JACKAL is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package called nest. It has the following capabilities:

• comparative modeling based on single, composite or multiple templates
• side-chain prediction
• modeling residue mutation, insertion or deletion
• loop prediction
• structure refinement
• reconstruction of protein missing atoms
• reconstruction of protein missing residues
• prediction of hydrogen atoms
• fast calculation of solvent accessible surface area
• structure superimposition