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)

Comparison of methods for deriving atomic charges from the electrostatic potential and moments. - Emma Sigfridsson; Ulf Ryde (J. Comput. Chem., 1998)

Quantum chemical geometry optimizations in proteins using crystallographic raw data. - Ulf Ryde; Lars Olsen; Kristina Nilsson (J. Comput. Chem., 2002)

Restrained point-charge models for disaccharides. - Emma Sigfridsson; Ulf Ryde; Bruce L. Bush (J. Comput. Chem., 2002)

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)

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)

An improved method to predict the entropy term with the MM/PBSA approach. - Jacob Kongsted; Ulf Ryde (J. Comput. Aided Mol. Des., 2009)

How accurate are continuum solvation models for drug-like molecules? - Jacob Kongsted; Pär Söderhjelm; Ulf Ryde (J. Comput. Aided Mol. Des., 2009)

Conformational dependence of charges in protein simulations. - Pär Söderhjelm; Ulf Ryde (J. Comput. Chem., 2009)

How to obtain statistically converged MM/GBSA results. - Samuel Genheden; Ulf Ryde (J. Comput. Chem., 2010)

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)

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. - Samuel Genheden; Ulf Ryde (J. Comput. Chem., 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)

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)

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)

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)

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)

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)

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)

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)

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 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)

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., 2017)

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)

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 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)

Can MM/GBSA calculations be sped up by system truncation? - Majda Misini Ignjatovic; Paulius Mikulskis; Pär Söderhjelm; Ulf Ryde (J. Comput. Chem., 2018)

Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations. - Meiting Wang; Hao Jiang; Ulf Ryde (J. Chem. Inf. Model., 2025)