I want to do protein protein flexible blind docking ..Please let me know how to do it?
Sargol Mazraedoost
- Prepare the proteins: Obtain 3D structures of both proteins (receptor and ligand). Clean the structures by removing water molecules, heteroatoms, and resolving any structural issues. Add hydrogen atoms and assign proper charges
- Define the search space: Since this is blind docking, you'll need to consider the entire surface of the receptor protein. Create a grid box that encompasses the entire receptor or a large portion of it.
- Set up flexibility parameters: Identify flexible residues in both the receptor and ligand proteins. This typically includes side chains of surface residues and loop regions.
- Choose a docking software: Popular options include: AutoDock Vina, HADDOCK, or Rosetta. Each has its strengths for protein-protein docking and handling flexibility.
- Perform the docking: Run multiple docking simulations to ensure adequate sampling of possible conformations. This process can be computationally intensive and may require a high-performance computing cluster.
- Analyze results: Examine the generated poses and their associated scores Look for clusters of similar poses, which may indicate likely binding sites. Evaluate the biological relevance of the predicted interactions.
- Refine and validate: Perform more focused docking on promising poses Use molecular dynamics simulations to further refine the structures. Compare results with experimental data if available.
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