Journal Articles

2025

25.03

Paciorek J.; Steinborn C.; Gordiy I.; Schmutzler D.; Barber D. M.; Wurst K.; Riniker S.; Magauer T.
external page Asymmetric Total Synthesis of Glauconic and Glaucanic Acid
Chem. Sci., 2025, 16, 4159 (open access).

25.02

Pultar F.; Thürlemann M.; Gordiy I.; Doloszeski E.; Riniker S.
external page Neural Network Potential with Multi-Resolution Approach Enables Accurate Prediction of Reaction Free Energies in Solution
J. Am. Chem. Soc., 2025, 147, 6835 (open access).
Preprint: external page arXiv:2411.19728 (2024).

25.01

Poliak P.; Bleiziffer P.; Pultar F.; Riniker S.; Oostenbrink C.
external page A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS
J. Comput. Chem., 2025, 46, e70053 (open access).

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2024

24.11

Waibl F.; Casagrande F.; Dey F.; Riniker S.
external page Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents
J. Chem. Inf. Model., 2024, 64, 7938 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2024-1zxff (2024)

24.10

Braun J.; Katzberger P.; Landrum G. A.; Riniker S.
external page Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings
J. Chem. Inf. Model., 2024, 64, 7917 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2024-b7sxm (2024)

24.09

Lehner M. T.; Katzberger P.; Maeder N.; Landrum G. A.; Riniker S.
external page DASH Properties: Estimating Atomic and Molecular Properties from a Dynamic Attention-Based Substructure Hierarchy
J. Chem. Phys., 2024, 161, 074103 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2024-0ks0p (2024)

24.08

Landrum G. A.; Braun J.; Katzberger P.; Lehner M. T.; Riniker S.
external page lwreg: A Lightweight System for Chemical Registration and Data Storage
J. Chem. Inf. Model., 2024, 64, 6247 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2024-zrfl9 (2024)

24.07

Katzberger P.; Riniker S.
external page General Graph Neural Network Based Implicit Solvation Model for Organic Molecules in Water
Chem. Sci., 2024, 15, 10794 (open access).
external page ChemSci Pick of the Week
Preprint: external page ChemRxiv 10.26434/chemrxiv-2024-z8725 (2024).  

24.06

Champion C.; Hünenberger P. H.; Riniker S.
external page Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations
J. Chem. Theory Comput., 2024, 20, 4350 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2024-qkw53 (2024).

24.05

Benzenberg L.; Katzberger P.; Wu R.; Metternich J.; Riniker S.; Zenobi R.
external page Probing the Stability of a β-Hairpin Scaffold After Desolvation
J. Phys. Chem. Lett., 2024, 15, 5041.

24.04

Champion C.; Lehner M.; Smith A. A.; Ferrage F.; Bolik-Coulon N.; Riniker S.
external page Unraveling Motion in Proteins by Combining NMR Relaxometry and Molecular Dynamics Simulations: A Case Study on Ubiquitin
J. Chem. Phys., 2024, 160, 104105 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2023-335gp (2023).

24.03

Landrum G. A.; Riniker S.
external page Combining IC50 or Ki Values From Different Sources is a Source of Significant Noise
J. Chem. Inf. Model., 2024, 64, 1560 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2024-2smhk (2024).

24.02

Isert C.; Atz K.; Riniker S.; Schneider G.
external page Exploring Protein-Ligand Binding Affinity Prediction with Electron Density-Based Geometric Deep Learning
RSC Adv., 2024, 14, 4492 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2023-585vf (2023).

24.01

Cotter E.; Pultar F.; Riniker S.; Altmann K.-H.
external page Experimental and Theoretical Studies on the Reactions of Aliphatic Imines with Isocyanates
Chem. Eur. J., 2024, 30, e202304272 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2023-twjpr (2023).

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2023

23.13

Landrum G. A.; Beckers M.; Lanini J.; Schneider N.; Stiefl N.; Riniker S.
external page SIMPD: an Algorithm for Generating Simulated Time Splits for Validating Machine Learning Approaches
J. Cheminf., 2023, 15, 119 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2023-x9pjf (2023).

