparison
CVPR '06 Proceedings of the 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition - Volume 1
3D object retrieval using the 3D shape impact descriptor
Pattern Recognition
Efficient 3-D model search and retrieval using generalized 3-D radon transforms
IEEE Transactions on Multimedia
SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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This paper presents a novel approach for fast rigid docking of proteins based on geometric complementarity. After extraction of the 3D molecular surface, a set of local surface patches is generated based on the local surface curvature. The shape complementarity between a pair of patches is calculated using an efficient shape descriptor, the Shape Impact Descriptor. The key property of the Shape Impact Descriptor is its rotation invariance, which obviates the need for taking an exhaustive set of rotations for each pair of patches. Thus, complementarity matching between two patches is reduced to a simple histogram matching. Finally, a condensed set of almost complementary pairs of surface patches is supplied as input to the final scoring step, where each pose is evaluated using a 3D distance grid. The experimental results prove that the proposed method demonstrates superior performance over other well-known geometry-based, rigid-docking approaches.