J-TM Align: Efficient Comparison of Protein Structure Based on TMAlign

Pietro      H. Guzzi; Pierangelo      Veltri; Mario      Cannataro

Abstract

Proteins interact among them and different interactions are represented as graphs named Protein to Protein Interaction (PPI) networks. From a physical point of view, interactions are performed by contacts among protein structure. Consequently, the study and the comparison of protein structure is an important field in Bioinformatics and Computational Biology. The TM-Align algorithm is a method that presents one of the best performance but is currently available only as a stand alone application with a simple command-line interface available only on Linux platforms. We provide a comprehensive tool, (J-TMAlign) allowing a graphical, easy to use, interface to access J-TMAlign functions and the possibility to visualize compared structure. Finally, J-TMAlign is based on a multi-threaded architecture enables user to submit multiple jobs that are executed in a concurrent and time-efficient way.

Keywords: Distributed processing, docking, multithreads, protein analysis, protein structure comparison, protein structure, wrappers, eukaryotic systems, Docking Algorithms, Fold Prediction Algorithms, JProt Align