Ulf Ryde

Publication Activity (10 Years)

Years Active: 1996-2018
Publications (10 Years): 8

Top Topics

Grand Challenge

Belief Propagation

Top Venues

J. Comput. Aided Mol. Des.

J. Comput. Chem.

J. Chem. Inf. Model.

Publications

Octav Caldararu, Martin A. Olsson, Majda Misini Ignjatovic, Meiting Wang, Ulf Ryde
Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods. J. Comput. Aided Mol. Des. 32 (10) (2018)
Francesco Manzoni, Ulf Ryde
Assessing the stability of free-energy perturbation calculations by performing variations in the method. J. Comput. Aided Mol. Des. 32 (4) (2018)
Majda Misini Ignjatovic, Paulius Mikulskis, Pär Söderhjelm, Ulf Ryde
Can MM/GBSA calculations be sped up by system truncation? J. Comput. Chem. 39 (7) (2018)
Martin A. Olsson, Alfonso T. García-Sosa, Ulf Ryde
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking. J. Comput. Aided Mol. Des. 32 (1) (2018)
Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde
Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? J. Chem. Inf. Model. 57 (11) (2017)
Octav Caldararu, Martin A. Olsson, Christoph Riplinger, Frank Neese, Ulf Ryde
Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). J. Comput. Aided Mol. Des. 31 (1) (2017)
Martin A. Olsson, Pär Söderhjelm, Ulf Ryde
Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. J. Comput. Chem. 37 (17) (2016)
Majda Misini Ignjatovic, Octav Caldararu, Geng Dong, Camila Muñoz-Gutiérrez, Francisco Adasme-Carreño, Ulf Ryde
Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations. J. Comput. Aided Mol. Des. 30 (9) (2016)
Samuel Genheden, Ulf Ryde, Pär Söderhjelm
Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. J. Comput. Chem. 36 (28) (2015)
Paulius Mikulskis, Daniela Cioloboc, Milica Andrejic, Sakshi Khare, Joakim Brorsson, Samuel Genheden, Ricardo A. Mata, Pär Söderhjelm, Ulf Ryde
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. J. Comput. Aided Mol. Des. 28 (4) (2014)
Paulius Mikulskis, Samuel Genheden, Ulf Ryde
A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities. J. Chem. Inf. Model. 54 (10) (2014)
Paulius Mikulskis, Samuel Genheden, Karin Wichmann, Ulf Ryde
A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections. J. Comput. Chem. 33 (12) (2012)
Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde
The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. J. Chem. Inf. Model. 52 (8) (2012)
Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde
Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. J. Comput. Aided Mol. Des. 26 (5) (2012)
Samuel Genheden, Ulf Ryde
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. J. Comput. Chem. 32 (2) (2011)
Samuel Genheden, Ingemar Nilsson, Ulf Ryde
Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA. J. Chem. Inf. Model. 51 (4) (2011)
Antonella Ciancetta, Samuel Genheden, Ulf Ryde
A QM/MM study of the binding of RAPTA ligands to cathepsin B. J. Comput. Aided Mol. Des. 25 (8) (2011)
Samuel Genheden, Ulf Ryde
How to obtain statistically converged MM/GBSA results. J. Comput. Chem. 31 (4) (2010)
Jacob Kongsted, Pär Söderhjelm, Ulf Ryde
How accurate are continuum solvation models for drug-like molecules? J. Comput. Aided Mol. Des. 23 (7) (2009)
Jacob Kongsted, Ulf Ryde
An improved method to predict the entropy term with the MM/PBSA approach. J. Comput. Aided Mol. Des. 23 (2) (2009)
Pär Söderhjelm, Ulf Ryde
Conformational dependence of charges in protein simulations. J. Comput. Chem. 30 (5) (2009)
Pär Söderhjelm, J. W. Krogh, Gunnar Karlström, Ulf Ryde, Roland Lindh
Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models. J. Comput. Chem. 28 (6) (2007)
Lubomír Rulísek, Kasper P. Jensen, Kristoffer Lundgren, Ulf Ryde
The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations. J. Comput. Chem. 27 (12) (2006)
Emma Sigfridsson, Ulf Ryde, Bruce L. Bush
Restrained point-charge models for disaccharides. J. Comput. Chem. 23 (3) (2002)
Ulf Ryde, Lars Olsen, Kristina Nilsson
Quantum chemical geometry optimizations in proteins using crystallographic raw data. J. Comput. Chem. 23 (11) (2002)
Emma Sigfridsson, Ulf Ryde
Comparison of methods for deriving atomic charges from the electrostatic potential and moments. J. Comput. Chem. 19 (4) (1998)
Ulf Ryde
The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations. J. Comput. Aided Mol. Des. 10 (2) (1996)