Concepedia

Integrating Molecular Docking and Molecular Dynamics Simulations

Lucianna Helene Santos, Rafaela Salgado Ferreira, Ernesto R. Caffarena

Methods in molecular biology · 2019 · 280 citations · 78 references

Concepts

Natural SciencesBiophysicsChemistryBiophysical ChemistryComputational ChemistryStructural BiologyMolecular DockingMolecular DynamicsMolecular ModelingMolecular SimulationProtein DockingProtein-ligand DockingDocking-based Drug DesignLigand-protein DockingMolecular Docking AnalysisProtein-ligand Recognition DynamicsSolvent Effects In Docking

References

78

VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 66.6K citations

Natural Sciences, Biophysics, Physics +12

UCSF Chimera—A visualization system for exploratory research and analysis

Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Journal of Computational Chemistry · 2004 · 47.8K citations

Computing, Bioinformatics, Visualization +17

Comparison of simple potential functions for simulating liquid water

William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura et al. · The Journal of Chemical Physics · 1983 · 42.1K citations

Natural Sciences, Chemistry, Physics +17

The Protein Data Bank

Helen M. Berman · Nucleic Acids Research · 2000 · 39.8K citations

Life Sciences, Biochemistry, Bioinformatics +10

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Oleg Trott, Arthur J. Olson · Journal of Computational Chemistry · 2009 · 37.1K citations · Full text

Pharmacy, Chemistry, Medicinal Chemistry +17