Journal Articles
Preprints
Katzberger P.; Riniker S.
General Graph Neural Network Based Implicit Solvation Model for Organic Molecules in Water
Preprint: external pageChemRxiv 10.26434/chemrxiv-2024-z8725call_made (2024).
Champion C.; Hünenberger P. H.; Riniker S.
Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations
Preprint: external pageChemRxiv 10.26434/chemrxiv-2024-qkw53call_made (2024).
2024
24.04
Champion C.; Lehner M.; Smith A. A.; Ferrage F.; Bolik-Coulon N.; Riniker S.
external pageUnraveling Motion in Proteins by Combining NMR Relaxometry and Molecular Dynamics Simulations: A Case Study on Ubiquitincall_made
J. Chem. Phys., 2024, 160, 104105 (open access).
Preprint: external pageChemRxiv 10.26434/chemrxiv-2023-335gpcall_made (2023).
24.03
Landrum G. A.; Riniker S.
external pageCombining IC50 or Ki Values From Different Sources is a Source of Significant Noisecall_made
J. Chem. Inf. Model., 2024, 64, 1560 (open access).
Preprint: external pageChemRxiv 10.26434/chemrxiv-2024-2smhkcall_made (2024).
24.02
Isert C.; Atz K.; Riniker S.; Schneider G.
external pageExploring Protein-Ligand Binding Affinity Prediction with Electron Density-Based Geometric Deep Learningcall_made
RSC Adv., 2024, 14, 4492 (open access).
Preprint: external pageChemRxiv 10.26434/chemrxiv-2023-585vfcall_made (2023).
24.01
Cotter E.; Pultar F.; Riniker S.; Altmann K.-H.
external pageExperimental and Theoretical Studies on the Reactions of Aliphatic Imines with Isocyanatescall_made
Chem. Eur. J., 2024, 30, e202304272 (open access).
Preprint: external pageChemRxiv 10.26434/chemrxiv-2023-twjprcall_made (2023).
2023
23.13
Landrum G. A.; Beckers M.; Lanini J.; Schneider N.; Stiefl N.; Riniker S.
external pageSIMPD: an Algorithm for Generating Simulated Time Splits for Validating Machine Learning Approachescall_made
J. Cheminf., 2023, 15, 119 (open access).
Preprint: external pageChemRxiv 10.26434/chemrxiv-2023-x9pjfcall_made (2023).
23.12
Kubincová A.; Riniker S., Hünenberger P. H.
external pageSimulation of Aqueous Solutes Using the Adaptive Solvent-Scaling (AdSoS) Schemecall_made
J. Chem. Phys., 2023, 159, 234102 (open access).
Preprint: external pageChemRxiv 10.26434/chemrxiv-2023-f1fqxcall_made (2023).
23.11
Thürlemann M.; Riniker S.
external pageHybrid Classical/Machine-Learning Force Fields for the Accurate Description of Molecular Condensed-Phase Systemscall_made
Chem. Sci., 2023, 14, 12661 (open access).
Preprint: external pagearXiv:2308.08984call_made (2023).
23.10
Champion C.; Gall R.; Ries B.; Rieder S. R.; Barros E. P.; Riniker S.
external pageAccelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinasescall_made
J. Chem. Inf. Model., 2023, 63, 7133.
Preprint: external pageChemRxiv 10.26434/chemrxiv-2023-kfh2scall_made (2023).
23.09
Lehner M. T.; Katzberger P.; Maeder N.; Schiebroek C. C. G.; Teetz J.; Landrum G. A.; Riniker S.
external pageDASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignmentcall_made
J. Chem. Inf. Model., 2023, 63, 6014 (open access).
Preprint: external pagearXiv:2305.15981call_made (2023).
23.08
Metternich J. B.; Katzberger P.; Kamenik A. S.; Tiwari P.; Wu R.; Riniker S.; Zenobi R.
external pageInfluence of the Fluorophore Mobility on Distance Measurements by Gas Phase FRETcall_made
J. Phys. Chem. A, 2023, 127, 5620.
Preprint: external pageChemRxiv 10.26434/chemrxiv-2023-fcnwgcall_made (2023).
