Molecular Docking for Drug Design and Analysis using MOE

Molecular docking with protein-ligand using the MOE software is a crucial step in drug discovery, allowing for the generation of stable adduct structures through interaction analysis. MOE offers various applications like structure-based design, and it integrates visualization, modeling, and simulations for protein 3D structure. The process involves setting parameters, finding active site residues, and refining the docking type. With MOE, diverse file formats can be read and structural conformations can be stored for later analysis.

• Molecular Docking
• Protein-Ligand Interaction
• Drug Design
• MOE Software
• Bioinformatics Analysis

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1. Molecular Docking Molecular Docking Molecular Docking of Protein-Ligand using MOE

2. Content Content Introduction Objectives Input & Output Methodology Docking Complex Analysis Conclusion

3. Introductio Introductio n n Molecular docking is an important approach for designing new drugs and vaccines and other bioinformatics analysis. It involves the interaction of two or more molecules to give the stable adduct. MOE is an efficient tool to perform molecular docking.

4. Molecular docking generates different possible adduct structures that are ranked and grouped together using scoring function in the software utilizing MOE.

5. Objectives Objectives Analyzes Analyzes MOE is a platform for drug discovery which provides applications such as structure-based design, fragment based design and others. Outcome Outcome Available on Available on MOE is a standalone program and can be installed on windows, Linux & MacOS. MOE integrates visualization, modeling and simulations for protein 3D structure.

6. Input & Output Input & Output Input Input Output Output MOE can read most common file formats (sdf, SMILES, pdb, mol2, FASTA) as well as the internal .moe file type are required for both biological receptor & Ligand. MOE results in the structural conformation for input files. The generated conformations can be stored and analyzed later.

7. Flow diagram showing the process of docking of protein-ligand

8. Docking Docking Provides docking of Biological receptor and ligand by setting parameters in Compute . Protonation Protonation QuickPrep can fix the protonation, bond lengths and other inaccuracies in the structure. Energy Energy Minimization Minimization Minimize the energy for receptor molecule by resetting the Gradient value. Refinement Refinement Selects the docking type to be Rigid Receptor or Induced Fit . Methodology Methodology Site Finder Site Finder Provides the list of active site residues present in biological receptor. Residues in SE Residues in SE Provides residues being docked on 3D structure of receptor.

9. Docking Complex Analysis Docking Complex Analysis Provides the poses or orientations of the ligand molecules, against which different values and scores are assigned 1st 2nd 3rd mol mol Surface Surface Provides visualization of docking complex by changing its surface Ligand Ligand Legend Legend Field Field Check the Ligand interactions of the docking complex Provides the active site residues interacting with the ligand molecule and interaction details 4th

10. Conclusion Conclusion MOE is a platform for drug discovery. It is a tool which integrates visualization, modeling and simulations, as well as methodology development for drug discovery, in one single package. It is an efficient tool to perform docking of a biological target against the ligand molecule.