The Fast Atomic Density Evaluator (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE) programs are designed to aid in the molecular modeling of proteins. 

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.

Flex is a simple display program that can show molecules and animation sequences from disk files or from network connections to running programs.

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.

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.

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.

DOT is program for docking macromolecules to other molecules of any size.

FADE and PADRE are programs for analyzing molecular shape and measuring shape complementarity for docked complexes.