23.07
Thürlemann M.; Riniker S.
external pageEnergy-Based Clustering: Fast and Robust Clustering of Data with Known Likelihood Functionscall_made
J. Chem. Phys., 2023, 159, 024105 (open access).
Editor's pick. Journal cover of issue external pageVolume 159, Issue 2call_made.
Preprint: external pagearXiv:2303.01104call_made (2023).
23.06
Katzberger P.; Riniker S.
external pageImplicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulationscall_made
J. Chem. Phys., 2023, 158, 204101 (open access).
Preprint: external pagearXiv:2302.09321call_made (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 pageDetermining the Gas-Phase Structures of alpha-Helical Peptides: Insights from Shape, Intramolecular Distance, and Microsolvation Assayscall_made
Nature Commun., 2023, 14, 2913 (open access).
23.04
Barros E. P.; Ries B.; Champion C.; Rieder S. R.; Riniker S.
external pageAccounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavitiescall_made
J. Chem. Inf. Model., 2023, 63, 1794 (open access).
Preprint: external pageChemRxiv:10.26434/chemrxiv-2022-sx77xcall_made (2022).
23.03
Thürlemann M.; Riniker S.
external pageAnisotropic Message Passing: Graph Neural Networks with Directional and Long-Range Interactionscall_made
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 pageLessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranescall_made
J. Med. Chem., 2023, 66, 2773 (open access).
Preprint: external pageChemRxiv:10.26434/chemrxiv-2022-9b47dcall_made (2022).
23.01
Volkamer A.; Riniker S.; Nittinger E.; Lanini J.; Grisoni F.; Evertsson E.; Rodríguez-Pérez R.; Schneider N.
external pageMachine Learning for Small Molecule Drug Discovery in Academia and Industrycall_made
Artif. Intel. Life Sci. 2023, 3, 100056 (open access).
2022
22.16
Rieder S. R.; Oliveira M. P.; Riniker S.; Hünenberger P. H.
external pageDevelopment of an Open-Source Software for Isomer Enumerationcall_made
J. Cheminf. 2023, 15, 10 (open access).
22.15
Thürlemann M.; Böselt L.; Riniker S.
external pageRegularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactionscall_made
J. Chem. Theory Comput. 2023, 19, 562 (open access).
Preprint: external pagearXiv:2206.00355call_made (2022).
22.14
Böselt L.; Aerts R.; Herrebout W.; Riniker S.
external pageImproving the IR Spectra Alignment Algorithm with Spectra Deconvolution and Combination with Raman or VCD Spectroscopycall_made
Phys. Chem. Chem. Phys. 2023, 25, 2063 (open access).
22.13
Fiala T.; Barros E. P.; Heeb R.; Riniker S.; Wennemers H.
external pagePredicting Collagen Triple Helix Stability Through Additive Effects of Terminal Residues and Capscall_made
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 pageFrame Shifts Affect the Stability of Collagen Triple Helicescall_made
J. Am. Chem. Soc. 2022, 144, 18642.
22.11
Stadelmann T.; Balmer C.; Riniker S.; Ebert M.-C.
external pageImpact of Solvent Interactions on 1H and 13C Chemical Shifts Investigated Using DFT and a Reference Dataset Recorded in CDCl3 and CCl4call_made
Phys. Chem. Chem. Phys. 2022, 24, 23551 (open access).
22.10
Hofstetter A.; Böselt L.; Riniker S.
external pageGraph Convolutional Neural Networks for (QM)ML/MM Molecular Dynamics Simulationscall_made
Phys. Chem. Chem. Phys. 2022, 24, 22497 (open access).
Preprint: external pagearXiv:2206.14422call_made (2022).
22.09
Rieder S. R.; Ries B.; Kubincová A.; Champion C.; Barros E. P.; Hünenberger P. H.; Riniker S.
external pageLeveraging the Sampling Efficiency of RE-EDS in OpenMM Using a Shifted Reaction-Field With an Atom-Based Cutoffcall_made
J. Chem. Phys. 2022, 157, 104117 (open access).
22.08
Stenström S.; Champion C.; Lehner M.; Bouvignies G.; Riniker S.; Ferrage F.
external pageHow Does it Really Move? Recent Progress in the Investigation of Protein Nanosecond Dynamics by NMR and Simulationcall_made
Curr. Opin. Struct. Biol. 2022, 77, 102459 (open access).
