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Analysis Tools

All the tools run on our compute cluster.
There are no limitations in the number or size of the sequences unless explicitely specified.

 

Modelling

Protein modelling and structure analysis tools

For licensing reasons, these tools must be installed locally on the user's computers.

In the Bioinformatics Lab @ CRS4, graphic tools run locally on the user's desktop, computer hungry tools run on the Janas compute Cluster.



Protein Modelling
MODELLER MODELLER is used for homology or comparative modelling of protein three-dimensional structures. The user provides an alignment of a sequence to be modelled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modelling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modelling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. Download
GROMACS GROMACS is a software for molecular dynamics simulations and energy minimization. It is free software, licensed under the GNU General Public License. We have installed the MPI version of GROMACS on our 48 nodes compute cluster here at CRS4.
Download
TINKER TINKER molecular modelling package is designed to be an easily used and flexible system of programs and routines for molecular mechanics and dynamics and energy-based and structural manipulation calculation. Download

Docking
ROSETTA DOCK
  • ROSETTA DOCK works by simultaneous optimization of side-chain conformation and rigid body position of the two docking partners. The former is performed by a packing algorithm, and the latter is performed by a rigid-body Monte Carlo Minimization (MCM) strategy. Our version of Rosetta Dock is implemented in the distributed environment provided by our 48 nodes compute cluster using the Sun GRID Engine. For more on the algorithm of Rosetta, see
Protein-Protein Docking with Simultaneous Optimization of Rigid Body Displacement and Side Chain Conformations, J.J. Gray, S.E. Moughan, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl and D. Baker, J. Mol. Biol., 331(1), 281-299 2003.

Download
3D_Dock
  • The 3D-dock suite is composed of 3 programs: FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. RPScore ( Residue level Pair potential Score ) uses a single distance constraint empirically derived pair potential to screen the ouptut from FTDock. A further improvement in the quality of the predictions can be gained by using MultiDock (Multiple copy side-chain refinement Dock ).

Download

Molecular Viewers
VMD VMD is a molecular visualization program for displaying, animating, and analysing large biomolecular systems using 3-D graphics and built-in scripting. Download
RasMol & Protein Explorer software for looking at macromolecules structure and its relation to function
Pymol
  • PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files).
Download
JME molecular applet, for depiction of small molecules. Download
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