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

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• LatFold - Global folding simulation using Pull-moves or Pivot-moves
• LatVec - Sequential/Co-translational 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 structures via cRMSD/dRMSD/GDT

Main Publications

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• 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

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• A PDF documentation for each tool is generated in the ‘doc’ subfolder of the package (pdflatex required).
  • LatSeF manual
  • LatFold manual
  • LatFit manual
• First steps for package compilation:
  • Download the source
  • Run ./configure
  • Run make
  • Run make install

Dependencies

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

Downloads

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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

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• Martin Mann
• Daniel Maticzka
• Rhodri Saunders - University of Oxford

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

LatFit is a 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 procedure

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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 center of mass of non-hydrogen side chain atoms as the side chain.

LatFit is embedded in our research field Simplified Protein Models.

Download and Documentation

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• A PDF documentation of LatFit is generated in the ‘doc’ subfolder of the package (pdflatex required) or can be accessed here:
  • LatFit manual
• First steps for package compilation:
  • Download the source
  • Run ./configure
  • Run make
  • Run make install

Contributing group members

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• Martin Mann
• Rhodri Saunders - University of Oxford