Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package nest.


Click here to download Jackal.

System requirements

The current version of Jackal supports the following platforms: SGI 6.5, Intel Linux and Sun solaris.



Jackal contains the following individual programs:

  • nest for building homology models based on 1) a single sequence-template alignment, 2) from multiple templates for the entire structure, or 3) from different templates used for different regions of the structure. It also carries out energy based structure refinement and can change an alignment based on energetic considerations.

  • loopy for loop prediction including mutation, insertion and deletion in a loop region.

  • scap for prediction of side-chain conformations on a given backbone. It can be used to predict the conformations of one or more residues that have been “mutated” in a particular structure.

  • profix for reconstruction of missing protein atoms and residues.

  • ctrip for getting coordinates of protein backbone atoms based on the coordinates of CAs.

  • conref for carrying out protein structure refinement.

  • minst for energy minimization of a protein structure using a smoothing energy technique.

  • addh for getting coordinates of hydrogen atoms.

  • surface for calculating the solvent accessible surface.

  • chi for calculating dihedral angles.

  • rotate for manipulating protein structure in dihedral angle space.

  • nalgn for protein structure superimposition based on a given sequence alignment.


Jackal is supported by a funding from the National Science Foundation and National Institutes of Health Grant # DBI-9904841 and 5 R37 GM30518.

Developed in the Honig Lab.


If you have questions about using Jackal, contact honigsoftware@zi.columbia.edu.