Power diagrams: properties, algorithms and applications
SIAM Journal on Computing
Three-dimensional alpha shapes
ACM Transactions on Graphics (TOG)
Finding and filling protein cavities using cellular logic operations
Journal of Molecular Graphics
Journal of Molecular Graphics
Spheres, molecules, and hidden surface removal
SCG '94 Proceedings of the tenth annual symposium on Computational geometry
On the definition and the construction of pockets in macromolecules
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
Voronoi diagram of a circle set from Voronoi diagram of a point set: topology
Computer Aided Geometric Design
Voronoi diagram of a circle set from Voronoi diagram of a point set: geometry
Computer Aided Geometric Design
Blending quadric surfaces with piecewise algebraic surfaces
Graphical Models
Viewing Geometric Protein Structures From Inside a CAVE
IEEE Computer Graphics and Applications
Dynamic maintenance and visualization of molecular surfaces
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Vertex-based boundary representation of nonmanifold geometric models
Vertex-based boundary representation of nonmanifold geometric models
Introduction to Algorithms, Third Edition
Introduction to Algorithms, Third Edition
Computer-Aided Design
Euclidean Voronoi diagram of 3D balls and its computation via tracing edges
Computer-Aided Design
An efficient algorithm for three-dimensional β-complex and β-shape via a quasi-triangulation
Proceedings of the 2007 ACM symposium on Solid and physical modeling
Molecular surfaces on proteins via beta shapes
Computer-Aided Design
Spatial and temporal competition as a two dimensional kinetic Voronoi diagram
Computer-Aided Design
Interaction interfaces in proteins via the Voronoi diagram of atoms
Computer-Aided Design
Manifoldization of β-shapes in O(n) time
Computer-Aided Design
Manifoldization of β-shapes by topology operators
GMP'08 Proceedings of the 5th international conference on Advances in geometric modeling and processing
Multi-resolution protein model
ICCSA'07 Proceedings of the 2007 international conference on Computational science and Its applications - Volume Part II
Topologies of surfaces on molecules and their computation in O(n) time
Computer-Aided Design
Quasi-worlds and quasi-operators on quasi-triangulations
Computer-Aided Design
Three-dimensional beta-shapes and beta-complexes via quasi-triangulation
Computer-Aided Design
Protein-ligand docking based on beta-shape
Transactions on computational science IX
Protein-ligand docking based on beta-shape
Transactions on computational science IX
Reduction of the search space in the edge-tracing algorithm for the voronoi diagram of 3d balls
ICCSA'06 Proceedings of the 6th international conference on Computational Science and Its Applications - Volume Part I
Anomalies in quasi-triangulations and beta-complexes of spherical atoms in molecules
Computer-Aided Design
| Hi-index | 0.00 |
A protein consists of atoms. Given a protein, the automatic recognition of depressed regions on the surface of the protein, often called docking sites or pockets, is important for the analysis of interaction between a protein and a ligand and facilitates fast development of new drugs. Presented in this paper is a geometric approach for the detection of docking sites using @b-shape which is based on the Voronoi diagram for atoms in Euclidean distance metric. We first propose a geometric construct called a @b-shape which represents the proximity among atoms on the surface of a protein. Then, using the @b-shape, which takes the size differences among different atoms into account, we present an algorithm to extract the pockets for the possible docking site on the surface of a protein.