EDPDB: a multifunctional tool for protein structure analysis

Abstract

EDPDB is a Fortran program that simplifies the analysis of protein structure and makes it easy to extract various types of geometrical and biologically relevant information for the molecule both in isolation as well as in its crystallographic context. EDPDB offers a large set of functions by which the user can evaluate, select and manipulate the coordinates of protein structures. Types of calculation available include the determination of solvent accessibility, bond lengths and torsion angles, determination of the van der Waals volume of a group of atoms, determination of the best-fit plane through a set of points, evaluation of crystal contacts between a molecule in a crystal and all symmetry-related molecules, and the determination of `hinge-bending' motion between protein domains. It is also possible to compare different structures, to perform coordinate manipulations and to edit coordinate files. The program augments the graphic analysis of protein structure by allowing the user to construct a simple set of commands that will rapidly screen an entire structure. It may also make special purpose analyses feasible without complicated programming.