22.07
Kamenik A. S.; Linker S. M.; Riniker S.
external pageMatching Simulations and Experiments of Conformationally Flexible Cyclic Peptides: Steps toward a Holistic View of Passive Membrane Permeabilitycall_made
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 pageReplica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Moleculescall_made
J. Chem. Inf. Model. 2022, 62, 3043 (open access).
Preprint external pagearXiv:2204.01396call_made (2022)
22.05
Rieder S. R.; Ries B.; Champion C.; Barros E. P.; Hünenberger P. H.; Riniker S.
external pageReplica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOScall_made
CHIMIA 2022, 76, 327 (open access).
22.04
Ries B.; Rieder S.; Rhiner C.; Hünenberger P. H.; Riniker S.
external pageRestraintMaker: A Graph-Based Approach to Select Distance Restraints in Free-Energy Calculations with Dual Topologycall_made
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 pagePolar/Apolar Interfaces Modulate the Conformational Behavior of Cyclic Peptides with Impact on Their Passive Membrane Permeabilitycall_made
RSC Advances 2022, 12, 5782 (open access).
22.02
Thürlemann M.; Böselt L.; Riniker S.
external pageLearning Atomic Multipoles: Prediction of the Electrostatic Potential with Equivariant Graph Neural Networkscall_made
J. Chem. Theory Comput. 2022, 18, 1701 (open access).
Preprint external pagearXiv:2110.05417call_made (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 pageIncorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometrycall_made
J. Chem. Inf. Model. 2022, 62, 472 (open access).
2021
21.17
Kamenik A. S.; Linker S. M.; Riniker S.
external pageEnhanced Sampling Without Borders: On Global Biasing Functions and How to Reweight Themcall_made
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 pageRelative Free-Energy Calculations for Scaffold Hopping-Type Transformations with an Automated RE-EDS Sampling Procedurecall_made
J. Comput.-Aided Mol. Des. 2022, 36, 117 (open access).
21.15
König G.; Ries B.; Hünenberger P. H.; Riniker S.
external pageEfficient Alchemical Intermediate States in Free Energy Calculations Using λ-EDScall_made
J. Chem. Theory Comput. 2021, 17, 5805.
21.14
Barros E. P.; Ries B.; Böselt L.; Champion C.; Riniker S.
external pageRecent Developments in Multiscale Free Energy Simulationscall_made
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 pageEffect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptidescall_made
J. Med. Chem. 2021, 64, 12761 (open access).
21.12
Weiss R. G.; Losfeld M.-E.; Aebi M.; Riniker S.
external pageN-Glycosylation Enhances Conformational Flexibility of Protein Disulfide Isomerase Revealed by Microsecond Molecular Dynamics and Markov State Modelingcall_made
J. Phys. Chem. B 2021, 125, 9467.
21.11
Kubincová A.; Riniker S.; Hünenberger P. H.
external pageSolvent Scaling as an Alternative to Coarse-graining in Adaptive-resolution Simulations: The Adaptive Solvent-Scaling (AdSoS) Schemecall_made
J. Chem. Phys. 2021, 155, 094107 (open access).
21.10
Linker S. M.; Wang S.; Ries B.; Stadelmann T.; Riniker S.
external pagePassing the Barrier – How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptidescall_made
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 pageMutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluationcall_made
J. Am. Chem. Soc. 2021, 143, 10389.
21.08
Esposito C.; Landrum G. A.; Schneider N.; Stiefl N.; Riniker S.
external pageGHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learningcall_made
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 pageGlycan-Protein Interactions Determine Kinetics of N-Glycan Remodelingcall_made
RSC Chem. Biol. 2021, 2, 917 (open access).
