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Sereina Riniker, Ph.D. - Publications

Affiliations: 
Chemistry Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
Area:
Computational Chemistry
Website:
http://www.riniker.ethz.ch/people/riniker
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67 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Rieder SR, Ries B, Kubincová A, Champion C, Barros EP, Hünenberger PH, Riniker S. Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff. The Journal of Chemical Physics. 157: 104117. PMID 36109239 DOI: 10.1063/5.0107935  0.303
2021 Esposito C, Landrum GA, Schneider N, Stiefl N, Riniker S. GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning. Journal of Chemical Information and Modeling. PMID 34100609 DOI: 10.1021/acs.jcim.1c00160  0.506
2020 van Gunsteren WF, Daura X, Fuchs PFJ, Hansen N, Horta BAC, Hünenberger PH, Mark AE, Pechlaner M, Riniker S, Oostenbrink C. 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. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 33377305 DOI: 10.1002/cphc.202000968  0.641
2020 Stadelmann T, Subramanian G, Menon S, Townsend CE, Lokey RS, Ebert MO, Riniker S. Connecting the conformational behavior of cyclic octadepsipeptides with their ionophoric property and membrane permeability. Organic & Biomolecular Chemistry. PMID 32902550 DOI: 10.1039/D0Ob01447H  0.344
2020 König G, Glaser N, Schroeder B, Kubincová A, Hünenberger PH, Riniker S. An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. Journal of Chemical Information and Modeling. PMID 32794763 DOI: 10.1021/Acs.Jcim.0C00520  0.321
2020 Esposito C, Wang S, Lange UEW, Oellien F, Riniker S. Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. Journal of Chemical Information and Modeling. PMID 32786699 DOI: 10.1021/Acs.Jcim.0C00525  0.351
2020 Gebhardt J, Kiesel M, Riniker S, Hansen N. Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients. Journal of Chemical Information and Modeling. PMID 32786697 DOI: 10.1021/Acs.Jcim.0C00479  0.408
2020 Awale M, Riniker S, Kramer C. Matched Molecular Series Analysis for ADME Property Prediction. Journal of Chemical Information and Modeling. PMID 32369360 DOI: 10.1021/Acs.Jcim.0C00269  0.34
2020 Wang S, Witek J, Landrum GA, Riniker S. Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. Journal of Chemical Information and Modeling. PMID 32155061 DOI: 10.1021/Acs.Jcim.0C00025  0.368
2019 Riniker S, Wang S, Bleiziffer P, Böselt L, Esposito C. Machine Learning with and for Molecular Dynamics Simulations. Chimia. 73: 1024-1027. PMID 31883555 DOI: 10.2533/Chimia.2019.1024  0.355
2019 Wang S, Riniker S. Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. Journal of Computer-Aided Molecular Design. PMID 31745704 DOI: 10.1007/S10822-019-00252-6  0.389
2019 Renevey A, Riniker S. Benchmarking Hybrid Atomistic/Coarse-Grained Schemes for Proteins with an Atomistic Water Layer. The Journal of Physical Chemistry. B. PMID 30916957 DOI: 10.1021/Acs.Jpcb.8B12149  0.364
2019 Böselt L, Sidler D, Kittelmann T, Stohner J, Zindel D, Wagner T, Riniker S. Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. Journal of Chemical Information and Modeling. PMID 30916954 DOI: 10.1021/Acs.Jcim.8B00789  0.339
2019 Sidler D, Riniker S. Fast Nosé-Hoover thermostat: molecular dynamics in quasi-thermodynamic equilibrium. Physical Chemistry Chemical Physics : Pccp. PMID 30810120 DOI: 10.1039/C8Cp06800C  0.333
2018 Sidler D, Lehner M, Frasch S, Cristófol-Clough M, Riniker S. Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. F1000research. 7: 1745. PMID 30997032 DOI: 10.12688/F1000Research.16715.3  0.355
2018 Witek J, Wang S, Schroeder B, Lingwood R, Dounas A, Roth HJ, Fouché M, Blatter M, Lemke O, Keller BG, Riniker S. Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. Journal of Chemical Information and Modeling. PMID 30457855 DOI: 10.1021/Acs.Jcim.8B00485  0.327
2018 Sidler D, Frasch S, Cristòfol-Clough M, Riniker S. Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations. The Journal of Chemical Physics. 148: 234105. PMID 29935522 DOI: 10.1063/1.5007132  0.373
2018 Riniker S. Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. Journal of Chemical Information and Modeling. PMID 29510041 DOI: 10.1021/Acs.Jcim.8B00042  0.358
2018 Bleiziffer P, Schaller K, Riniker S. Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations. Journal of Chemical Information and Modeling. PMID 29461814 DOI: 10.1021/Acs.Jcim.7B00663  0.388
2017 Witek J, Mühlbauer M, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S. Interconversion Rates Between Conformational States as Rationale for the Membrane Permeability of Cyclosporines. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 28921848 DOI: 10.1002/Cphc.201700995  0.331
2017 van Gunsteren WF, Daura X, Hansen N, Mark A, Oostenbrink C, Riniker S, Smith L. Validation of Molecular Simulation: An Overview of Issues. Angewandte Chemie (International Ed. in English). PMID 28682472 DOI: 10.1002/Anie.201702945  0.671
