Parallel Protein Docking Tool (PPTP) system is performing a shape based process of protein docking using spherical harmonics. The software is made from the scratch in C++. Input data are two PDB (Protein Data Bank) les and desired docking parameters. The PDB les hold information about coordination of protein atoms in three dimensional space. Protein structures are transformed with spherical functions which allow fast rotation and translation of 3D shapes in space. By translation and rotation (with a given resolution of angles and distance) the surface complementarity is tested for each orientation of two proteins in 3D space. The orientations are then ranked according to the given scores. The output PDB le now holds orientations with best scores ready for visualization. As a part of the system the tool for visualization of molecules is developed. It's purpose is to provide a visualization of molecule structure in all phases of protein docking process. The visualizator also allows interactive translation and rotation of input proteins and evaluation of their complementarity in real time.


Developer team: Nino Antulov-Fantulin, Igor Čanadi, Matija Piškorec, Ivan Sović

Project Leader: Mile Šikić