Ulf Ryde - RankMe

28 papers Journal 28

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations. J. Chem. Inf. Model. Meiting Wang, Hao Jiang, Ulf Ryde
2018	J	`jnl`	Assessing the stability of free-energy perturbation calculations by performing variations in the method. J. Comput. Aided Mol. Des. Francesco Manzoni, Ulf Ryde
2018	J	`jnl`	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. Martin A. Olsson, Alfonso T. García-Sosa, Ulf Ryde
2018	J	`jnl`	Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods. J. Comput. Aided Mol. Des. Octav Caldararu, Martin A. Olsson, Majda Misini Ignjatovic, Meiting Wang, Ulf Ryde
2018	J	`jnl`	Can MM/GBSA calculations be sped up by system truncation? J. Comput. Chem. Majda Misini Ignjatovic, Paulius Mikulskis, Pär Söderhjelm, Ulf Ryde
2017	J	`jnl`	Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). J. Comput. Aided Mol. Des. Octav Caldararu, Martin A. Olsson, Christoph Riplinger, Frank Neese, Ulf Ryde
2017	J	`jnl`	Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? J. Chem. Inf. Model. Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde
2016	J	`jnl`	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. Majda Misini Ignjatovic, Octav Caldararu, Geng Dong, Camila Muñoz-Gutiérrez, Francisco Adasme-Carreño, Ulf Ryde
2016	J	`jnl`	Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. J. Comput. Chem. Martin A. Olsson, Pär Söderhjelm, Ulf Ryde
2015	J	`jnl`	Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. J. Comput. Chem. Samuel Genheden, Ulf Ryde, Pär Söderhjelm
2014	J	`jnl`	A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities. J. Chem. Inf. Model. Paulius Mikulskis, Samuel Genheden, Ulf Ryde
2014	J	`jnl`	Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. J. Comput. Aided Mol. Des. Paulius Mikulskis, Daniela Cioloboc, Milica Andrejic, Sakshi Khare, Joakim Brorsson, Samuel Genheden, Ricardo A. Mata, Pär Söderhjelm, Ulf Ryde
2012	J	`jnl`	A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections. J. Comput. Chem. Paulius Mikulskis, Samuel Genheden, Karin Wichmann, Ulf Ryde
2012	J	`jnl`	Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. J. Comput. Aided Mol. Des. Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde
2012	J	`jnl`	The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. J. Chem. Inf. Model. Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde
2011	J	`jnl`	A QM/MM study of the binding of RAPTA ligands to cathepsin B. J. Comput. Aided Mol. Des. Antonella Ciancetta, Samuel Genheden, Ulf Ryde
2011	J	`jnl`	A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. J. Comput. Chem. Samuel Genheden, Ulf Ryde
2011	J	`jnl`	Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA. J. Chem. Inf. Model. Samuel Genheden, Ingemar Nilsson, Ulf Ryde
2010	J	`jnl`	How to obtain statistically converged MM/GBSA results. J. Comput. Chem. Samuel Genheden, Ulf Ryde
2009	J	`jnl`	An improved method to predict the entropy term with the MM/PBSA approach. J. Comput. Aided Mol. Des. Jacob Kongsted, Ulf Ryde
2009	J	`jnl`	Conformational dependence of charges in protein simulations. J. Comput. Chem. Pär Söderhjelm, Ulf Ryde
2009	J	`jnl`	How accurate are continuum solvation models for drug-like molecules? J. Comput. Aided Mol. Des. Jacob Kongsted, Pär Söderhjelm, Ulf Ryde
2007	J	`jnl`	Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models. J. Comput. Chem. Pär Söderhjelm, J. W. Krogh, Gunnar Karlström, Ulf Ryde, Roland Lindh
2006	J	`jnl`	The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations. J. Comput. Chem. Lubomír Rulísek, Kasper P. Jensen, Kristoffer Lundgren, Ulf Ryde
2002	J	`jnl`	Quantum chemical geometry optimizations in proteins using crystallographic raw data. J. Comput. Chem. Ulf Ryde, Lars Olsen, Kristina Nilsson
2002	J	`jnl`	Restrained point-charge models for disaccharides. J. Comput. Chem. Emma Sigfridsson, Ulf Ryde, Bruce L. Bush
1998	J	`jnl`	Comparison of methods for deriving atomic charges from the electrostatic potential and moments. J. Comput. Chem. Emma Sigfridsson, Ulf Ryde
1996	J	`jnl`	The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations. J. Comput. Aided Mol. Des. Ulf Ryde