Using molecular docking and molecular dynamics to investigate protein-ligand interactions
Connor J. Morris, Dennis Della Corte
Abstract
Molecular docking and molecular dynamics (MD) are powerful tools used to investigate protein-ligand interactions. Molecular docking programs predict the binding pose and affinity of a protein-ligand complex, while MD can be used to incorporate flexibility into docking calculations and gain further information on the kinetics and stability of the protein-ligand bond. This review covers state-of-the-art methods of using molecular docking and MD to explore protein-ligand interactions, with emphasis on application to drug discovery. We also call for further research on combining common molecular docking and MD methods.
Topics & Concepts
Docking (animal)Protein–ligand dockingMolecular dynamicsSearching the conformational space for dockingLigand (biochemistry)Computational biologyChemistryComputer scienceComputational chemistryProtein structureVirtual screeningBiologyBiochemistryReceptorNursingMedicineComputational Drug Discovery MethodsProtein Structure and DynamicsClick Chemistry and Applications