Chapter

Chapter 22.1 Protein geometry: volumes, areas and distances

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 22. Molecular geometry and features

  1. M. Gerstein,
  2. F. M. Richards

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000885

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Gerstein, M. and Richards, F. M. 2012. Protein geometry: volumes, areas and distances. International Tables for Crystallography. F:22:22.1:703–712.

Author Information

  1. Department of Molecular Biophysics & Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA

Publication History

  1. Published Online: 14 APR 2012

SEARCH

Abstract

In this chapter, methods for the calculation of the volumes and areas of proteins are surveyed. The application of Voronoi polyhedra to the calculation of volumes is focused on, with a discussion of how this construction is made and various aspects of it, including the calculation of standard sets of protein volumes. Various measures for protein surface areas, including the accessible surface area, are also discussed.

Keywords:

  • molecular surface;
  • molecular volumes;
  • surface areas;
  • surface‐area calculation;
  • surfaces;
  • Voronoi construction;
  • Voronoi polyhedra