23.12

Kubincová A.; Riniker S., Hünenberger P. H.
external page Simulation of Aqueous Solutes Using the Adaptive Solvent-Scaling (AdSoS) Scheme
J. Chem. Phys., 2023, 159, 234102 (open access).
Preprint: external page ChemRxiv 10.26434/chemrxiv-2023-f1fqx (2023).

23.11

Thürlemann M.; Riniker S.
external page Hybrid Classical/Machine-Learning Force Fields for the Accurate Description of Molecular Condensed-Phase Systems
Chem. Sci., 2023, 14, 12661 (open access).
Preprint: external page arXiv:2308.08984 (2023).

23.10

Champion C.; Gall R.; Ries B.; Rieder S. R.; Barros E. P.; Riniker S.
external page Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases
J. Chem. Inf. Model., 2023, 63, 7133.
Preprint: external page ChemRxiv 10.26434/chemrxiv-2023-kfh2s (2023).

23.09

Lehner M. T.; Katzberger P.; Maeder N.; Schiebroek C. C. G.; Teetz J.; Landrum G. A.; Riniker S.
external page DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment
J. Chem. Inf. Model., 2023, 63, 6014 (open access).
Preprint: external page arXiv:2305.15981 (2023).

23.08

Metternich J. B.; Katzberger P.; Kamenik A. S.; Tiwari P.; Wu R.; Riniker S.; Zenobi R.
external page Influence of the Fluorophore Mobility on Distance Measurements by Gas Phase FRET
J. Phys. Chem. A, 2023, 127, 5620.
Preprint: external page ChemRxiv 10.26434/chemrxiv-2023-fcnwg (2023).

23.07

Thürlemann M.; Riniker S.
external page Energy-Based Clustering: Fast and Robust Clustering of Data with Known Likelihood Functions
J. Chem. Phys., 2023, 159, 024105 (open access).
Editor's pick. Journal cover of issue external page Volume 159, Issue 2.
Preprint: external page arXiv:2303.01104 (2023).

23.06

Katzberger P.; Riniker S.
external page Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
J. Chem. Phys., 2023, 158, 204101 (open access).
Preprint: external page arXiv:2302.09321 (2023).

23.05

Wu R.; Metternich J. B.; Kamenik A. S.; Tiwari P.; Harrison J. A.; Kessen D.; Akay H.; Benzenberg J. R.; Chan T.-W. D.; Riniker S.; Zenobi R.
external page Determining the Gas-Phase Structures of alpha-Helical Peptides: Insights from Shape, Intramolecular Distance, and Microsolvation Assays
Nature Commun., 2023, 14, 2913 (open access).

23.04

Barros E. P.; Ries B.; Champion C.; Rieder S. R.; Riniker S.
external page Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities
J. Chem. Inf. Model., 2023, 63, 1794 (open access).
Preprint: external page ChemRxiv:10.26434/chemrxiv-2022-sx77x (2022).

23.03

Thürlemann M.; Riniker S.
external page Anisotropic Message Passing: Graph Neural Networks with Directional and Long-Range Interactions
International Conference on Learning Representations (ICLR) 2023 (open access).

23.02

Linker S. M.; Schellhaas C.; Kamenik A. S.; Veldhuizen M. M.; Waibl F.; Roth H.-J.; Fouché M.; Rodde S.; Riniker S.
external page Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes
J. Med. Chem., 2023, 66, 2773 (open access).
Preprint: external page ChemRxiv:10.26434/chemrxiv-2022-9b47d (2022).

23.01

Volkamer A.; Riniker S.; Nittinger E.; Lanini J.; Grisoni F.; Evertsson E.; Rodríguez-Pérez R.; Schneider N.
external page Machine Learning for Small Molecule Drug Discovery in Academia and Industry
Artif. Intel. Life Sci. 2023, 3, 100056 (open access).

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2022

22.16

Rieder S. R.; Oliveira M. P.; Riniker S.; Hünenberger P. H.
external page Development of an Open-Source Software for Isomer Enumeration
J. Cheminf. 2023, 15, 10  (open access).

