WebThe ASA is closely related to the concept of the solvent-excluded surface (also known as the molecular surface or Connolly surface), which is imagined as a cavity in bulk solvent (effectively the inverse of the solvent-accessible surface).It is also calculated in practice via a rolling-ball algorithm developed by Fred Richards and independently implemented three … WebMotivation: Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the Cartesian grid, which is necessary for simulating many biomolecular electrostatic and ion channel models.
Physics:Accessible surface area - HandWiki
The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square angstroms (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in … See more Shrake–Rupley algorithm The Shrake–Rupley algorithm is a numerical method that draws a mesh of points equidistant from each atom of the molecule and uses the number of these points that are … See more Accessible surface area is often used when calculating the transfer free energy required to move a biomolecule from an aqueous solvent to a non-polar solvent, such as a lipid environment. The LCPO method is also used when calculating implicit solvent effects … See more • Network Science, Part 5: Solvent-Accessible Surfaces • AREAIMOL is a command line tool in the CCP4 Program Suite for calculating ASA. See more The ASA is closely related to the concept of the solvent-excluded surface (also known as the Connolly's molecular surface area or simply Connolly surface), which is imagined as a cavity … See more • Implicit solvation • Van der Waals surface • VADAR tool for analyzing peptide and protein structures • Relative accessible surface area See more WebApr 3, 2024 · The solvent-excluded surface (SES1) of a molecule is an important geometrical property relevant to its solvation in aqueous solution and its interactions with … kapil dev black and white
ESES: Software for Eulerian solvent excluded surface
WebSep 5, 1984 · The solvent accessible surface of a solute molecule is the surface of closest approach of the centres of solvent molecules where both solute and solvent are represented by hard spheres (Fig. 1). Computationally, this surface is denned as the van der Waals envelope of the solute molecule expanded by the radius of the solvent sphere about each … WebBioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes … WebApr 3, 2024 · The solvent-excluded surface (SES1) of a molecule is an important geometrical property relevant to its solvation in aqueous solution and its interactions with other molecules. In this paper we present an accurate and robust analytic algorithm suitable for a large-scale SES analysis. The accuracy and robustness of our algorithm are made … kapil dev highest score in odi