Operating systems: Windows, MacOS and Linux.

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

Chem-Path-Tracker 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 Chem-Path-Tracker.

Chem-Path-Tracker 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 Chem-Path-Tracker plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ .

The Chem-Path-Tracker 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 chemPathTracker.zip file to a directory in the disk.
3. Run the installer available in the directory of chemPathTracker. (If it does not work type in a terminal shell the command: wish install.tcl)
4. Once this procedure is complete the Chem-Path-Tracker plugin can be found at the VMD extensions menu (PortoBioComp»Chem-Path-Tracker).

Note: Tcl/tk software must be installed on the computer (http://www.activestate.com/activetcl/downloads).

This next tutorial provides some guidelines regarding the Chem-Path-Tracker plug-in:

• Chem-Path-tracker Tutorial