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Ulf Ryde
Publications
- 2018
- [j27]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): 211-224 (2018) - [j26]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): 529-536 (2018) - [j25]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): 1027-1046 (2018) - [j24]Majda Misini Ignjatovic, Paulius Mikulskis, Pär Söderhjelm, Ulf Ryde:
Can MM/GBSA calculations be sped up by system truncation? J. Comput. Chem. 39(7): 361-372 (2018) - 2017
- [j23]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): 87-106 (2017) - [j22]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): 2865-2873 (2017) - 2016
- [j21]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): 707-730 (2016) - [j20]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): 1589-1600 (2016) - 2015
- [j19]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): 2114-2124 (2015) - 2014
- [j18]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): 375-400 (2014) - [j17]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): 2794-2806 (2014) - 2012
- [j16]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): 527-541 (2012) - [j15]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): 1179-1189 (2012) - [j14]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): 2079-2088 (2012) - 2011
- [j13]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): 729-742 (2011) - [j12]Samuel Genheden, Ulf Ryde:
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. J. Comput. Chem. 32(2): 187-195 (2011) - [j11]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): 947-958 (2011) - 2010
- [j10]Samuel Genheden, Ulf Ryde:
How to obtain statistically converged MM/GBSA results. J. Comput. Chem. 31(4): 837-846 (2010) - 2009
- [j9]Jacob Kongsted, Ulf Ryde:
An improved method to predict the entropy term with the MM/PBSA approach. J. Comput. Aided Mol. Des. 23(2): 63-71 (2009) - [j8]Jacob Kongsted, Pär Söderhjelm, Ulf Ryde:
How accurate are continuum solvation models for drug-like molecules? J. Comput. Aided Mol. Des. 23(7): 395-409 (2009) - [j7]Pär Söderhjelm, Ulf Ryde:
Conformational dependence of charges in protein simulations. J. Comput. Chem. 30(5): 750-760 (2009) - 2007
- [j6]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): 1083-1090 (2007) - 2006
- [j5]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): 1398-1414 (2006) - 2002
- [j3]Ulf Ryde, Lars Olsen, Kristina Nilsson:
Quantum chemical geometry optimizations in proteins using crystallographic raw data. J. Comput. Chem. 23(11): 1058-1070 (2002)
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