22.15

Thürlemann M.; Böselt L.; Riniker S.
external page Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions
J. Chem. Theory Comput. 2023, 19, 562 (open access).
Preprint: external page arXiv:2206.00355 (2022).

22.14

Böselt L.; Aerts R.; Herrebout W.; Riniker S.
external page Improving the IR Spectra Alignment Algorithm with Spectra Deconvolution and Combination with Raman or VCD Spectroscopy
Phys. Chem. Chem. Phys. 2023, 25, 2063 (open access).

22.13

Fiala T.; Barros E. P.; Heeb R.; Riniker S.; Wennemers H.
external page Predicting Collagen Triple Helix Stability Through Additive Effects of Terminal Residues and Caps
Angew. Chem. Int. Ed. 2022, 62, e202214728 (open access).

22.12

Fiala T.; Barros E. P.; Ebert M.-O.; Ruijsenaars E.; Riniker S.; Wennemers H.
external page Frame Shifts Affect the Stability of Collagen Triple Helices
J. Am. Chem. Soc. 2022, 144, 18642.

22.11

Stadelmann T.; Balmer C.; Riniker S.; Ebert M.-C.
external page Impact of Solvent Interactions on ¹H and ¹³C Chemical Shifts Investigated Using DFT and a Reference Dataset Recorded in CDCl₃ and CCl₄
Phys. Chem. Chem. Phys. 2022, 24, 23551 (open access).

22.10

Hofstetter A.; Böselt L.; Riniker S.
external page Graph Convolutional Neural Networks for (QM)ML/MM Molecular Dynamics Simulations
Phys. Chem. Chem. Phys. 2022, 24, 22497 (open access).
Preprint: external page arXiv:2206.14422 (2022).

22.09

Rieder S. R.; Ries B.; Kubincová A.; Champion C.; Barros E. P.; Hünenberger P. H.; Riniker S.
external page Leveraging the Sampling Efficiency of RE-EDS in OpenMM Using a Shifted Reaction-Field With an Atom-Based Cutoff
J. Chem. Phys. 2022, 157, 104117 (open access).

22.08

Stenström S.; Champion C.; Lehner M.; Bouvignies G.; Riniker S.; Ferrage F.
external page How Does it Really Move? Recent Progress in the Investigation of Protein Nanosecond Dynamics by NMR and Simulation
Curr. Opin. Struct. Biol. 2022, 77, 102459 (open access).

22.07

Kamenik A. S.; Linker S. M.; Riniker S.
external page Matching Simulations and Experiments of Conformationally Flexible Cyclic Peptides: Steps toward a Holistic View of Passive Membrane Permeability
ACS Book "Approaching the Next Inflection in Peptide Therapeutics: Attaining Cell Permeability and Oral Bioavailability" 2022, Ch. 5, pp. 137--154.

22.06

Rieder S. R.; Ries B.; Schaller K.; Champion C.; Barros E. P.; Hünenberger P. H.; Riniker S.
external page Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules
J. Chem. Inf. Model. 2022, 62, 3043 (open access).
Preprint external page arXiv:2204.01396 (2022)

22.05

Rieder S. R.; Ries B.; Champion C.; Barros E. P.; Hünenberger P. H.; Riniker S.
external page Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS
CHIMIA 2022, 76, 327 (open access).

22.04

Ries B.; Rieder S.; Rhiner C.; Hünenberger P. H.; Riniker S.
external page RestraintMaker: A Graph-Based Approach to Select Distance Restraints in Free-Energy Calculations with Dual Topology
J. Comput.-Aided Mol. Des. 2022, 36, 175 (open access).

22.03

Linker S. M.; Schellhaas C.; Ries B.; Roth H.-J.; Fouché M.; Rodde S.; Riniker S.
external page Polar/Apolar Interfaces Modulate the Conformational Behavior of Cyclic Peptides with Impact on Their Passive Membrane Permeability
RSC Advances 2022, 12, 5782 (open access).

