S. Riniker

发表

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

Andreas P. Eichenberger, W. V. van Gunsteren, S. Riniker, 2012, European Biophysics Journal.

Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems.

S. Riniker, Lennard Böselt, Moritz Thürlemann, 2020, Journal of chemical theory and computation.

The importance of N-methylations for the stability of the $$\beta ^{6.3}$$β6.3-helical conformation of polytheonamide B

S. Riniker, A. Renevey, 2017, European Biophysics Journal.

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

Andreas P. Eichenberger, A. Mark, Nathan Schmid, 2011, European Biophysics Journal.

Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff.

P. Hünenberger, S. Riniker, Alžbeta Kubincová, 2020, Physical chemistry chemical physics : PCCP.

Connecting the conformational behavior of cyclic octadepsipeptides with their ionophoric property and membrane permeability†

Chad E. Townsend, M. Ebert, G. Subramanian, 2020, Organic & biomolecular chemistry.

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

B. Meier, M. Ernst, S. Riniker, 2019, Angewandte Chemie.

Fast Nosé-Hoover thermostat: molecular dynamics in quasi-thermodynamic equilibrium.

S. Riniker, D. Sidler, Sereina Riniker, 2019, Physical chemistry chemical physics : PCCP.

Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations

S. Riniker, D. Sidler, M. Lehner, 2018, F1000Research.

Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations

S. Riniker, D. Sidler, M. Lehner, 2019, F1000Research.

A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds

M. Künzler, M. Aebi, J. Naismith, 2018, Science Advances.

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.

Pascal T. Merz, P. Hünenberger, S. Riniker, 2016, Journal of chemical theory and computation.

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

P. Hünenberger, S. Riniker, Benjamin Ries, 2022, Journal of Computer-Aided Molecular Design.

Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system.

W. V. van Gunsteren, S. Riniker, 2012, The Journal of chemical physics.

Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water.

W. V. van Gunsteren, S. Riniker, Zhixiong Lin, 2013, Journal of chemical theory and computation.

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

B. Keller, S. Riniker, A. Meissner, 2017, Chemphyschem : a European journal of chemical physics and physical chemistry.

Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: a molecular dynamics simulation study.

W. V. van Gunsteren, B. Thijssen, P. Hünenberger, 2012, Chemphyschem : a European journal of chemical physics and physical chemistry.

Beyond the Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutions.

S. Riniker, Patrick Bleiziffer, D. Sidler, 2019, Journal of chemical theory and computation.

Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions

S. Riniker, Lennard Böselt, Moritz Thürlemann, 2022, Journal of chemical theory and computation.

Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules

Emília P. Barros, E. P. Barros, S. Riniker, 2022, J. Chem. Inf. Model..

Graph Convolutional Neural Networks for (QM)ML/MM Molecular Dynamics Simulations

S. Riniker, Albert Hofstetter, Lennard Boselt, 2022, 2206.14422.

Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules

Emília P. Barros, P. Hünenberger, E. P. Barros, 2022, J. Chem. Inf. Model..

Rapid Sampling of Folding Equilibria of β-Peptides in Methanol Using a Supramolecular Solvent Model.

W. V. van Gunsteren, S. Riniker, Wei Huang, 2014, Journal of chemical theory and computation.

Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase.

Andreas P. Eichenberger, W. V. van Gunsteren, S. Riniker, 2015, Journal of chemical theory and computation.

Cross-Linked Collagen Triple Helices by Oxime Ligation.

S. Riniker, H. Wennemers, Jagna Witek, 2017, Journal of the American Chemical Society.

Toward the elucidation of the mechanism for passive membrane permeability of cyclic peptides.

S. Riniker, 2019, Future medicinal chemistry.

A New Family of Rigid Dienone Musks Challenges the Perceptive Range of the Human Olfactory Receptor OR5AN1

Stephanie M. Linker, A. Natsch, S. Riniker, 2020 .

Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions.

S. Riniker, A. Renevey, Sereina Riniker, 2017, The Journal of chemical physics.

Graph-convolutional neural networks for (QM)ML/MM molecular dynamics simulations.

