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Sidler D.; Christófol-Clough M.; Riniker S.
Efficient Round-Trip Time Optimisation for Replica-Exchange Enveloping Distribution Sampling (RE-EDS)
J. Chem. Theory Comput. 2017, 13, 3020.


Riniker S.
Molecular dynamics fingerprints (MDFP): Machine-learning from MD data to predict free-energy differences
J. Chem. Inf. Model. 2017, 57, 276.


Renevey A.; Riniker S.
Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions
J. Chem. Phys. 2017, 146, 124131.



Sidler D.; Schwaninger A.; Riniker S.
Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation
J. Chem. Phys. 2016, 145, 154114.


Renevey A.; Riniker S.
The importance of N-methylations for the stability of β6.3-helical conformation of polytheonamide B
Eur. Biophys. J. 2016, 46, 363.


Fuchs S. W.; Lackner G.; Morinaka B. I.; Riniker S.; Jörn P.
A lanthipeptide-like motif guides peptide epimerization by radical SAM epimerases - implications for RiPP evolution
Angew. Chem. Int. Ed. 2016, 55, 12330.


Witek J.;  Keller B. G.; Blatter M.; Meissner A.; Wagner T.; Riniker S.
Kinetic models of cyclosporin A in polar and apolar environment reveal multiple congruent states
J. Chem. Inf. Model. 2016, 56, 1547.


Horta B. A. C.; Merz P. T.; Fuchs P. F. J.; Dolenc J.; Riniker S.; Hünenberger P. H.
GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set
J. Chem. Theory Comput. 2016, 12, 3825.




Riniker S.; Landrum G. A.
Better informed distance geometry: using what we know to improve conformation generation
J. Chem. Inf. Model. 2015, 55, 2562.


Riniker S.
Method development for classical molecular dynamics simulations: Coarse-graining and free energy calculations
Bunsen-Magazin 2015, 17 (6/2015), 228.


Eichenberger A.; Huang W.; Riniker S.; van Gunsteren W. F.
A supra-atomic coarse-grained GROMOS force field for aliphatic hydrocarbons in the liquid phase
J. Chem. Theory Comput. 2015, 11, 2925.


Mortier J.; Rakers C.; Bermudez M.; Murgueitio M. S.; Riniker S.; Wolber G.
The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes
Drug Discov. Today 2015, 20, 686.


Eichenberger A.; van Gunsteren W. F.; Riniker S.; von Ziegler L.; Hansen N.
The key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured states
BBA General Subjects 2015, 1850, 983.




Don C.; Riniker S.
Scents and Sense: In silico perspectives on olfactory receptors
J. Comput. Chem. 2014, 35, 2279.


Riniker S.
Crossing the boundaries within computational chemistry: from molecular dynamis to cheminformatics and back
CHIMIA 2014, 68, 620.


Huang W.; Riniker S.; van Gunsteren W. F.
Rapid sampling of folding equilibria of β‐peptides in methanol using a supramolecular solvent model
J. Chem. Theory Comput. 2014, 10, 2213.


Riniker S.; Wang Y.; Jenkins J. L.; Landrum G. A.
Using information from historical high-throughput screens to predict active compounds
J. Chem. Inf. Model. 2014, 54, 1880.




Riniker S.; Fechner N., Landrum G. A.
Heterogeneous classifier fusion for ligand-based virtual screening: or, how decision making by committee can be a good thing
J. Chem. Inf. Model. 2013, 53, 2829.


Riniker S., Landrum G. A.
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods
J. Cheminf. 2013, 5, 43.


Riniker S.; Landrum G. A.
Open-source platform to benchmark fingerprints for ligand-based virtual screening
J. Cheminf. 2013, 5, 26.


Lin Z.; Riniker S.; van Gunsteren W. F.
Free enthalpy differences between α-, π-, and 310-helices of an atomic level fine-grained alanine deca-peptide solvated in supra-molecular coarse-grained water
J. Chem. Theory Comput. 2013, 9, 1328.


Meier K.; Choutko A.; Dolenc J.; Eichenberger A.; Riniker S.; van Gunsteren W. F.
Multi-resolution simulation of biomolecular systems: a review of methodological issues
Angew. Chem. Int. Ed. 2013, 52, 2820.