Preprint external pagebioRxiv 10.1101/2020.12.01.406371call_made (2020)
21.06
Egli J.; Esposito C.; Müri M.; Riniker S.; Wennemers H.
external pageInfluence of Lipidation on the Folding and Stability of Collagen Triple Helices – An Experimental and Theoretical Studycall_made
J. Am. Chem. Soc. 2021, 143, 5937.
21.05
Böselt L.; Thürlemann M.; Riniker S.
external pageMachine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systemscall_made
J. Chem. Theory Comput. 2021, 17, 2641 (open access).
Preprint external pagearXiv:2010.11610call_made (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 pageModulation of the Passive Permeability of Semi-Peptidic Macrocycles. N- and C-Methylations Fine-tune Conformation and Propertiescall_made
J. Med. Chem. 2021, 64, 5365.
21.03
Ries B.; Linker S.; Hahn D.; König G.; Riniker S.
external pageEnsembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulationscall_made
J. Chem. Inf. Model. 2021, 61, 560.
21.02
Weiss R. G.; Ries B.; Wang S.; Riniker S.
external pageVolume-Scaled Common Nearest Neighbor Clustering Algorithm with Free-Energy Hierarchycall_made
J. Chem. Phys. 2021, 154, 084106 (open access).
21.01
Awale M.; Hert J.; Guasch L.; Riniker S.; Kramer C.
external pageThe Playbooks of Medicinal Chemistry Design Movescall_made
J. Chem. Inf. Model. 2021, 61, 729.
2020
20.16
Linker S. M.; Weiss R. G.; Riniker S.
external pageConnecting Dynamic Reweighting Algorithms: Derivation of the Dynamic Reweighting Family Treecall_made
J. Chem. Phys. 2020, 153, 234106 (open access).
20.15
Armacost K. A.; Riniker S.; Cournia Z.
external pageExploring Novel Directions in Free Energy Calculations (Editorial)call_made
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 pageOn the Effect of the Various Assumptions and Approximations used in Molecular Simulation on the Properties of Bio-Molecular Systems: Overview and Perspective on Issuescall_made
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 pageSystematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanescall_made
J. Chem. Theory Comput. 2020, 16, 7525 (open access).
20.12
Wang S.; Riniker S.
external pageMachine Learning in the Area of Molecular Dynamics Simulationscall_made
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 pageReaction-field Electrostatics in Molecular Dynamics Simulations: Development of a Conservative Scheme Compatible with an Atomic Cutoffcall_made
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 pageAn Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Samplingcall_made
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 pageConnecting the Conformational Behavior of Cyclic Octadepsipeptides With Their Ionophoric Property and Membrane Permeabilitycall_made
Org. Biomol. Chem. 2020, 18, 7110 (open access).
20.08
Gebhardt J.; Kiesel M.; Riniker S.; Hansen N.
external pageCombining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficientscall_made
J. Chem. Inf. Model. 2020, 60, 5319.
20.07
Esposito C.; Wang S.; Lange U. E. W.; Oellien F.; Riniker S.
external pageCombining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substratescall_made
J. Chem. Inf. Model. 2020, 60, 4730.
20.06
König G.; Riniker S.
external pageOn the Faithfulness of Molecular Mechanics Representations of Proteins Towards Quantum-mechanical Energy Surfacescall_made
Interface Focus 2020, 10, 20190121.
20.05
Böselt L.; Doetzer R.; Steiner S.; Stritzinger M.; Salzmann S.; Riniker S.
external pageDetermining the Regio- and Relative Stereochemistry of Small and Drug-like Molecules Using an Alignment Algorithm for Infrared Spectracall_made
Anal. Chem. 2020, 92, 9124.
20.04
Awale M.; Riniker S.; Kramer C.
external pageMatched Molecular Series Analysis for ADME Property Predictioncall_made
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 pageA New Family of Rigid Dienone Musks Challenges the Perceptive Range of the Human Olfactory Receptor OR5AN1call_made
Synlett 2020, 31, 972.
external pageSynlett Best Paper Award 2020call_made
20.02
Wang S.; Witek J.; Landrum G. A.; Riniker S.
external pageImproving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferencescall_made
J. Chem. Inf. Model. 2020, 60, 2044 (open access).
20.01
Armacost K. A.; Riniker S.; Cournia Z.
external pageNovel Directions in Free Energy Methods and Applications (Editorial)call_made
J. Chem. Inf. Model. 2020, 60, 1.
2019
19.08
Wang S.; Riniker S.
external pageUse of Molecular Dynamics Fingerprints (MDFPs) in SAMPL6 Octanol-Water logP Blind Challengecall_made
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 pageMachine Learning With and For Molecular Dynamics Simulationscall_made
CHIMIA 2019, 73, 1024.
