Are there any computational tools or method present through which one can observe the conformational changes in model complex after Molecular docking and MD simulation? For example what will happen to active site and allosteric site after the binding of the peptide drug to it?
Fariba Heidarizadeh
Molecular Dynamics (MD) simulations: MD simulations can be used to track the conformational changes in the model complex after protein-peptide molecular docking. MD simulations simulate the movement of atoms in the system over time, providing insights into the dynamic behavior of the protein-peptide complex. Principal Component Analysis (PCA): PCA can be used to analyze the conformational changes in the model complex after protein-peptide molecular docking. PCA analyzes the collective motion of atoms in the protein-peptide complex, providing a low-dimensional representation of the conformational changes. Normal Mode Analysis (NMA): NMA can be used to predict the collective motion of the protein-peptide complex after molecular docking. NMA analyzes the low-frequency modes of the protein-peptide complex, which correspond to the global conformational changes. Free Energy Perturbation (FEP): FEP can be used to calculate the free energy changes associated with the conformational changes in the protein-peptide complex after molecular docking. FEP calculates the energy difference between two different conformations of the protein-peptide complex, providing insights into the stability of the complex. Distance-based metrics: Distance-based metrics such as root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) can be used to track the conformational changes in the protein-peptide complex after molecular docking. RMSD calculates the distance between two different conformations of the protein-peptide complex, while RMSF calculates the deviation of atoms in the protein-peptide complex over time.
There are several insilico tools available for tracking the conformational changes in the model complex after protein-peptide molecular docking. Here are some of them:
These insilico tools can provide valuable insights into the conformational changes in the protein-peptide complex after molecular docking and aid in the design of new drugs or peptides targeting specific proteins.
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