Works by Riniker, Sereina

Results: 35

α-Cyclodextrin Host-Guest Binding: A Computational Study of the Different Driving Forces.

Published in:

Helvetica Chimica Acta, 2010, v. 93, n. 12, p. 2318, doi. 10.1002/hlca.201000251

By:

Riniker, Sereina;
Daura, Xavier;
van Gunsteren, Wilfred F.

Publication type:

Article

Open-source platform to benchmark fingerprints for ligand-based virtual screening.

Published in:

Journal of Cheminformatics, 2013, v. 5, n. 1, p. 1, doi. 10.1186/1758-2946-5-26

By:

Riniker, Sereina;
Landrum, Gregory A.

Publication type:

Article

Cover Feature: Experimental and Theoretical Studies on the Reactions of Aliphatic Imines with Isocyanates (Chem. Eur. J. 14/2024).

Published in:

2024

By:

Cotter, Etienne;
Pultar, Felix;
Riniker, Sereina;
Altmann, Karl‐Heinz

Publication type:

Correction Notice

Experimental and Theoretical Studies on the Reactions of Aliphatic Imines with Isocyanates.

Published in:

Chemistry - A European Journal, 2024, v. 30, n. 14, p. 1, doi. 10.1002/chem.202304272

By:

Cotter, Etienne;
Pultar, Felix;
Riniker, Sereina;
Altmann, Karl‐Heinz

Publication type:

Article

Predicting Collagen Triple Helix Stability through Additive Effects of Terminal Residues and Caps.

Published in:

Angewandte Chemie, 2023, v. 135, n. 3, p. 1, doi. 10.1002/ange.202214728

By:

Fiala, Tomas;
Barros, Emilia P.;
Heeb, Rahel;
Riniker, Sereina;
Wennemers, Helma

Publication type:

Article

Localized and Collective Motions in HET‐s(218‐289) Fibrils from Combined NMR Relaxation and MD Simulation.

Published in:

Angewandte Chemie, 2019, v. 131, n. 28, p. 9483, doi. 10.1002/ange.201901929

By:

Smith, Albert A.;
Ernst, Matthias;
Riniker, Sereina;
Meier, Beat H.

Publication type:

Article

SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00787-9

By:

Landrum, Gregory A.;
Beckers, Maximilian;
Lanini, Jessica;
Schneider, Nadine;
Stiefl, Nikolaus;
Riniker, Sereina

Publication type:

Article

Development of an open-source software for isomer enumeration.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-022-00677-6

By:

Rieder, Salomé R.;
Oliveira, Marina P.;
Riniker, Sereina;
Hünenberger, Philippe H.

Publication type:

Article

A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS.

Published in:

Journal of Computational Chemistry, 2025, v. 46, n. 5, p. 1, doi. 10.1002/jcc.70053

By:

Poliak, Peter;
Bleiziffer, Patrick;
Pultar, Felix;
Riniker, Sereina;
Oostenbrink, Chris

Publication type:

Article

Temperature Dependence of the Dielectric Permittivity of Acetic Acid, Propionic Acid and Their Methyl Esters: A Molecular Dynamics Simulation Study.

Published in:

ChemPhysChem, 2012, v. 13, n. 5, p. 1182, doi. 10.1002/cphc.201100949

By:

Riniker, Sereina;
Horta, Bruno A. C.;
Thijssen, Bram;
Gupta, Saumya;
van Gunsteren, Wilfred F.;
Hünenberger, Philippe H.

Publication type:

Article

Multi-Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues.

Published in:

Angewandte Chemie International Edition, 2013, v. 52, n. 10, p. 2820, doi. 10.1002/anie.201205408

By:

Meier, Katharina;
Choutko, Alexandra;
Dolenc, Jozica;
Eichenberger, Andreas P.;
Riniker, Sereina;
van Gunsteren, Wilfred F.

Publication type:

Article

Free enthalpies of replacing water molecules in protein binding pockets.

Published in:

Journal of Computer-Aided Molecular Design, 2012, v. 26, n. 12, p. 1293, doi. 10.1007/s10822-012-9620-8

By:

Riniker, Sereina;
Barandun, Luzi;
Diederich, François;
Krämer, Oliver;
Steffen, Andreas;
Gunsteren, Wilfred

Publication type:

Article

Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.

