Concepedia

Molecular dynamics to enhance structure-based virtual screening on cathepsin B

Mitja Ogrizek, Samo Lešnik, Izidor Sosič, Milan Hodošček, Bojana Mirković, Janko Kos, Dušanka Janežič, Stanislav Gobec, Janez Konc

Journal of Computer-Aided Molecular Design · 2015 · 27 citations · 22 references

DOI

Concepts

References

22

VMD: Visual molecular dynamics

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

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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

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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

, , +17

Open Babel: An open chemical toolbox

Noel M. O’Boyle, Michael Banck, Craig A. James et al. · Journal of Cheminformatics · 2011 · 11.1K citations · Full text

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CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields

Kenno Vanommeslaeghe, Elizabeth Hatcher, Chitrangada Acharya et al. · Journal of Computational Chemistry · 2009 · 7.5K citations · Full text

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