Prediction of Protein Structure and Interaction by GALAXY Protein Modeling Programs

In this review, recently developed GALAXY protein modeling programs are introduced and advantages and disadvantages of these programs for both program users and method developers are discussed. The GALAXY package consists of the template-based modeling program GalaxyTBM, the loop/terminus modeling program GalaxyLoop, the model refinement program GalaxyRefine, the homo-oligomer prediction program GalaxyGemini, and the protein-ligand docking program GalaxyDock. These programs have been tested with some success in community-wide competition Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments. For the development of these programs, modeling problems have been posed as global optimization problems of designed energy functions. The free energy functions of GALAXY have been carefully designed by combining physical chemistry principles and structure and sequence information. Efficient conformational search methods such as conformational space annealing and triaxial loop closure have been employed. Freely accessible web servers of the modeling programs are available at http://galaxy.seoklab.org, and some programs can be downloaded from http://galaxy.seoklab.org/softwares.