Institute of Computer Science
University Freiburg

LatPack - Folding studies for arbitrary lattice protein models

LatPack is a collection of tools related to the folding simulations of lattice-protein models with arbitrary energy function.

It is therefore embedded in our research field Simplified Protein Models.

Available tools

Main Publications




Contributing group members

LatFit - PDB fitting for 3D side chain lattice protein models

side chain lattice protein fit

LatFit is tool allowing for the creation of high resolution models of full atom protein structures in lattice models.
It enables the fitting of backbone and side chain models of a given protein in PDB format. The method applied is sketched in the following.

The procedure

latfit workflow

We follow a chain elongation procedure similar to that described by Park and Levitt (JMB,1995). Residues are placed on the lattice sequentially starting from the amino terminus, for each residue placement the current best lattice fit is iteratively extended. Each extension is evaluated via RMSD, and the best fit further extended until full chain length is achieved.
The coordinates fitted are user defined. By default LatFit takes the C_alpha atom coordinates for the backbone and the centre of mass of non-hydrogen side chain atoms as the side chain. A cartoon of the LatFit workflow is given on the right (click for larger version).
For details about the method applied and its parameters see the LatFit manual below.

LatFit is embedded in our research field Simplified Protein Models.

Download and Documentation

  • A pdf documentation of LatFit is generated in the 'doc' subfolder of the package (pdflatex required) or can be accessed here:

  • LatFit is distributed within the LatPack tools package

  • First steps for package compilation:
    • download the source
    • run './configure'
    • run 'make'
    • run 'make install'

Contributing group members