One of the most important geometric structures of a protein is the Connolly surface of protein since a Connolly surface plays an important role in protein folding, docking, interactions between proteins, amongst other...One of the most important geometric structures of a protein is the Connolly surface of protein since a Connolly surface plays an important role in protein folding, docking, interactions between proteins, amongst other things. This paper presents an algorithm for precisely and efficiently computing the Connolly surface of a protein using a proposed geometric construct called β-shape based on the Voronoi diagram of atoms in the protein. Given the Voronoi diagram of atoms based on the Euclidean distance from the atom surfaces, the proposed algorithm first computes a β-shape with an appropriate probe. Then, the Connolly surface is computed by employing the blending operation on the atomic complex of the protein by the given probe.展开更多
We consider the modeling and simulation by means of multiwavelets on many patches. Our focus is on molecular surfaces which are represented in the form of Solvent Excluded Surfaces that are featured by smooth blending...We consider the modeling and simulation by means of multiwavelets on many patches. Our focus is on molecular surfaces which are represented in the form of Solvent Excluded Surfaces that are featured by smooth blendings between the constituting atoms. The wavelet bases are constructed on the unit square which maps bijectively onto the patches embedded in the space. The cavity which designates the surface bounding a molecular model is acquired from the nuclei coordinates and the Van-der-Waals radii. We use multi-wavelets for which the wavelet basis functions are organized hierarchically on several levels. Our assembly of the linear system is accomplished by using a hierarchical tree which enables the treatment of large molecules admitting thousands of patches. Along with the patch construction, some wavelet simulation outcomes which are applied to realistic patches are reported.展开更多
The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well ...The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field.In this work,two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface:the blobby surface,an implicit Gaussian atom centered surface,and the skin surface.As figures of merit,we considered surface differentiability and surface area continuity with respect to atom positions,and the agreement with explicit solvent simulations.Geometric analysis seems to privilege the skin to the blobby surface,and points to an unexpected relationship between the non connectedness of the surface,caused by interstices in the solute volume,and the surface area dependence on atomic centers.In order to assess the ability to reproduce explicit solvent results,specific software tools have been developed to enable the use of the skin surface in PoissonBoltzmann calculations with the DelPhi solver.The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.展开更多
文摘One of the most important geometric structures of a protein is the Connolly surface of protein since a Connolly surface plays an important role in protein folding, docking, interactions between proteins, amongst other things. This paper presents an algorithm for precisely and efficiently computing the Connolly surface of a protein using a proposed geometric construct called β-shape based on the Voronoi diagram of atoms in the protein. Given the Voronoi diagram of atoms based on the Euclidean distance from the atom surfaces, the proposed algorithm first computes a β-shape with an appropriate probe. Then, the Connolly surface is computed by employing the blending operation on the atomic complex of the protein by the given probe.
文摘We consider the modeling and simulation by means of multiwavelets on many patches. Our focus is on molecular surfaces which are represented in the form of Solvent Excluded Surfaces that are featured by smooth blendings between the constituting atoms. The wavelet bases are constructed on the unit square which maps bijectively onto the patches embedded in the space. The cavity which designates the surface bounding a molecular model is acquired from the nuclei coordinates and the Van-der-Waals radii. We use multi-wavelets for which the wavelet basis functions are organized hierarchically on several levels. Our assembly of the linear system is accomplished by using a hierarchical tree which enables the treatment of large molecules admitting thousands of patches. Along with the patch construction, some wavelet simulation outcomes which are applied to realistic patches are reported.
基金supported by NIGMS,NIH,grant number,1R01GM093937-01.
文摘The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field.In this work,two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface:the blobby surface,an implicit Gaussian atom centered surface,and the skin surface.As figures of merit,we considered surface differentiability and surface area continuity with respect to atom positions,and the agreement with explicit solvent simulations.Geometric analysis seems to privilege the skin to the blobby surface,and points to an unexpected relationship between the non connectedness of the surface,caused by interstices in the solute volume,and the surface area dependence on atomic centers.In order to assess the ability to reproduce explicit solvent results,specific software tools have been developed to enable the use of the skin surface in PoissonBoltzmann calculations with the DelPhi solver.The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.