19.06
Smith A. A.; Ernst M.; Riniker S.; Meier B. H.
external pageLocalized and Collective Motions in HET-s(218-289) Fibrils From Combined NMR Relaxation and MD Simulationcall_made
Angew. Chem. Int Ed. 2019, 58, 9383.
19.05
Renevey A.; Riniker S.
external pageBenchmarking Hybrid Atomistic/Coarse-Grained Schemes for Proteins with an Atomistic Water Layercall_made
J. Phys. Chem. B 2019, 123, 3033.
19.04
Böselt L.; Sidler D.; Kittelmann T.; Stohner J.; Zindel D.; Wagner T.; Riniker S.
external pageDetermination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism (VCD) Spectra Alignment Algorithmcall_made
J. Chem. Inf. Model. 2019, 59, 1826.
19.03
Sidler D.; Bleiziffer P.; Riniker S.
external pageBeyond Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutionscall_made
J. Chem. Theory Comput. 2019, 15, 2492.
19.02
Sidler D.; Riniker S.
external pageFast Nosé-Hoover Thermostat: Molecular Dynamics in Quasi-thermodynamic Equilibriumcall_made
Phys. Chem. Chem. Phys. 2019, 21, 6059 (open access).
19.01
Riniker S.
external pageTowards the Elucidation of the Mechanism for Passive Membrane Permeability of Cyclic Peptidescall_made
Future Med. Chem. 2019, 11, 637.
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 pageRationalization of the membrane permeability differences in a series of analogue cyclic decapeptidescall_made
J. Chem. Inf. Model. 2018, 59, 294.
18.07
Riniker S.
external pageResearch strategies in computational chemistrycall_made
Infozine 2018, S2, 24-25. PDF
18.06
Sidler D.; Lehner M.; Frasch S.; Cristófol-Clough M.; Riniker S.
external pageDensity artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulationscall_made
F1000Research 2018, 7, 1745 (open access)
18.05
Volkamer A.; Riniker S.
external pageTransition from Academia to Industry and Backcall_made
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 pageA Molecular Mechanism for the Enzymatic Methylation of Nitrogen Atoms within Peptide Bondscall_made
Science Adv. 2018, 4, eaat2720 (open access).
18.03
Sidler D.; Frasch S.; Christòfol Clough M.; Riniker S.
external pageAnisotropic Reaction Field Correction for Long-Range Electrostatic Interactions in Molecular Dynamics Simulationscall_made
J. Chem. Phys. 2018, 148, 234105.
18.02
Riniker S.
external pageFixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overviewcall_made
J. Chem. Inf. Model. 2018, 58, 565.
18.01
Bleiziffer P.; Schaller K.; Riniker S.
external pageMachine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculationscall_made
J. Chem. Inf. Model. 2018, 58, 579 (open access).
external pageErratumcall_made: J. Chem. Inf. Model. 2023.
2017
17.07
Witek J.; Mühlbauer M.; Keller B. G.; Blatter M.; Meissner A.; Wagner T.; Riniker S.
external pageInterconversion Rates Between Conformational States as Rationale for the Membrane Permeability of Cyclosporinescall_made
ChemPhysChem 2017, 18, 3309.
17.06
Hentzen N. B.; Smeenk L. E. J.; Witek J.; Riniker S.; Wennemers H.
external pageCross-Linked Collagen Triple Helices by Oxime Ligationcall_made
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 pageVirtual-screening workflow tutorials and prospective results from the Teach-Discover-Treat competition 2014 against malariacall_made
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 pageValidation of Molecular Simulation: An Overview of Issuescall_made
Angew. Chem. Int. Ed. 2018, 57, 884.
