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Surface Diver

User's Manual

VERSION 1.0
Tue 25 Nov 2008

Introduction

Mapping of physicochemical features onto surfaces of biomolecules can provide valuable insights into their function. Such information can be used to characterize and identify similarities within surface regions of proteins or nucleic acids. The Surface Diver quantitatively describes various physicochemical properties such as hydrophobicity, charge density, and electrostatic potential on the protein surface, using a method based on 3D Spherical Harmonic Decomposition. The method introduces a compact representation of a given property defined on the surface of the molecule using a finite set of rotation-invariant descriptors. Rotation-invariance of these descriptors allows one to compare proteins within a given set with respect to their shape and physicochemical properties without the need for any prior structural alignement.


General

Requirements

Installation

S2kit

References

License

Usage

File formats

Interactive mode

Non-interactive mode

Keywords

Output

Scripts

Visualization


Theory & Methods

Molecular surface representation
Hydrophobicity maps
Charge maps
Electrostatic potentials
Spherical Harmonics Decomposition
Similarities within Surface Regions of Proteins



Maciej Dlugosz