Protein's Segmentation and Surface Analyzer

The main purpose of this package is to give a fast and precise tool for proteins features detection. The package models protein surface starting from atom locations from PDB files. A 3D matrix is created by using Van der Walls volumes. Algorithms for curvature analysis and for pocket and protrusion detection can be found in papers. An open list of package features is :

• Loading of 3D proteins volume from PDB files.
• Proteins space filling representations and visualization.
• Basic 3D Mathematical Morphology operators.
• Marching Cubes algorithm for Protein surface triangulation (SES, SAS or single features).
• 3D Convex Hull algorithm (QHULL).
• Surface curvature detectors (IDCC - Heat Diffusion).
• Pocket, tunnel and protrusion detection.
• Convexity tree representation and data structure.
• Parameters set evaluation for each protein’s pocket/protrusion.
• Surfaces or volumes storing on .obj files.
• Export workspace pocket/protrusion files to the EGI package.

The program is still under heavy development and more features will be added soon.

Screenshots

Contact

Telephone:  +39 0382 985486
E-mail:  riccardo.gatti@unipv.it