Packages
CCMS Software Abstracts
DOT
DOT is a package for examining cellular metabolism, finding the most stable relative orientations between two proteins, studying protein subunit aggregation, performing computer-aided drug design, and solving problems of cellular signaling and expression.
How to obtain shape
Shape
Shape is a package for analysis of molecular
surfaces. It includes programs for determining whether a point is in
a groove or crevice in a surface, and for determining the largest
sphere that can fit at a location.
How to obtain shape
Flex
Flex is a simple display program that can show
molecules and animation sequences from disk files or from network
connections to running programs -- for example, a molecular dynamics
simulation. A library of communication routines is included which
makes it very simple to add this real-time display ability to any
program.
How to obtain flex
PDBtool
PDBtool is a UNIX based tool for browsing the features of a single
macromolecular structure supplied in PDB format. PDBtool includes
structure verification and limited query capabilities.
PDBtool is currently in Beta Test. To be a tester contact Phil Bourne
(bourne@sdsc.edu).
WPDB
WPDB (the Protein Data Bank through Microsoft Windows) is a PC based
software package comprising a compressed version of all or parts of the
PDB and a set of tools to query features of a single structure or perform a
comparative analysis on multiple structures with emphasis on sequence
alignment and structure superposition. WPDB is described in the paper
by Shindyalov and Bourne, (1995) J. App. Cryst. 28(6)
847-852.
How to obtain WPDB
XtalView
XTALVIEW is a package for X-ray crystal structure solution from the
point at which data is collected through the fitting of a molecular
model into an electron density map. XtalView runs on ordinary
workstations and does not require 3-D hardware.
How to obtain xtalview