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After performing molecular docking, you select the protein-ligand complex's final pose and use the prime module for MMGBSA calculations. Also, you can calculate the MMGBSA after the simulation.

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Glide and MM-GBSA (Molecular Mechanics/Generalized Born Surface Area) are widely employed techniques in molecular docking and the computation of binding free energies. To acquire Glide docking scores and MM-GBSA scores, you can follow these general procedures:

Step 1: Prepare Your System

• Start by readying your target protein and ligands for docking and binding energy calculations. This entails tasks such as introducing hydrogen atoms, assigning charges, and generating suitable input files. Software tools like Schrödinger's Maestro or PyMOL are often employed for this purpose.

Step 2: Conduct Glide Docking

• Employ the Schrödinger Glide software to carry out molecular docking. Begin by defining the receptor grid, outlining the active or binding site on the protein. Next, prepare and specify the ligand files. Execute the Glide docking calculations, which will yield docking scores and ligand poses.

Step 3: Analyze Glide Docking Outcomes

• Subsequent to the docking process, you will have a collection of ligand poses and associated docking scores. These results should be meticulously scrutinized to identify the most favorable ligand poses and those with promising docking scores.

Step 4: Execute MM-GBSA Calculations

• To compute MM-GBSA scores, it is necessary to utilize specialized software or custom scripts. Schrödinger's Prime MM-GBSA module is a commonly utilized tool for this purpose. Input the ligand-protein complexes that were obtained through Glide docking. Configure the parameters for the MM-GBSA calculations. Run the MM-GBSA calculations to estimate the binding free energies.

Step 5: Analyze MM-GBSA Results

• Examine the MM-GBSA results thoroughly to acquire estimates of binding free energy values for your ligand-protein complexes. These values offer insights into binding strength and facilitate the ranking of ligands based on their binding affinity.

It's crucial to remember that the specific steps and commands may vary depending on the software being employed. The Schrödinger suite, including Glide and Prime, is commonly utilized for these calculations. Additionally, the interpretation of Glide docking scores and MM-GBSA results should be approached with caution, as they provide estimates and may not always precisely predict binding affinities. Validation and comparison with experimental data are essential for assessing the reliability of these calculations.