Adepth

Adepth computes atomic depths and heights in macromolecules using a signed distance function (SDF) to enable precise geometric and surface analyses.

Key Features:

• Depth and Height Representation: Calculates both atomic depth and height within macromolecules to provide dual geometric descriptors of atomic positions.
• Signed Distance Function (SDF) Utilization: Represents atomic depths via a signed distance function computed on grid points within a rectangular box enclosing the macromolecule, with tri-linear interpolation of SDF values at the nearest surrounding grid points.
• Iso-surface Computation: Computes iso-surfaces for atomic depths to represent spatial distributions at specified distances from the molecular surface.
• Visualization Outputs: Generates macromolecular shape representations at varying distances from the surface for visualization and structural analysis.
• High Accuracy and Performance: In benchmarks on an artificial molecule with known atomic depths, achieved an average accuracy of 1.6% at a grid spacing of 0.5 Å, compared with DEPTH's 7.5%.

Scientific Applications:

• Structural Analysis: Detailed examination of macromolecular surfaces and internal structures.
• Drug Design: Identification of potential binding sites and optimization of ligand conformations.
• Molecular Modeling: Enhanced visualization and interpretation of molecular dynamics simulations.

Methodology:

Adepth computes an SDF on grid points within a rectangular box enclosing the macromolecule and derives atomic depths via tri-linear interpolation of nearest SDF values, and it computes iso-surfaces of depth.