List of works - Sereina Riniker

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

scientific article

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

scientific article

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

scientific article published on 24 August 2018

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

article

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

article

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

scientific article published on 07 January 2012

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

scientific article published on 27 March 2019

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

scientific article published on 17 November 2015

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

scientific article published on 11 March 2019

Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

scholarly article by Sereina Riniker et al published 24 November 2011 in Journal of Physical Chemistry

Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol

scientific article

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

scientific article published in July 2011

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

scientific article published on 01 December 2020

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

scientific article published on 09 September 2020

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

scientific article published on 12 September 2017

Cross-Linked Collagen Triple Helices by Oxime Ligation

scientific article published on 5 September 2017

Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back

article

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

scientific article published on 30 April 2011

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

scientific article published on 5 November 2018

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

scientific article published on 27 March 2019

Development of an open-source software for isomer enumeration

scientific article published on 22 January 2023

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

scientific article published on 06 September 2021

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

scientific article

Exploring Novel Directions in Free Energy Calculations

scientific article published on 01 November 2020

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

scientific article published on 6 March 2018

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

scientific article published on 6 February 2013

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

scientific article published on 7 July 2011

Free enthalpies of replacing water molecules in protein binding pockets

scientific article published on 18 December 2012

Heterogeneous classifier fusion for ligand-based virtual screening: or, how decision making by committee can be a good thing.

scientific article published on 14 November 2013

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

scientific article published on 20 March 2020

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

scientific article published in 2023

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

scientific article published on 17 September 2017

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

scientific article

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

scientific article published on 03 February 2022

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

scientific article published in 2023

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

scientific article published on 05 June 2019

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

scientific article published on 05 April 2021

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

scientific article published on 20 February 2018

Matched Molecular Series Analysis for ADME Property Prediction

scientific article published on 05 May 2020

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

article

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

scientific article

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

scientific article published on 18 February 2013

New functionalities in the GROMOS biomolecular simulation software

scientific article published on 11 November 2011

Novel Directions in Free Energy Methods and Applications

scientific article published on 01 January 2020

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

scientific article published on 08 June 2012

On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase

article

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

scientific article published on 11 November 2011

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

scientific article published on 16 October 2020

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

scientific article (publication date: 30 May 2013)

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

scientific article published on 16 February 2022

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

scientific article published on June 2014

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

scientific article published on 04 December 2018

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

scientific article published on 12 November 2020

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

scientific article

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

scientific article

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

scientific article published in 2022

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

scientific article published on 22 March 2022

Scents and sense: in silico perspectives on olfactory receptors

scientific article

Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods

scientific article published on 24 September 2013

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

scientific article

Structural Effects of an Atomic-Level Layer of Water Molecules around Proteins Solvated in Supra-Molecular Coarse-Grained Water

scientific article published on 20 July 2012

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

scientific article published on 23 June 2015

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

scientific article published on 24 November 2020

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

article

Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations

scientific article published on October 2009

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

scientific article

The importance of N-methylations for the stability of the β⁶·³-helical conformation of polytheonamide B.

scientific article

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

scientific article published on 18 September 2014

Transition from Academia to Industry and Back

scientific article published on 30 July 2018

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

scientific article published on 19 November 2019

Using information from historical high-throughput screens to predict active compounds.

scientific article published on 26 June 2014

Validation of Molecular Simulation: An Overview of Issues

scientific article

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

scientific article published on 17 July 2017

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

scientific article published on 19 February 2018

List of works by Sereina Riniker

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

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

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

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

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

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

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

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

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

Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol

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

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

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

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

Cross-Linked Collagen Triple Helices by Oxime Ligation

Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back

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

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

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

Development of an open-source software for isomer enumeration

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

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

Exploring Novel Directions in Free Energy Calculations

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

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

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

Free enthalpies of replacing water molecules in protein binding pockets

Heterogeneous classifier fusion for ligand-based virtual screening: or, how decision making by committee can be a good thing.

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

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

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

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

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

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

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

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

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

Matched Molecular Series Analysis for ADME Property Prediction

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

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

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

New functionalities in the GROMOS biomolecular simulation software

Novel Directions in Free Energy Methods and Applications

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

On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase

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

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

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

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

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

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

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

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

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

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

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

Scents and sense: in silico perspectives on olfactory receptors

Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods

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

Structural Effects of an Atomic-Level Layer of Water Molecules around Proteins Solvated in Supra-Molecular Coarse-Grained Water

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

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

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

Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations

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

The importance of N-methylations for the stability of the β⁶·³-helical conformation of polytheonamide B.

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

Transition from Academia to Industry and Back

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

Using information from historical high-throughput screens to predict active compounds.

Validation of Molecular Simulation: An Overview of Issues

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

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