|
Biopredicta |
BioPredicta module allows to perform all biomolecule related activities, such as homology modeling, protein analysis and to study protein - ligand interactions. In order to study protein-ligand interactions, a protein structure of interest can be collected from database if 3D crystal structure is known or can be built using template based homology modeling facility. The protein analysis facility of BioPredicta helps to check/repair geometry of protein structure and visualization of various protein cavities before undertaking any protein-ligand interaction study. The molecular docking facility of BioPredicta helps in understanding of mode of binding of ligands to their receptors for successful design of more efficient drugs.
|
|
|
MEP mapped on Channel of retinoic acid receptor beta |
| Advantages |
| * |
Allows the biomolecule handling facilities. Starting from simple visualization as well as editing of protein, this module allows more complex modeling activities like generation of homology model of protein, model validation analysis and molecular docking studies. |
| * |
Allows analysis of protein cavities in terms of shape and electrostatic as well as hydrophobic properties, which further will provide clues for optimization of ligand design. |
|
| |
|
| Features |
Homology Modeling Homology modeling feature of BioPredicta allows execution of the BLAST program for the protein sequence to be modeled to get the template sequence for modeling. This allows selection of template protein for building homology model. This also enables both manual and automated homology modeling from the selected template. |
| Protein Analysis |
The protein analysis feature of Biopredicta allows: |
| * |
Performing protein local geometry check |
| * |
Identification of residues crossing in protein model |
| * |
Visualization of Ramachandran plot |
| * |
Cavity identification |
| * |
Channel identification |
| * |
Ligand interaction visualizer. |
|
|
Molecular Docking
|
The Molecular Docking feature allows rapid identification of the binding mode of ligands to their receptors. This could be done using systematic methods (Grid) or stochastic method (genetic algorithm). Various scoring functions like PLP score, XCscore and Steric + Electrostatic are available for evaluation of the docked poses. |
