Operating systems: Windows, MacOS and Linux.

Contacts : João Ribeiro Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos

BioPathFinder is a bioinformatic tool that allows to locate functionally relevant chemical motifs in protein structures.

The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed BioPathFinder.

BioPathFinder is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra’s algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation.

In order to run the BioPathFinder plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ .

The BioPathFinder plug-in runs in any platform where VMD runs, i.e., Windows, OSX and LINUX.

1. Install the VMD software ( if you haven't yet installed).
2. Extract biopathfinder.zip file to a directory in the disk.
3. Once unpacked, we need to let VMD know of this location. To do so, edit your VMD start-up file and add the biopathfinder plugin directory to the auto_path variable (see below).
4. Once this procedure is complete the BioPathFinder plugin can be found at the VMD extensions menu (CompBioComp»BioPathFinder).

• Edit the file located at $HOME/.vmdrc.
• For example if the VMD_Magazine directory is locate at /home/nuno/VMD_Magazine, add to the file the following lines to the end of the file:

 lappend auto_path /home/nuno/biopathfinder
 
 vmd_install_extension VBox "::VBox::vBox" "PortoBioComp/BioPathFinder"

• Edit the file located at C:\Documents and Settings\User directory\.vmdrc.
• If the VMD_Magazine directory is locate at c:\biopathfinder then the following lines should be added to the end of the .vmdrc file.

 lappend auto_path c:\biopathfinder
 
 vmd_install_extension VBox "::VBox::vBox" "PortoBioComp/BioPathFinder"

• This tutorial provides a short guideline to the biopathfinder plug-in: Example No1