22.02

Thürlemann M.; Böselt L.; Riniker S.
external page Learning Atomic Multipoles: Prediction of the Electrostatic Potential with Equivariant Graph Neural Networks
J. Chem. Theory Comput. 2022, 18, 1701 (open access).
Preprint external page arXiv:2110.05417 (2021)

22.01

Wang S.; Krummenacher K.; Landrum G. A.; Sellers B.; Di Lello P.; Robinson S.; Martin B.; Holden J.; Tom J.; Murthy A.; Popovych N.; Riniker S.
external page Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry
J. Chem. Inf. Model. 2022, 62, 472 (open access).

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2021

21.17

Kamenik A. S.; Linker S. M.; Riniker S.
external page Enhanced Sampling Without Borders: On Global Biasing Functions and How to Reweight Them
Phys. Chem. Chem. Phys. 2021, 24, 1225 (open access).

21.16

Ries B.; Normak K.; Weiss R. G.; Rieder S.; Barros E. P.; Champion C.; König G.; Riniker S.
external page Relative Free-Energy Calculations for Scaffold Hopping-Type Transformations with an Automated RE-EDS Sampling Procedure
J. Comput.-Aided Mol. Des. 2022, 36, 117 (open access).

21.15

König G.; Ries B.; Hünenberger P. H.; Riniker S.
external page Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-EDS
J. Chem. Theory Comput. 2021, 17, 5805.

21.14

Barros E. P.; Ries B.; Böselt L.; Champion C.; Riniker S.
external page Recent Developments in Multiscale Free Energy Simulations
Curr. Opin. Struct. Biol. 2021, 72, 55 (open access).

21.13

Wang S.; König G.; Roth H.-J.; Fouché M.; Rodde S.; Riniker S.
external page Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides
J. Med. Chem. 2021, 64, 12761 (open access).

21.12

Weiss R. G.; Losfeld M.-E.; Aebi M.; Riniker S.
external page N-Glycosylation Enhances Conformational Flexibility of Protein Disulfide Isomerase Revealed by Microsecond Molecular Dynamics and Markov State Modeling
J. Phys. Chem. B 2021, 125, 9467.

21.11

Kubincová A.; Riniker S.; Hünenberger P. H.
external page Solvent Scaling as an Alternative to Coarse-graining in Adaptive-resolution Simulations: The Adaptive Solvent-Scaling (AdSoS) Scheme
J. Chem. Phys. 2021, 155, 094107 (open access).

21.10

Linker S. M.; Wang S.; Ries B.; Stadelmann T.; Riniker S.
external page Passing the Barrier – How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides
CHIMIA 2021, 75, 518 (open access).

21.09

Pultar F.; Hansen M.; Wolfrum S.; Böselt L.; Frois-Martins R.; Bloch S.; Kravina A.; Pehlivanoglu D.; Schaffer C.; Leibundgut-Landmann S.; Riniker S.; Carreira E.
external page Mutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluation
J. Am. Chem. Soc. 2021, 143, 10389.

21.08

Esposito C.; Landrum G. A.; Schneider N.; Stiefl N.; Riniker S.
external page GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning
J. Chem. Inf. Model. 2021, 61, 2623 (open access).

21.07

Mathew C.; Weiss R. G.; Giese C.; Lin C.-W.; Losfeld M.-E.; Glockshuber R.; Riniker S.; Aebi M.
external page Glycan-Protein Interactions Determine Kinetics of N-Glycan Remodeling
RSC Chem. Biol. 2021, 2, 917 (open access).
Preprint external page bioRxiv 10.1101/2020.12.01.406371 (2020)

21.06

Egli J.; Esposito C.; Müri M.; Riniker S.; Wennemers H.
external page Influence of Lipidation on the Folding and Stability of Collagen Triple Helices – An Experimental and Theoretical Study
J. Am. Chem. Soc. 2021, 143, 5937.

