"MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling 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. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac."
1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics,
John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.
2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali.
Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol.
Struct. 29, 291-325, 2000.
3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints.
J. Mol. Biol. 234, 779-815, 1993.
4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures,
Protein Science 9. 1753-1773, 2000.
We currently add interface to the optimization function of MODELLER, we plan to support the comparative modeling features of MODELLER.
To obtain MODELLER visit : http://www.salilab.org/modeller/download_installation.html
Once MODELLER is installed edit patho_ePMV/extension/liste.txt to provide the pathtoModeller modlib library, e.g.:
Windows "C:\Program Files\Modeller9v8\mnodlib"
Alternatively you can use the Add Extension in the extension menu from the gui.
Note : for windows users the MODELLER installation automatically put the MODELLER library in the python Path. Thus MODELLER will be automatically available in ePMV. We currently have tested XP and Vista.
Once modeller is available, a new menu item become available in the extension Window menu. This will open our simple MODELLER dialog. This dialog apply on the current molecule in ePMV. This dialog is active only if the use Modeller options was check before loading/browsing for a Molecule. (Edit->Option).
The dialog is decompose in 3 part :
you can specify if you want to store the simulation trajectory
you can specify an interactive simulation where you can drag atom/group of atom, spline point or bones for stearing the simulation (mini or md)
you can specify the number of step of simulation per frame/redraw for the real time mode
you can update the coordinate for the simulation from the screen using the specified geometry.
Here is a simple demonstration in C4D:
no real-time, specify the maximum number of iteration and click minimized to see your molecule going alive and trying to reach a better conformation
no real-time, specify the maximum number of iteration and the temperature then click run MD to see your molecule going alive.