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

LatFold - Global folding simulation using Pull-moves or Pivot-moves
LatVec - Sequential/Co-tranlational folding simulation
LatFit - Fitting of a real PDB protein structure onto a lattice
LatConv - Conversion between structure representations (including PDB format)
LatNum - Counting the number of possible non-symmetric structures
LatMap - Compare different structure via cRMSD/dRMSD/GDT

Main Publications

Martin Mann, Daniel Maticzka, Rhodri Saunders, and Rolf Backofen.
Classifying protein-like sequences in arbitrary lattice protein models using LatPack.
In HFSP Journal, 2 no. 6 pp. 396, 2008.
Special issue on protein folding: experimental and theoretical approaches.

Supplementary data can be obtained HERE .

Documentation

A pdf documentation for each tool is generated in the 'doc' subfolder of the package (pdflatex required).
First steps for package compilation:
- download the source
- run './configure'
- run 'make'
- run 'make install'

Dependencies

the Bioinformatic Utility library - BIU (INCLUDED)
the Energy Landscape Library - ELL (for LatFold only - can be disabled)

Downloads

You can download the LatPack source code including configure scripts :
- latpack-1.9.1.tar.gz - 2016-08-08 - [ BIU(2.3.7) included ] [ for latFold : ELL(3.2.4) ]
- latpack-1.9.0.tar.gz - 2010-12-16 - [ BIU(2.3.5) included ] [ for latFold : ELL(3.1.2) ]
- latpack-1.6.4.tar.gz - 2009-03-09 - [ BIU(2.0.0) included ] [ for latFold : ELL(2.3.0) ]

Contributing group members

Martin Mann
Daniel Maticzka
Rhodri Saunders - University of Oxford

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

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

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 manual
LatFit is distributed within the LatPack tools package
- latpack-source-download
First steps for package compilation:
- download the source
- run './configure'
- run 'make'
- run 'make install'

Contributing group members

Martin Mann
Rhodri Saunders - University of Oxford