Schrödinger

1. Prepare the protein-ligand complex using Maestro.

2. Generate a library of ligand analogs.

3. Perform docking studies using Glide to identify promising analogs.

4. Calculate binding free energies using FEP.

5. Select the analogs with the highest predicted affinity for synthesis and experimental validation.

1. Create a model of the polymer structure.

2. Perform molecular dynamics simulations to assess its stability and mechanical properties.

3. Modify the polymer structure and repeat the simulations.

4. Use the simulation results to optimize the polymer composition for maximum strength.

5. Validate the design experimentally.

1. Analyze the protein structure to identify potential instability hotspots.

2. Generate a library of protein variants with mutations at these hotspots.

3. Predict the stability of each variant using computational methods.

4. Select the most stable variants for experimental characterization.

5. Test the activity and stability of the engineered enzymes under relevant conditions.

1. Prepare the protein structure.

2. Dock a large library of compounds into the protein binding site using Glide.

3. Score the docking poses and select the top-scoring compounds.

4. Perform more accurate binding free energy calculations using FEP for the selected compounds.

5. Purchase and test the most promising compounds in vitro.

1. Input the target molecule into RetroSynth.

2. Analyze the suggested synthetic routes.

3. Evaluate the feasibility and cost of each route.

4. Select the optimal route based on available reagents and equipment.

5. Perform the synthesis in the lab.