21.05

Böselt L.; Thürlemann M.; Riniker S.
external page Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems
J. Chem. Theory Comput. 2021, 17, 2641 (open access).
Preprint external page arXiv:2010.11610 (2020)

21.04

Comeau C.; Ries B.; Stadelmann T.; Tremblay J.; Poulet S.; Froehlich U.; Côté J.; Boudreault P.-L.; Derbali R. M.; Sarret P.; Grandbois M.; Leclair G.; Riniker S.; Marsault E.
external page Modulation of the Passive Permeability of Semi-Peptidic Macrocycles. N- and C-Methylations Fine-tune Conformation and Properties
J. Med. Chem. 2021, 64, 5365.

21.03

Ries B.; Linker S.; Hahn D.; König G.; Riniker S.
external page Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations
J. Chem. Inf. Model. 2021, 61, 560.

21.02

Weiss R. G.; Ries B.; Wang S.; Riniker S.
external page Volume-Scaled Common Nearest Neighbor Clustering Algorithm with Free-Energy Hierarchy
J. Chem. Phys. 2021, 154, 084106 (open access).

21.01

Awale M.; Hert J.; Guasch L.; Riniker S.; Kramer C.
external page The Playbooks of Medicinal Chemistry Design Moves
J. Chem. Inf. Model. 2021, 61, 729.

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2020

20.16

Linker S. M.; Weiss R. G.; Riniker S.
external page Connecting Dynamic Reweighting Algorithms: Derivation of the Dynamic Reweighting Family Tree
J. Chem. Phys. 2020, 153, 234106 (open access).

20.15

Armacost K. A.; Riniker S.; Cournia Z.
external page Exploring Novel Directions in Free Energy Calculations (Editorial)
J. Chem. Inf. Model. 2020, 60, 5283 (open access).

20.14

van Gunsteren W. F.; Daura X.; Fuchs P. F. J.; Hansen N.; Horta B. A. C.; Hünenberger P. H.; Mark A. E.; Pechlaner M.; Riniker S.; Oostenbrink C.
external page On the Effect of the Various Assumptions and Approximations used in Molecular Simulation on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues
ChemPhysChem 2021, 22, 264.

20.13

Oliveira M. P.; Andrey M.; Rieder S. R.; Kern L.; Hahn D. F.; Riniker S.; Horta B. A. C.; Hünenberger P. H.
external page Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes
J. Chem. Theory Comput. 2020, 16, 7525 (open access).

20.12

Wang S.; Riniker S.
external page Machine Learning in the Area of Molecular Dynamics Simulations
in the book "Artificial Intelligence in Drug Discovery", The Royal Society of Chemistry, 2021, Chapter 9, pp. 184-214.

20.11

Kubincová A.; Riniker S.; Hünenberger P. H.
external page Reaction-field Electrostatics in Molecular Dynamics Simulations: Development of a Conservative Scheme Compatible with an Atomic Cutoff
Phys. Chem. Chem. Phys. 2020, 22, 26419 (open access).

20.10

König G.; Glaser N.; Schroeder B.; Kubincová A.; Hünenberger P. H.; Riniker S.
external page An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling
J. Chem. Inf. Model. 2020, 60, 5407.

20.09

Stadelmann T.; Subramanian G.; Menon S.; Townsend C.; Lokey S.; Ebert M.-O.; Riniker S.
external page Connecting the Conformational Behavior of Cyclic Octadepsipeptides With Their Ionophoric Property and Membrane Permeability
Org. Biomol. Chem. 2020, 18, 7110 (open access).

20.08

Gebhardt J.; Kiesel M.; Riniker S.; Hansen N.
external page Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients
J. Chem. Inf. Model. 2020, 60, 5319.

20.07

Esposito C.; Wang S.; Lange U. E. W.; Oellien F.; Riniker S.
external page Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates
J. Chem. Inf. Model. 2020, 60, 4730.

20.06

König G.; Riniker S.
external page On the Faithfulness of Molecular Mechanics Representations of Proteins Towards Quantum-mechanical Energy Surfaces
Interface Focus 2020, 10, 20190121.

