Table of ContentsMolecular 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 |
Author: Office97
Email: Mark.Gerstein@Yale.edu Home Page: http://bioinfo.mbb.yale.edu/course Other information: |