17.03
Sidler D.; Christófol-Clough M.; Riniker S.
external pageEfficient Round-Trip Time Optimisation for Replica-Exchange Enveloping Distribution Sampling (RE-EDS)call_made
J. Chem. Theory Comput. 2017, 13, 3020.
17.02
Riniker S.
external pageMolecular dynamics fingerprints (MDFP): Machine-learning from MD data to predict free-energy differencescall_made
J. Chem. Inf. Model. 2017, 57, 726.
17.01
Renevey A.; Riniker S.
external pageImproved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactionscall_made
J. Chem. Phys. 2017, 146, 124131.
2016
16.05
Sidler D.; Schwaninger A.; Riniker S.
external pageReplica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulationcall_made
J. Chem. Phys. 2016, 145, 154114.
16.04
Renevey A.; Riniker S.
external pageThe importance of N-methylations for the stability of β6.3-helical conformation of polytheonamide Bcall_made
Eur. Biophys. J. 2016, 46, 363.
16.03
Fuchs S. W.; Lackner G.; Morinaka B. I.; Riniker S.; Piel J.
external pageA lanthipeptide-like motif guides peptide epimerization by radical SAM epimerases - implications for RiPP evolutioncall_made
Angew. Chem. Int. Ed. 2016, 55, 12330.
16.02
Witek J.; Keller B. G.; Blatter M.; Meissner A.; Wagner T.; Riniker S.
external pageKinetic models of cyclosporin A in polar and apolar environment reveal multiple congruent statescall_made
J. Chem. Inf. Model. 2016, 56, 1547.
external pageErratumcall_made: 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 pageGROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter setcall_made
J. Chem. Theory Comput. 2016, 12, 3825.
2015
15.05
Riniker S.; Landrum G. A.
external pageBetter informed distance geometry: using what we know to improve conformation generationcall_made
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 pageA supra-atomic coarse-grained GROMOS force field for aliphatic hydrocarbons in the liquid phasecall_made
J. Chem. Theory Comput. 2015, 11, 2925.
15.02
Mortier J.; Rakers C.; Bermudez M.; Murgueitio M. S.; Riniker S.; Wolber G.
external pageThe impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexescall_made
Drug Discov. Today 2015, 20, 686.
15.01
Eichenberger A.; van Gunsteren W. F.; Riniker S.; von Ziegler L.; Hansen N.
external pageThe key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured statescall_made
BBA General Subjects 2015, 1850, 983.
2014
14.04
Don C.; Riniker S.
external pageScents and Sense: In silico perspectives on olfactory receptorscall_made
J. Comput. Chem. 2014, 35, 2279.
14.03
Riniker S.
external pageCrossing the boundaries within computational chemistry: from molecular dynamis to cheminformatics and backcall_made
CHIMIA 2014, 68, 620.
14.02
Huang W.; Riniker S.; van Gunsteren W. F.
external pageRapid sampling of folding equilibria of β‐peptides in methanol using a supramolecular solvent modelcall_made
J. Chem. Theory Comput. 2014, 10, 2213.
14.01
Riniker S.; Wang Y.; Jenkins J. L.; Landrum G. A.
external pageUsing information from historical high-throughput screens to predict active compoundscall_made
J. Chem. Inf. Model. 2014, 54, 1880.
2013
13.05
Riniker S.; Fechner N., Landrum G. A.
external pageHeterogeneous classifier fusion for ligand-based virtual screening: or, how decision making by committee can be a good thingcall_made
J. Chem. Inf. Model. 2013, 53, 2829.
13.04
Riniker S., Landrum G. A.
external pageSimilarity maps - a visualization strategy for molecular fingerprints and machine-learning methodscall_made
J. Cheminf. 2013, 5, 43.
13.03
Riniker S.; Landrum G. A.
external pageOpen-source platform to benchmark fingerprints for ligand-based virtual screeningcall_made
J. Cheminf. 2013, 5, 26.
13.02
Lin Z.; Riniker S.; van Gunsteren W. F.
external pageFree enthalpy differences between α-, π-, and 310-helices of an atomic level fine-grained alanine deca-peptide solvated in supra-molecular coarse-grained watercall_made
J. Chem. Theory Comput. 2013, 9, 1328.
13.01
Meier K.; Choutko A.; Dolenc J.; Eichenberger A.; Riniker S.; van Gunsteren W. F.
external pageMulti-resolution simulation of biomolecular systems: a review of methodological issuescall_made
Angew. Chem. Int. Ed. 2013, 52, 2820.