20.05

Böselt L.; Doetzer R.; Steiner S.; Stritzinger M.; Salzmann S.; Riniker S.
external page Determining the Regio- and Relative Stereochemistry of Small and Drug-like Molecules Using an Alignment Algorithm for Infrared Spectra
Anal. Chem. 2020, 92, 9124.

20.04

Awale M.; Riniker S.; Kramer C.
external page Matched Molecular Series Analysis for ADME Property Prediction
J. Chem. Inf. Model. 2020, 60, 2903.

20.03

Liu J.; Hürlimann V.; Emter R.; Natsch A.; Esposito C.; Linker S. M.; Zou Y.; Zhou Q.; Wang Q.; Riniker S.; Kraft P.
external page A New Family of Rigid Dienone Musks Challenges the Perceptive Range of the Human Olfactory Receptor OR5AN1
Synlett 2020, 31, 972.
external page Synlett Best Paper Award 2020

20.02

Wang S.; Witek J.; Landrum G. A.; Riniker S.
external page Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences
J. Chem. Inf. Model. 2020, 60, 2044 (open access).

20.01

Armacost K. A.; Riniker S.; Cournia Z.
external page Novel Directions in Free Energy Methods and Applications (Editorial)
J. Chem. Inf. Model. 2020, 60, 1.

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2019

19.08

Wang S.; Riniker S.
external page Use of Molecular Dynamics Fingerprints (MDFPs) in SAMPL6 Octanol-Water logP Blind Challenge
J. Comput.-Aided Mol. Des. 2019, 34, 393.
Author's accepted manuscript (open access).

19.07

Riniker S.; Wang S.; Bleiziffer P.; Böselt L.; Esposito C.
external page Machine Learning With and For Molecular Dynamics Simulations
CHIMIA 2019, 73, 1024.

19.06

Smith A. A.; Ernst M.; Riniker S.; Meier B. H.
external page Localized and Collective Motions in HET-s(218-289) Fibrils From Combined NMR Relaxation and MD Simulation
Angew. Chem. Int Ed. 2019, 58, 9383.

19.05

Renevey A.; Riniker S.
external page Benchmarking Hybrid Atomistic/Coarse-Grained Schemes for Proteins with an Atomistic Water Layer
J. Phys. Chem. B 2019, 123, 3033.

19.04

Böselt L.; Sidler D.; Kittelmann T.; Stohner J.; Zindel D.; Wagner T.; Riniker S.
external page Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism (VCD) Spectra Alignment Algorithm
J. Chem. Inf. Model. 2019, 59, 1826.

19.03

Sidler D.; Bleiziffer P.; Riniker S.
external page Beyond Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutions
J. Chem. Theory Comput. 2019, 15, 2492.

19.02

Sidler D.; Riniker S.
external page Fast Nosé-Hoover Thermostat: Molecular Dynamics in Quasi-thermodynamic Equilibrium
Phys. Chem. Chem. Phys. 2019, 21, 6059 (open access).

19.01

Riniker S.
external page Towards the Elucidation of the Mechanism for Passive Membrane Permeability of Cyclic Peptides
Future Med. Chem. 2019, 11, 637.

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2018

18.08

Witek J.; Wang S.; Schroeder B.; Lingwood R.; Dounas A.; Roth H.-J.; Fouché M.; Blatter M.; Lemke O.; Keller B.; Riniker S.
external page Rationalization of the membrane permeability differences in a series of analogue cyclic decapeptides
J. Chem. Inf. Model. 2018, 59, 294.

18.07

Riniker S.
external page Research strategies in computational chemistry
Infozine 2018, S2, 24-25. PDF

18.06

Sidler D.; Lehner M.; Frasch S.; Cristófol-Clough M.; Riniker S.
external page Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations
F1000Research 2018, 7, 1745 (open access)

18.05

Volkamer A.; Riniker S.
external page Transition from Academia to Industry and Back
J. Chem. Inf. Model. 2018, 58, 1469-1472.

18.04

Song H.; van der Velden N. S.; Shiran S. L.; Bleiziffer P.; Zach C.; Sieber R.; Imani A. S.; Krausbeck F.; Aebi M.; Freeman M. F.; Riniker S.; Künzler M.; Naismith J. H.
external page A Molecular Mechanism for the Enzymatic Methylation of Nitrogen Atoms within Peptide Bonds
Science Adv. 2018, 4, eaat2720 (open access).

