10 100001 0512 MSF-VATHAUER

MSF-VATHAUER is a protein engineering software suite developed by the Max Planck Institute for Biophysical Chemistry. It consists of a set of tools for the analysis of protein structures, design of new proteins, the validation and verification of protein structures, and optimization of protein-ligand structures. 1. Protein pre-processing: This module is used to clean up experimental protein structures, refine the coordinates of a protein and analyze its quality. 2. Protein design: This module enables the user to design new molecules for a desired application, based on protein structure, sequence and binding energy. 3. Protein verification: This module is used to verify that a protein structure is stable and free of steric clashes, and to identify any potential issues. 4. Protein optimization: This module is used to optimize protein-ligand interactions and to ensure an optimal fit between the protein and the ligand. 5. Advanced molecular visualization: This module is used to create visualizations of proteins and complex protein-ligand interactions. 6. Model quality assessment: This module is used to assess the quality of protein models by pinpointing possible local or global structure problems. 7. Parameter generation: This module enables the user to generate atomic parameters that reflect the physics of protein–ligand interactions for protein docking and dynamics simulations. 8. Protein-ligand docking: This module is used to predict protein-ligand complexes and to optimize their binding affinity. 9. Molecular dynamics analysis: This module enables the user to study the dynamics of a protein-ligand complex in order to gain insight into their behavior. 10. Protein-ligand structure optimization: This module is used to minimize the energy of protein-ligand complexes and to identify the most stable structures.