S. Riniker, Lennard Böselt, Albert Hofstetter, 2022, Physical chemistry chemical physics : PCCP.

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

Andreas P. Eichenberger, W. V. van Gunsteren, S. Riniker, 2012, European Biophysics Journal.

Improving the IR spectra alignment algorithm with spectra deconvolution and combination with Raman or VCD spectroscopy

S. Riniker, Lennard Böselt, W. Herrebout, 2022, Physical chemistry chemical physics : PCCP.

Determining the Regio- and Relative Stereochemistry of Small and Drug-like Molecules Using an Alignment Algorithm for Infrared Spectra.

S. Riniker, Lennard Böselt, S. Steiner, 2020, Analytical chemistry.

Mutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluation.

E. Carreira, S. Leibundgut-Landmann, S. Riniker, 2021, Journal of the American Chemical Society.

Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation

Sereina Riniker, Gregory A. Landrum, S. Riniker, 2015, J. Chem. Inf. Model..

Recent developments in multiscale free energy simulations.

Emília P. Barros, E. P. Barros, S. Riniker, 2021, Current opinion in structural biology.

Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes

Stephanie M. Linker, H. Roth, S. Riniker, 2023, Journal of medicinal chemistry.

Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides.

H. Roth, S. Riniker, Shuzhe Wang, 2021, Journal of medicinal chemistry.

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

Stephanie M. Linker, S. Riniker, Shuzhe Wang, 2021, Chimia.

Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties.

S. Poulet, R. Derbali, S. Riniker, 2021, Journal of medicinal chemistry.

Connecting dynamic reweighting Algorithms: Derivation of the dynamic reweighting family tree.

Sereina Riniker, Stephanie M Linker, R Gregor Weiß, 2020, The Journal of chemical physics.

Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides

Shuzhe Wang, Sereina Riniker, Oliver Lemke, 2018, J. Chem. Inf. Model..

Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States

Marie-Claude Blatter, Sereina Riniker, Jagna Witek, 2016, J. Chem. Inf. Model..

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

Shuzhe Wang, Sereina Riniker, S. Riniker, 2019, Journal of Computer-Aided Molecular Design.

Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences

Sereina Riniker, S. Riniker, Sereina Riniker, 2017, J. Chem. Inf. Model..

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

Wei Huang, Wilfred F. van Gunsteren, Sereina Riniker, 2012, J. Comput. Chem..

Using Information from Historical High-Throughput Screens to Predict Active Compounds

Yuan Wang, Jeremy L. Jenkins, Sereina Riniker, 2014, J. Chem. Inf. Model..

The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes.

Gerhard Wolber, Christin Rakers, Sereina Riniker, 2015, Drug discovery today.

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.

X. Daura, A. Mark, W. V. van Gunsteren, 2020, Chemphyschem : a European journal of chemical physics and physical chemistry.

Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates

Frank Oellien, Shuzhe Wang, Sereina Riniker, 2020, J. Chem. Inf. Model..

Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water.

Andreas P. Eichenberger, W. V. van Gunsteren, S. Riniker, 2012, The journal of physical chemistry. B.

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview

Sereina Riniker, S. Riniker, Sereina Riniker, 2018, J. Chem. Inf. Model..

Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability

Stephanie M. Linker, H. Roth, S. Riniker, 2022, RSC advances.

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes.

David F. Hahn, P. Hünenberger, S. Riniker, 2020, Journal of chemical theory and computation.

How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation.

G. Bouvignies, F. Ferrage, S. Riniker, 2022, Current opinion in structural biology.

Glycan–protein interactions determine kinetics of N-glycan remodeling

R. Glockshuber, M. Aebi, S. Riniker, 2021, RSC chemical biology.

Glycan-Protein Interactions Determine Kinetics of N-Glycan Remodeling

R. Glockshuber, M. Aebi, R. Weiss, 2020, bioRxiv.

Scents and sense: In silico perspectives on olfactory receptors

Sereina Riniker, C. G. Don, Charleen G. Don, 2014, J. Comput. Chem..

