On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces

por König, Gerhard, Riniker, Sereina
Publicado en Interface Focus (2020)

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: The performance of relative free energy calculations

por König, Gerhard, Brooks, Bernard R.
Publicado 2011

Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations

por König, Gerhard, Brooks, Bernard R.
Publicado en Biochim Biophys Acta (2014)

Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability

por König, Gerhard, Bruckner, Stefan, Boresch, Stefan
Publicado 2013

Advances in 3D geo-information sciences

por Kolbe, Thomas H., König, Gerhard., Nagel, Claus.
Publicado 2011

Computing eigenvectors of block tridiagonal matrices based on twisted block factorizations

por König, Gerhard, Moldaschl, Michael, Gansterer, Wilfried N.
Publicado 2012

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

por König, Gerhard, Hudson, Phillip S., Boresch, Stefan, Woodcock, H. Lee
Publicado 2014

Predicting hydration free energies with a hybrid QM/MM approach: An evaluation of implicit and explicit solvation models in SAMPL4

por König, Gerhard, Pickard, Frank C., Mei, Ye, Brooks, Bernard R.
Publicado 2014

On the convergence of multi-scale free energy simulations

por König, Gerhard, Brooks, Bernard R., Thiel, Walter, York, Darrin M.
Publicado en Mol Simul (2018)

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods

por Konig, Gerhard, Miller, Benjamin T., Boresch, Stefan, Wu, Xiongwu, Brooks, Bernard R.
Publicado en J Chem Theory Comput (2012)

A Comparison of Methods to Reweight from Classical Molecular Simulations to QM/MM Potentials

por Dybeck, Eric C., König, Gerhard, Brooks, Bernard R., Shirts, Michael R.
Publicado en J Chem Theory Comput (2016)

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

por Tao, Peng, Sodt, Alexander J., Shao, Yihan, König, Gerhard, Brooks, Bernard R.
Publicado 2014

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations

por Pickard, Frank C., König, Gerhard, Simmonett, Andrew C., Shao, Yihan, Brooks, Bernard R.
Publicado en Bioorg Med Chem (2016)

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

por Sodt, Alexander J., Mei, Ye, König, Gerhard, Tao, Peng, Steele, Ryan P., Brooks, Bernard R., Shao, Yihan
Publicado en J Phys Chem A (2014)

Absolute binding free energies for octa-acids and guests in SAMPL5: Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge

por Tofoleanu, Florentina, Lee, Juyong, Pickard, Frank C., König, Gerhard, Huang, Jing, Baek, Minkyung, Seok, Chaok, Brooks, Bernard R.
Publicado en J Comput Aided Mol Des (2016)

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

por König, Gerhard, Pickard, Frank C., Huang, Jing, Thiel, Walter, MacKerell, Alexander D., Brooks, Bernard R., York, Darrin M.
Publicado en Molecules (2018)

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

por Lee, Juyong, Tofoleanu, Florentina, Pickard, Frank C., König, Gerhard, Huang, Jing, Damjanović, Ana, Baek, Minkyung, Seok, Chaok, Brooks, Bernard R.
Publicado en J Comput Aided Mol Des (2016)

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Method

por König, Gerhard, Mei, Ye, Pickard, Frank C., Simmonett, Andrew C., Miller, Benjamin T., Herbert, John M., Woodcock, H. Lee, Brooks, Bernard R., Shao, Yihan
Publicado en J Chem Theory Comput (2015)

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical (QM/MM) Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

por Huang, Jing, Mei, Ye, König, Gerhard, Simmonett, Andrew C., Pickard, Frank C., Wu, Qin, Wang, Lee-Ping, MacKerell, Alexander D., Brooks, Bernard R., Shao, Yihan
Publicado en J Chem Theory Comput (2017)