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The Journal of Physical Chemistry. B|August 8, 2017
Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum RefinementLili Cao, Octav Caldararu, Ulf RydeJournal of Chemical Theory and Computation|October 27, 2018
Predicting Relative Binding Affinity Using Nonequilibrium QM/MM SimulationsMeiting Wang, Ye Mei, Ulf RydeThe Journal of Physical Chemistry. B|February 7, 2008
Protonation of the proximal histidine ligand in heme peroxidasesJimmy Heimdal, Patrik Rydberg, Ulf RydeThe Journal of Physical Chemistry. A|November 7, 2008
Prediction of activation energies for aromatic oxidation by cytochrome P450Patrik Rydberg, Ulf Ryde, Lars OlsenJournal of Chemical Information and Modeling|September 30, 2014
A large-scale test of free-energy simulation estimates of protein-ligand binding affinitiesPaulius Mikulskis, Samuel Genheden, Ulf RydeJournal of Inorganic Biochemistry|March 23, 2021
Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenaseJustin Bergmann, Esko Oksanen, Ulf RydeJournal of Molecular Modeling|May 30, 2014
Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approachPaulius Mikulskis, Samuel Genheden, Ulf RydePlos One|September 26, 2013
Virtual screening models for prediction of HIV-1 RT associated RNase H inhibitionVasanthanathan Poongavanam, Jacob KongstedJournal of Chemical Information and Modeling|October 30, 2024
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial LibrariesLaust Moesgaard, Jacob KongstedJournal of Computational Chemistry|July 13, 2002
Quantum chemical geometry optimizations in proteins using crystallographic raw dataUlf Ryde, Lars Olsen, Kristina NilssonPageof 47