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

Sereina Riniker, Gregory A. Landrum, S. Riniker, 2013, Journal of Cheminformatics.

Virtual-screening workflow tutorials and prospective results from the Teach-Discover-Treat competition 2014 against malaria

Floriane Montanari, Gregory A Landrum, Sereina Riniker, 2018, F1000Research.

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

Wilfred F. van Gunsteren, Xavier Daura, Sereina Riniker, 2011, J. Comput. Aided Mol. Des..

The importance of N-methylations for the stability of the $$\beta ^{6.3}$$β6.3-helical conformation of polytheonamide B

S. Riniker, A. Renevey, Sereina Riniker, 2017, European Biophysics Journal.

Validation of Molecular Simulation: An Overview of Issues.

Chris Oostenbrink, Xavier Daura, Sereina Riniker, 2018, Angewandte Chemie.

On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces

Gerhard König, Sereina Riniker, S. Riniker, 2020, Interface Focus.

Learning Atomic Multipoles: Prediction of the Electrostatic Potential with Equivariant Graph Neural Networks.

S. Riniker, Lennard Böselt, Moritz Thürlemann, 2021, Journal of chemical theory and computation.

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

J. Piel, S. Riniker, B. I. Morinaka, 2016, Angewandte Chemie.

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

Emília P. Barros, E. P. Barros, S. Riniker, 2022, Journal of Computer-Aided Molecular Design.

Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling.

P. Hünenberger, S. Riniker, Gerhard König, 2021, Journal of chemical theory and computation.

An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling

Sereina Riniker, Gerhard Koenig, Nina Glaser, 2020, J. Chem. Inf. Model..

Efficient Round-Trip Time Optimization for Replica-Exchange Enveloping Distribution Sampling (RE-EDS).

Sereina Riniker, Dominik Sidler, Michael Cristòfol-Clough, 2017, Journal of chemical theory and computation.

Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation.

Sereina Riniker, Dominik Sidler, Arthur Schwaninger, 2016, The Journal of chemical physics.

Implicit solvent approach based on generalized Born and transferable graph neural networks for molecular dynamics simulations.

S. Riniker, Paul Katzberger, Sereina Riniker, 2023, The Journal of chemical physics.

Enhanced sampling without borders: on global biasing functions and how to reweight them

Stephanie M. Linker, S. Riniker, A. S. Kamenik, 2021, Physical chemistry chemical physics : PCCP.

Machine Learning for Small Molecule Drug Discovery in Academia and Industry

Andrea Volkamer, F. Grisoni, S. Riniker, 2023, Artificial Intelligence in the Life Sciences.

Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients

Niels Hansen, Sereina Riniker, Julia Gebhardt, 2020, J. Chem. Inf. Model..

Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations

S. Riniker, D. Sidler, M. Lehner, 2018, F1000Research.

Exploring Novel Directions in Free Energy Calculations

Zoe Cournia, Sereina Riniker, Kira A Armacost, 2020, J. Chem. Inf. Model..

Multi-resolution simulation of biomolecular systems: a review of methodological issues.

Wilfred F van Gunsteren, Sereina Riniker, Jozica Dolenc, 2013, Angewandte Chemie.

Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations

Sereina Riniker, Patrick Bleiziffer, Kay Schaller, 2018, J. Chem. Inf. Model..

Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.

Wilfred F van Gunsteren, Sereina Riniker, Alan E Mark, 2011, The Journal of chemical physics.

On developing coarse-grained models for biomolecular simulation: a review.

Wilfred F van Gunsteren, Sereina Riniker, Jane R. Allison, 2012, Physical chemistry chemical physics : PCCP.

Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme.

P. Hünenberger, S. Riniker, Alžbeta Kubincová, 2021, The Journal of chemical physics.

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

Wilfred F van Gunsteren, Sereina Riniker, W. V. van Gunsteren, 2011, The Journal of chemical physics.