18.03

Sidler D.; Frasch S.; Christòfol Clough M.; Riniker S.
external page Anisotropic Reaction Field Correction for Long-Range Electrostatic Interactions in Molecular Dynamics Simulations
J. Chem. Phys. 2018, 148, 234105.

18.02

Riniker S.
external page Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview
J. Chem. Inf. Model. 2018, 58, 565.

18.01

Bleiziffer P.; Schaller K.; Riniker S.
external page Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations
J. Chem. Inf. Model. 2018, 58, 579 (open access).
external page Erratum: J. Chem. Inf. Model. 2023.

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2017

17.07

Witek J.; Mühlbauer M.; Keller B. G.; Blatter M.; Meissner A.; Wagner T.; Riniker S.
external page Interconversion Rates Between Conformational States as Rationale for the Membrane Permeability of Cyclosporines
ChemPhysChem 2017, 18, 3309.

17.06

Hentzen N. B.; Smeenk L. E. J.; Witek J.; Riniker S.; Wennemers H.
external page Cross-Linked Collagen Triple Helices by Oxime Ligation
J. Am. Chem. Soc. 2017, 139, 12815.

17.05

Riniker S.; Landrum G. A.; Montanari F.; Villalba S. D.; Maier J.; Jansen J. M.; Walters W. P.; Shelat A. A.
external page Virtual-screening workflow tutorials and prospective results from the Teach-Discover-Treat competition 2014 against malaria
F1000Research 2017, 6, 1136 (open access).

17.04

van Gunsteren W. F.; Daura X.; Hansen N.; Mark A.; Oostenbrink C.; Riniker S.; Smith L.
external page Validation of Molecular Simulation: An Overview of Issues
Angew. Chem. Int. Ed. 2018, 57, 884.

17.03

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

17.02

Riniker S.
external page Molecular dynamics fingerprints (MDFP): Machine-learning from MD data to predict free-energy differences
J. Chem. Inf. Model. 2017, 57, 726.

17.01

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

2016

16.05

Sidler D.; Schwaninger A.; Riniker S.
external page 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.

16.04

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

16.03

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

16.02

Witek J.;  Keller B. G.; Blatter M.; Meissner A.; Wagner T.; Riniker S.
external page Kinetic models of cyclosporin A in polar and apolar environment reveal multiple congruent states
J. Chem. Inf. Model. 2016, 56, 1547.
external page Erratum: J. Chem. Inf. Model. 2017, 57, 2393.  

16.01

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

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2015

15.05

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

15.04

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

15.03

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

15.02

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

15.01

Eichenberger A.; van Gunsteren W. F.; Riniker S.; von Ziegler L.; Hansen N.
external page 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.

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2014

14.04

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

14.03

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

14.02

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

14.01

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

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2013

13.05

Riniker S.; Fechner N., Landrum G. A.
external page 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.

13.04

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

13.03

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

13.02

Lin Z.; Riniker S.; van Gunsteren W. F.
external page 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.

13.01

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

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2012

12.10

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

12.09

Riniker S.; Eichenberger A. P.; van Gunsteren W. F.
external page 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.

12.08

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

12.07

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

12.06

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

12.05

Horta B. A. C.; Lin Z.; Huang W.; Riniker S.; van Gunsteren W. F.; Hünenberger P. H.
external page 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.

12.04

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

12.03

Hansen N.; Dolenc J.; Knecht M.; Riniker S.; van Gunsteren W. F.
external page 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.

12.02

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

12.01

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.
external page New functionalities in the GROMOS biomolecular simulation software
J. Comput. Chem. 2012, 33, 340.

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2011

11.07

Lin Z.; Liu H.; Riniker S.; van Gunsteren W. F.
external page 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.

11.06

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

11.05

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

11.04

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

11.03

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

11.02

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

11.01

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

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2010

10.01

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

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