Molecular Biophysics & Biochemistry 447b3 / 747b3 Bioinformatics

Other Aspects of Structure, Besides just Comparing Atom Positions

What is Protein Geometry?

Surfaces (slides 1-10 from website)

Packing at Interfaces

Classic Papers

Packing ~ VDW force

Close-packing is Default

Water v. Argon

Voronoi Volumes

Calclating Volumes with Voronoi polyhedra

Voronoi Volumes, the Natural Way to Measure Packing

Delauney Triangulation, the Natural Way to Define Packing Neighbors

Properties of Voronoi Polyhedra

Voronoi diagrams are generally useful, beyond proteins

Volume Calc Methods (slides 20-40 from website)

Atoms have different sizes

Set of VDW Radii

Standard Residue Volumes

Standard Core Volumes (Prelim.)

Small Packing Changes Significant

Packing defines the “Correct Definition” of the Protein Surface

Defining Surfaces from Packing: Convex Hull and Layers of Waters

Defining a Surface from the Faces of Voronoi Polyhedra

Accessible Surface as a Time-averaged Water Layer

The Hydration Surface: Trying to Model Real Water