N-Glycosylation Enhances Conformational Flexibility of Protein Disulfide Isomerase Revealed by Microsecond Molecular Dynamics and Markov State Modeling.

M. Aebi, S. Riniker, Marie-Estelle Losfeld, 2021, The journal of physical chemistry. B.

Sereina Riniker, Gregory A. Landrum, S. Riniker, 2013, Journal of Cheminformatics.

The key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured states.

Lukas M. von Ziegler, Andreas P. Eichenberger, W. V. van Gunsteren, 2015, Biochimica et biophysica acta.

New functionalities in the GROMOS biomolecular simulation software

Wilfred F. van Gunsteren, Daan P. Geerke, Sereina Riniker, 2012, J. Comput. Chem..

Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations.

S. Riniker, D. Sidler, S. Frasch, 2018, Journal of Chemical Physics.

Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities

Emília P. Barros, E. P. Barros, S. Riniker, 2023, J. Chem. Inf. Model..

Influence of the Fluorophore Mobility on Distance Measurements by Gas-Phase FRET.

R. Zenobi, S. Riniker, A. S. Kamenik, 2023, The journal of physical chemistry. A.

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

R. Zenobi, S. Riniker, A. S. Kamenik, 2023, Nature communications.

Matched Molecular Series Analysis for ADME Property Prediction

Christian Kramer, Sereina Riniker, Mahendra Awale, 2020, J. Chem. Inf. Model..

Free enthalpies of replacing water molecules in protein binding pockets

Wilfred F. van Gunsteren, Sereina Riniker, Andreas Steffen, 2012, Journal of Computer-Aided Molecular Design.

Influence of Lipidation on the Folding and Stability of Collagen Triple Helices-An Experimental and Theoretical Study.

S. Riniker, H. Wennemers, Jasmine Egli, 2021, Journal of the American Chemical Society.

Benchmarking Hybrid Atomistic/Coarse-Grained Schemes for Proteins with an Atomistic Water Layer.

S. Riniker, A. Renevey, Sereina Riniker, 2019, The journal of physical chemistry. B.

Frame Shifts Affect the Stability of Collagen Triple Helices.

Emília P. Barros, M. Ebert, E. P. Barros, 2022, Journal of the American Chemical Society.

Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm

Sereina Riniker, Trixie Wagner, Dominik Sidler, 2019, J. Chem. Inf. Model..

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.

Wilfred F van Gunsteren, Sereina Riniker, Zhixiong Lin, 2011, Journal of chemical theory and computation.

A NISOTROPIC M ESSAGE P ASSING : G RAPH N EURAL N ETWORKS WITH D IRECTIONAL AND L ONG -R ANGE I NTERACTIONS

S. Riniker, Moritz Thürlemann, Sereina Riniker, 2023 .

Development of an open-source software for isomer enumeration

P. Hünenberger, S. Riniker, Salomé R Rieder, 2023, Journal of Cheminformatics.

Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

Wilfred F van Gunsteren, Chris Oostenbrink, Sereina Riniker, 2011, The journal of physical chemistry. B.

Novel Directions in Free Energy Methods and Applications

Zoe Cournia, Sereina Riniker, Kira A Armacost, 2020, J. Chem. Inf. Model..

GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning

Sereina Riniker, Nadine Schneider, Gregory A. Landrum, 2021, J. Chem. Inf. Model..

Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences

Gregory A Landrum, Shuzhe Wang, Sereina Riniker, 2020, J. Chem. Inf. Model..

α‐Cyclodextrin Host–Guest Binding: A Computational Study of the Different Driving Forces

X. Daura, W. F. Gunsteren, S. Riniker, 2010 .

Energy-based clustering: Fast and robust clustering of data with known likelihood functions.

S. Riniker, Moritz Thürlemann, Sereina Riniker, 2023, The Journal of chemical physics.

Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry

Benjamin D. Sellers, Anastasia C. Murthy, N. Popovych, 2022, J. Chem. Inf. Model..

Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing

Sereina Riniker, Nikolas Fechner, Gregory A. Landrum, 2013, J. Chem. Inf. Model..