2012
12.10
Riniker S.; Barandun L. J.; Diederich F.; Krämer O.; Steffen A.; van Gunsteren W. F.
external pageFree enthalpies of replacing water molecules in protein binding pocketscall_made
J. Comput. Aided Mol. Des. 2012, 26, 1293.
12.09
Riniker S.; Eichenberger A. P.; van Gunsteren W. F.
external pageStructural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained watercall_made
J. Phys. Chem. B 2012, 116, 8873.
12.08
Riniker S.; Eichenberger A. P.; van Gunsteren W. F.
external pageSolvating atomic level fine-grained proteins in supra-molecular coarse-grained water for molecular dynamics simulationscall_made
Eur. Biophys. J. 2012, 41, 647.
12.07
Riniker S.; van Gunsteren W. F.
external pageMixing coarse-grained and fine-grained water in molecular dynamics simulations of a single systemcall_made
J. Chem. Phys. 2012, 137, 044120.
external pageErratumcall_made: J. Chem. Phys. 2017, 146, 129901.
12.06
Riniker S.; Allison J. R.; van Gunsteren W. F.
external pageOn developing coarse-grained models for biomolecular simulation: a reviewcall_made
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 pageReoptimized 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 methanolcall_made
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 pageTemperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: a molecular dynamics simulation studycall_made
ChemPhysChem 2012, 13, 1182.
12.03
Hansen N.; Dolenc J.; Knecht M.; Riniker S.; van Gunsteren W. F.
external pageAssessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solutioncall_made
J. Comput. Chem. 2012, 33, 640.
12.02
Allison J.; Riniker S.; van Gunsteren W. F.
external pageCoarse-grained models for the solvents dimethyl sulfoxide, chloroform and methanolcall_made
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 pageNew functionalities in the GROMOS biomolecular simulation softwarecall_made
J. Comput. Chem. 2012, 33, 340.
2011
11.07
Lin Z.; Liu H.; Riniker S.; van Gunsteren W. F.
external pageOn the use of enveloping distribution sampling (EDS) to compute free enthalpy differences between different conformational states of molecules: application to 310-, α- and π-helicescall_made
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 pageCalculation of relative free energies for ligand-protein binding, solvation and conformational transitions using the GROMOS softwarecall_made
J. Phys. Chem. B 2011, 115, 13570.
11.05
Dolenc J.; Riniker S.; Gaspari R.; Daura X.; van Gunsteren W. F.
external pageFree energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinitiescall_made
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 pageComparison of enveloping distribution sampling and thermodynamic integration to calculate relative binding free energies of phenylethanolamine N-methyltransferasecall_made
J. Chem. Phys. 2011, 135, 024105.
11.03
Riniker S.; van Gunsteren W. F.
external pageA simple, efficient polarisable coarse-grained water model for molecular dynamics simulationscall_made
J. Chem. Phys. 2011, 134, 084110.
11.02
Riniker S.; Kunz A. E.; van Gunsteren W. F.
external pageOn the calculation of the dielectric permittivity and relaxation of molecular models in the liquid phasecall_made
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 pageDefinition and testing of the GROMOS force field versions: 54A7 and 54B7call_made
Eur. Biophys. J. 2011, 40, 843.
2010
10.01
Riniker S.; Daura X.; van Gunsteren W. F.
external pageα-Cyclodextrin host-guest binding: a computational study of the different driving forcescall_made
Helv. Chim. Acta 2010, 93, 2318.
2009
09.01
Gattin Z.; Riniker S.; Hore P. J.; Mok K. H.; van Gunsteren W. F.
external pageTemperature and urea induced denaturation of the TRP-cage mini protein TC5b: a simulation study consistent with experimental observationscall_made
Protein Sci. 2009, 18, 2090.