Ulf Ryde

According to our database, Ulf Ryde authored at least 27 papers between 1996 and 2018.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of five.

2018

Can MM/GBSA calculations be sped up by system truncation?

Majda Misini Ignjatovic, Paulius Mikulskis, Pär Söderhjelm, Ulf Ryde

J. Comput. Chem., 2018

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.

Martin A. Olsson, Alfonso T. García-Sosa, Ulf Ryde

J. Comput. Aided Mol. Des., 2018

Assessing the stability of free-energy perturbation calculations by performing variations in the method.

Francesco Manzoni, Ulf Ryde

J. Comput. Aided Mol. Des., 2018

Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods.

Octav Caldararu, Martin A. Olsson, Majda Misini Ignjatovic, Meiting Wang, Ulf Ryde

J. Comput. Aided Mol. Des., 2018

2017

Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?

Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde

J. Chem. Inf. Model., November, 2017

Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).

Octav Caldararu, Martin A. Olsson, Christoph Riplinger, Frank Neese, Ulf Ryde

J. Comput. Aided Mol. Des., 2017

2016

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

Martin A. Olsson, Pär Söderhjelm, Ulf Ryde

J. Comput. Chem., 2016

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

Majda Misini Ignjatovic, Octav Caldararu, Geng Dong, Camila Muñoz-Gutiérrez, Francisco Adasme-Carreño, Ulf Ryde

J. Comput. Aided Mol. Des., 2016

2015

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model.

Samuel Genheden, Ulf Ryde, Pär Söderhjelm

J. Comput. Chem., 2015

2014

A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities.

Paulius Mikulskis, Samuel Genheden, Ulf Ryde

J. Chem. Inf. Model., 2014

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.

Paulius Mikulskis, Daniela Cioloboc, Milica Andrejic, Sakshi Khare, Joakim Brorsson, Samuel Genheden, Ricardo A. Mata, Pär Söderhjelm, Ulf Ryde

J. Comput. Aided Mol. Des., 2014

2012

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant.

Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde

J. Chem. Inf. Model., 2012

A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections.

Paulius Mikulskis, Samuel Genheden, Karin Wichmann, Ulf Ryde

J. Comput. Chem., 2012

Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.

Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde

J. Comput. Aided Mol. Des., 2012

2011

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA.

Samuel Genheden, Ingemar Nilsson, Ulf Ryde

J. Chem. Inf. Model., 2011

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations.

Samuel Genheden, Ulf Ryde

J. Comput. Chem., 2011

A QM/MM study of the binding of RAPTA ligands to cathepsin B.

Antonella Ciancetta, Samuel Genheden, Ulf Ryde

J. Comput. Aided Mol. Des., 2011

2010

How to obtain statistically converged MM/GBSA results.

Samuel Genheden, Ulf Ryde

J. Comput. Chem., 2010

2009

Conformational dependence of charges in protein simulations.

Pär Söderhjelm, Ulf Ryde

J. Comput. Chem., 2009

How accurate are continuum solvation models for drug-like molecules?

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde

J. Comput. Aided Mol. Des., 2009

An improved method to predict the entropy term with the MM/PBSA approach.

Jacob Kongsted, Ulf Ryde

J. Comput. Aided Mol. Des., 2009

2007

Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models.

Pär Söderhjelm, J. W. Krogh, Gunnar Karlström, Ulf Ryde, Roland Lindh

J. Comput. Chem., 2007

2006

The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations.

Lubomír Rulísek, Kasper P. Jensen, Kristoffer Lundgren, Ulf Ryde

J. Comput. Chem., 2006

2002

Restrained point-charge models for disaccharides.

Emma Sigfridsson, Ulf Ryde, Bruce L. Bush

J. Comput. Chem., 2002

Quantum chemical geometry optimizations in proteins using crystallographic raw data.

Ulf Ryde, Lars Olsen, Kristina Nilsson

J. Comput. Chem., 2002

1998

Comparison of methods for deriving atomic charges from the electrostatic potential and moments.

Emma Sigfridsson, Ulf Ryde

J. Comput. Chem., 1998

1996

The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations.

Ulf Ryde

J. Comput. Aided Mol. Des., 1996