Published in:

Journal of Computer-Aided Molecular Design, 2011, v. 25, n. 8, p. 709, doi. 10.1007/s10822-011-9453-x

By:

Dolenc, Jožica;
Riniker, Sereina;
Gaspari, Roberto;
Daura, Xavier;
van Gunsteren, Wilfred F.

Publication type:

Article

Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38463-z

By:

Wu, Ri;
Metternich, Jonas B.;
Kamenik, Anna S.;
Tiwari, Prince;
Harrison, Julian A.;
Kessen, Dennis;
Akay, Hasan;
Benzenberg, Lukas R.;
Chan, T.-W. Dominic;
Riniker, Sereina;
Zenobi, Renato

Publication type:

Article

Predicting Collagen Triple Helix Stability through Additive Effects of Terminal Residues and Caps.

Published in:

Angewandte Chemie International Edition, 2023, v. 62, n. 3, p. 1, doi. 10.1002/anie.202214728

By:

Fiala, Tomas;
Barros, Emilia P.;
Heeb, Rahel;
Riniker, Sereina;
Wennemers, Helma

Publication type:

Article

Localized and Collective Motions in HET‐s(218‐289) Fibrils from Combined NMR Relaxation and MD Simulation.

Published in:

Angewandte Chemie International Edition, 2019, v. 58, n. 28, p. 9383, doi. 10.1002/anie.201901929

By:

Smith, Albert A.;
Ernst, Matthias;
Riniker, Sereina;
Meier, Beat H.

Publication type:

Article

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio‐Molecular Systems: Overview and Perspective on Issues.

Published in:

ChemPhysChem, 2021, v. 22, n. 3, p. 264, doi. 10.1002/cphc.202000968

By:

Gunsteren, Wilfred F.;
Daura, Xavier;
Fuchs, Patrick F. J.;
Hansen, Niels;
Horta, Bruno A. C.;
Hünenberger, Philippe H.;
Mark, Alan E.;
Pechlaner, Maria;
Riniker, Sereina;
Oostenbrink, Chris

Publication type:

Article

Interconversion Rates between Conformational States as Rationale for the Membrane Permeability of Cyclosporines.

Published in:

ChemPhysChem, 2017, v. 18, n. 23, p. 3309, doi. 10.1002/cphc.201700995

By:

Witek, Jagna;
Mühlbauer, Max;
Keller, Bettina G.;
Blatter, Markus;
Meissner, Axel;
Wagner, Trixie;
Riniker, Sereina

Publication type:

Article

Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS.

Published in:

Chimia, 2022, v. 76, n. 4, p. 327, doi. 10.2533/chimia.2022.327

By:

Rieder, Salomé R.;
Ries, Benjamin;
Champion, Candide;
Barros, Emilia P.;
Hünenberger, Philippe H.;
Riniker, Sereina

Publication type:

Article

Passing the Barrier – How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides.

Published in:

Chimia, 2021, v. 75, n. 6, p. 518, doi. 10.2533/chimia.2021.518

By:

Linker, Stephanie M.;
Wang, Shuzhe;
Ries, Benjamin;
Stadelmann, Thomas;
Riniker, Sereina

Publication type:

Article

Scents and sense: In silico perspectives on olfactory receptors.

Published in:

Journal of Computational Chemistry, 2014, v. 35, n. 32, p. 2279, doi. 10.1002/jcc.23757

By:

Don, Charleen G.;
Riniker, Sereina

Publication type:

Article

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.

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 24, p. 1907, doi. 10.1002/jcc.23021

By:

Horta, Bruno A. C.;
Lin, Zhixiong;
Huang, Wei;
Riniker, Sereina;
van Gunsteren, Wilfred F.;
Hünenberger, Philippe H.

Publication type:

Article

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution.

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 6, p. 640, doi. 10.1002/jcc.22879

By:

Hansen, Niels;
Dolenc, Jožica;
Knecht, Matthias;
Riniker, Sereina;
van Gunsteren, Wilfred F.

Publication type:

Article

New functionalities in the GROMOS biomolecular simulation software.

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 3, p. 340, doi. 10.1002/jcc.21954

By:

Kunz, Anna-Pitschna E.;
Allison, Jane R.;
Geerke, Daan P.;
Horta, Bruno A. C.;
Hünenberger, Philippe H.;
Riniker, Sereina;
Schmid, Nathan;
van Gunsteren, Wilfred F.

