Consolv: Consolv is a tool for predicting whether water molecules bound to the surface of a protein are likely to be conserved or displaced in other, independently-solve crystallographic structures of the same protein.

ProFlex: MSU ProFlex (formerly called FIRST) predicts the rigid and flexible regions in a protein structure, given a Protein Data Bank (PDB) file including polar hydrogen atoms.

ROCK: The Rigidly Optimized Conformational Kinetics (ROCK) tool searches protein conformations in a random-walk style; concentrating on flexible regions of the protein.

Sequery: Searches the sequences of the protein structures in the Protein Data Bank (PDB) for a particular pattern of residues, including exact matches, matrix calculated substitutions, and user-defined substitutions.

SLIDE: SLIDE is a computational screening and docking tool designed to find ligands with good steric and chemical complementarity to the known three-dimensional structure of a protein's binding site.

SSA: The Superpositional Structure Assignment (SSA) Software automates the assignment of the secondary structure of a peptide from its atomic coordinates in PDB format based on their superposition with sequences of ideal secondary structure.

StoneHinge: Provides protein hinge prediction by determining the consensus of ProFlex and DomDecomp defined domains and intervening hinges.

WatCH: Calculates and analyzes conserved water molecule binding sites among a series of crystallographic structures of the same protein using heirarchical cluster analysis.