Riniker S.; Barandun L. J.; Diederich F.; Krämer O.; Steffen A.; van Gunsteren W. F.
Free enthalpies of replacing water molecules in protein binding pockets
J. Comput. Aided Mol. Des. 2012, 26, 1293.


Riniker S.; Eichenberger A. P.; van Gunsteren W. F.
Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water
J. Phys. Chem. B 2012, 116, 8873.


Riniker S.; Eichenberger A. P.; van Gunsteren W. F.
Solvating atomic level fine-grained proteins in supra-molecular coarse-grained water for molecular dynamics simulations
Eur. Biophys. J. 2012, 41, 647.


Riniker S.; van Gunsteren W. F.
Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system
J. Chem. Phys. 2012, 137, 044120.
Erratum: J. Chem. Phys. 2017, 146, 129901.


Riniker S.; Allison J. R.; van Gunsteren W. F.
On developing coarse-grained models for biomolecular simulation: a review
Phys. Chem. Chem. Phys. 2012, 14, 12423.


Horta B. A. C.; Lin Z.; Huang W.; Riniker S.; van Gunsteren W. F.; Hünenberger P. H.
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol
J. Comput. Chem. 2012, 33, 1907.


Riniker S.; Horta B. A. C.; Thijssen B.; Gupta S.; van Gunsteren W. F.; Hünenberger P. H.
Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: a molecular dynamics simulation study
ChemPhysChem 2012, 13, 1182.


Hansen N.; Dolenc J.; Knecht M.; Riniker S.; van Gunsteren W. F.
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution
J. Comput. Chem. 2012, 33, 640.


Allison J.; Riniker S.; van Gunsteren W. F.
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform and methanol
J. Chem. Phys. 2012, 136, 054505.


Kunz A. P. E.; Allison J. R.; Geerke D. P.; Horta B. A. C.; Hünenberger P. H.; Riniker S.; Schmid N.; van Gunsteren W. F.
New functionalities in the GROMOS biomolecular simulation software
J. Comput. Chem. 2012, 33, 340.




Lin Z.; Liu H.; Riniker S.; van Gunsteren W. F.
On the use of enveloping distribution sampling (EDS) to compute free enthalpy differences between different conformational states of molecules: application to 310-, α- and π-helices
J. Chem. Theory Comput. 2011, 7, 3884.


Riniker S.; Christ C. D.; Hansen H. S.; Hünenberger P. H.; Oostenbrink C.; Steiner D.; van Gunsteren W. F.
Calculation of relative free energies for ligand-protein binding, solvation and conformational transitions using the GROMOS software
J. Phys. Chem. B 2011, 115, 13570.


Dolenc J.; Riniker S.; Gaspari R.; Daura X.; van Gunsteren W. F.
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities
J. Comput. Aided Mol. Des. 2011, 25, 709.


Riniker S.; Christ C. D.; Hansen N.; Mark A. E.; Nair P. C.; van Gunsteren W. F.
Comparison of enveloping distribution sampling and thermodynamic integration to calculate relative binding free energies of phenylethanolamine N-methyltransferase
J. Chem. Phys. 2011, 135, 024105.


Riniker S.; van Gunsteren W. F.
A simple, efficient polarisable coarse-grained water model for molecular dynamics simulations
J. Chem. Phys. 2011, 134, 084110.


Riniker S.; Kunz A. E.; van Gunsteren W. F.
On the calculation of the dielectric permittivity and relaxation of molecular models in the liquid phase
J. Chem. Theory Comput. 2011, 7, 1469.


Schmid N.; Eichenberger A. P.; Choutko A.; Riniker S.; Winger M.; Mark A. E.; van Gunsteren W. F.
Definition and testing of the GROMOS force field versions: 54A7 and 54B7
Eur. Biophys. J. 2011, 40, 843.




Riniker S.; Daura X.; van Gunsteren W. F.
α-Cyclodextrin host-guest binding: a computational study of the different driving forces
Helv. Chim. Acta 2010, 93, 2318.




Gattin Z.; Riniker S.; Hore P. J.; Mok K. H.; van Gunsteren W. F.
Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: a simulation study consistent with experimental observations
Protein Sci. 2009, 18, 2090.


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