Software for protein engineering

Current version: 4.0.0
Released: MAR/17/2008
Updated: APR/4/2008

Introduction

The program TRITON is a graphical tool for computational aided protein engineering. It implements methodology of computational site-directed mutagenesis to design new protein mutants with required properties. It uses the external program MODELLER to model structures of new protein mutants based on the wild-type structure by homology modelling method. Subsequently, properties of these protein mutants are modelled. For enzymes, chemical reactions are modelled using semi-empirical quantum mechanical program MOPAC. Qualitative prediction of mutant activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of the active site residues during the reaction. Ligand-protein binding properties can be studied by docking methodology using the external program AutoDock. Ligand binding modes and afinities of individual protein mutants are obtained as a result. Binding properties can also be analysed by visualisation of affinity maps or by calculation of electrostatic potential interactions between ligand and individual residues of the binding site. The program TRITON offers graphical tools for preparation of the input files and for visualisation of output data. The program uses projects to organize computational data.

The program TRITON is available for Linux operating system. Version for MS Windows is under development. Executable files are available free of chargefor non-commercial users. See License Agreement for details.
 
 

New in Version 4.0

  • Docking projects with new docking wizard are available for docking ligands to proteins using the external program AutoDock.
  • Visualisations of output structures from docking, visualisation of affinity maps.
  • New version of MODELLER and MOPAC are now supported: MODELLER 9v3, MOPAC 7.1, MOPAC2007.
  • Better support for work with multiple structures. Easier changes of colors and rendering.
  • Fitting of structures using RMSD minimization.
  • New tools for adding hydrogens to atoms.
  • New bubble helps which describe usage of mouse and keyboard in TRITON and provide detailed information for items in wizard.
  • Preconfigurations can be used to save and recall current selection/visibility/color/rendering of atoms/molecules.
  • Simle animations of molecules in AVI format can be easily created.
  • New Geometry Graph allows user to visualize changes of distances, angles and torsion angles for selected atoms the modeled reaction.
 
 

Last update: March 17, 2008