Publication type:

Article

Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte.

Published in:

Angewandte Chemie, 2018, v. 130, n. 4, p. 894, doi. 10.1002/ange.201702945

By:

van Gunsteren, Wilfred F.;
Riniker, Sereina;
Daura, Xavier;
Hansen, Niels;
Mark, Alan E.;
Oostenbrink, Chris;
Smith, Lorna J.

Publication type:

Article

A Lanthipeptide-like N-Terminal Leader Region Guides Peptide Epimerization by Radical SAM Epimerases: Implications for RiPP Evolution.

Published in:

Angewandte Chemie, 2016, v. 128, n. 40, p. 12518, doi. 10.1002/ange.201602863

By:

Fuchs, Sebastian W.;
Lackner, Gerald;
Morinaka, Brandon I.;
Morishita, Yohei;
Asai, Teigo;
Riniker, Sereina;
Piel, Jörn

Publication type:

Article

Biomolekulare Simulationen mit mehreren Auflösungsniveaus: ein Überblick über methodische Aspekte.

Published in:

Angewandte Chemie, 2013, v. 125, n. 10, p. 2888, doi. 10.1002/ange.201205408

By:

Meier, Katharina;
Choutko, Alexandra;
Dolenc, Jozica;
Eichenberger, Andreas P.;
Riniker, Sereina;
van Gunsteren, Wilfred F.

Publication type:

Article

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology.

Published in:

Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 3, p. 175, doi. 10.1007/s10822-022-00445-6

By:

Ries, Benjamin;
Rieder, Salomé;
Rhiner, Clemens;
Hünenberger, Philippe H.;
Riniker, Sereina

Publication type:

Article

Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.

Published in:

Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 2, p. 117, doi. 10.1007/s10822-021-00436-z

By:

Ries, Benjamin;
Normak, Karl;
Weiß, R. Gregor;
Rieder, Salomé;
Barros, Emília P.;
Champion, Candide;
König, Gerhard;
Riniker, Sereina

Publication type:

Article

Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol–water log P blind challenge.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 4, p. 393, doi. 10.1007/s10822-019-00252-6

By:

Wang, Shuzhe;
Riniker, Sereina

Publication type:

Article

The importance of N-methylations for the stability of the $$\beta ^{6.3}$$ -helical conformation of polytheonamide B.

Published in:

European Biophysics Journal, 2017, v. 46, n. 4, p. 363, doi. 10.1007/s00249-016-1179-1

By:

Renevey, Annick;
Riniker, Sereina

Publication type:

Article

Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.

Published in:

European Biophysics Journal, 2012, v. 41, n. 8, p. 647, doi. 10.1007/s00249-012-0837-1

By:

Riniker, Sereina;
Eichenberger, Andreas;
van Gunsteren, Wilfred

Publication type:

Article

Definition and testing of the GROMOS force-field versions 54A7 and 54B7.

Published in:

European Biophysics Journal, 2011, v. 40, n. 7, p. 843, doi. 10.1007/s00249-011-0700-9

By:

Schmid, Nathan;
Eichenberger, Andreas;
Choutko, Alexandra;
Riniker, Sereina;
Winger, Moritz;
Mark, Alan;
Gunsteren, Wilfred

Publication type:

Article

Validation of Molecular Simulation: An Overview of Issues.

Published in:

Angewandte Chemie International Edition, 2018, v. 57, n. 4, p. 884, doi. 10.1002/anie.201702945

By:

van Gunsteren, Wilfred F.;
Riniker, Sereina;
Daura, Xavier;
Hansen, Niels;
Mark, Alan E.;
Oostenbrink, Chris;
Smith, Lorna J.

Publication type:

Article

A Lanthipeptide-like N-Terminal Leader Region Guides Peptide Epimerization by Radical SAM Epimerases: Implications for RiPP Evolution.

Published in:

Angewandte Chemie International Edition, 2016, v. 55, n. 40, p. 12330, doi. 10.1002/anie.201602863

By:

Fuchs, Sebastian W.;
Lackner, Gerald;
Morinaka, Brandon I.;
Morishita, Yohei;
Asai, Teigo;
Riniker, Sereina;
Piel, Jörn

Publication type:

Article