2017 Sidler D, Cristofol Clough M, Riniker S. Efficient Round-Trip Time Optimisation for Replica-Exchange Enveloping Distribution Sampling (RE-EDS). Journal of Chemical Theory and Computation. PMID 28510459 DOI: 10.1021/Acs.Jctc.7B00286  0.353
2017 Riniker S, van Gunsteren WF. Erratum: "Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system" [J. Chem. Phys. 137, 044120 (2012)]. The Journal of Chemical Physics. 146: 129901. PMID 28388170 DOI: 10.1063/1.4979127  0.511
2017 Renevey A, Riniker S. Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions. The Journal of Chemical Physics. 146: 124131. PMID 28388132 DOI: 10.1063/1.4979128  0.419
2017 Riniker S. Molecular Dynamics Fingerprints (MDFP): Machine-Learning from MD Data to Predict Free-Energy Differences. Journal of Chemical Information and Modeling. PMID 28368113 DOI: 10.1021/Acs.Jcim.6B00778  0.427
2017 van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte Angewandte Chemie. 130: 894-915. DOI: 10.1002/Ange.201702945  0.469
2016 Sidler D, Schwaninger A, Riniker S. Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation. The Journal of Chemical Physics. 145: 154114. PMID 27782485 DOI: 10.1063/1.4964781  0.367
2016 Witek J, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S. Kinetic models of cyclosporin A in polar and apolar environment reveal multiple congruent conformational states. Journal of Chemical Information and Modeling. PMID 27387150 DOI: 10.1021/Acs.Jcim.6B00251  0.391
2016 Horta BA, Merz PT, Fuchs PF, Dolenc J, Riniker S, Hünenberger PH. A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set. Journal of Chemical Theory and Computation. PMID 27248705 DOI: 10.1021/Acs.Jctc.6B00187  0.346
2015 Eichenberger AP, Huang W, Riniker S, van Gunsteren WF. Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase. Journal of Chemical Theory and Computation. 11: 2925-2937. PMID 26575730 DOI: 10.1021/Acs.Jctc.5B00295  0.534
2015 Riniker S, Landrum G. Better Informed Distance Geometry: Using What We Know to Improve Conformation Generation. Journal of Chemical Information and Modeling. PMID 26575315 DOI: 10.1021/Acs.Jcim.5B00654  0.687
2015 Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G. The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes. Drug Discovery Today. 20: 686-702. PMID 25615716 DOI: 10.1016/J.Drudis.2015.01.003  0.37
2015 Eichenberger AP, van Gunsteren WF, Riniker S, von Ziegler L, Hansen N. The key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured states. Biochimica Et Biophysica Acta. 1850: 983-95. PMID 25239199 DOI: 10.1016/J.Bbagen.2014.09.014  0.478
2014 Huang W, Riniker S, van Gunsteren WF. Rapid Sampling of Folding Equilibria of β-Peptides in Methanol Using a Supramolecular Solvent Model. Journal of Chemical Theory and Computation. 10: 2213-23. PMID 26580745 DOI: 10.1021/Ct500048C  0.562
2014 Riniker S. Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back. Chimia. 68: 620-3. PMID 25437781 DOI: 10.2533/Chimia.2014.620  0.332
2014 Don CG, Riniker S. Scents and sense: In silico perspectives on olfactory receptors Journal of Computational Chemistry. 35: 2279-2287. PMID 25327850 DOI: 10.1002/Jcc.23757  0.318
2014 Riniker S, Wang Y, Jenkins JL, Landrum GA. Using information from historical high-throughput screens to predict active compounds Journal of Chemical Information and Modeling. 54: 1880-1891. PMID 24933016 DOI: 10.1021/Ci500190P  0.647
2014 Huang W, Riniker S, Van Gunsteren WF. Rapid sampling of folding equilibria of β-peptides in methanol using a supramolecular solvent model Journal of Chemical Theory and Computation. 10: 2213-2223. DOI: 10.1021/ct500048c  0.391
2013 Lin Z, Riniker S, van Gunsteren WF. Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water. Journal of Chemical Theory and Computation. 9: 1328-33. PMID 26587595 DOI: 10.1021/Ct3010497  0.566
2013 Riniker S, Fechner N, Landrum GA. Heterogeneous classifier fusion for ligand-based virtual screening: Or, how decision making by committee can be a good thing Journal of Chemical Information and Modeling. 53: 2829-2836. PMID 24171408 DOI: 10.1021/Ci400466R  0.672
2013 Riniker S, Landrum GA. Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. Journal of Cheminformatics. 5: 43. PMID 24063533 DOI: 10.1186/1758-2946-5-43  0.68
2013 Riniker S, Landrum GA. Open-source platform to benchmark fingerprints for ligand-based virtual screening. Journal of Cheminformatics. 5: 26. PMID 23721588 DOI: 10.1186/1758-2946-5-26  0.665
2013 Meier K, Choutko A, Dolenc J, Eichenberger AP, Riniker S, van Gunsteren WF. Multi-resolution simulation of biomolecular systems: a review of methodological issues. Angewandte Chemie (International Ed. in English). 52: 2820-34. PMID 23417997 DOI: 10.1002/Anie.201205408  0.529
2013 Riniker S, Landrum GA. Similarity maps - A visualization strategy for molecular fingerprints and machine-learning methods Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-43  0.614
2013 Riniker S, Landrum GA. Open-source platform to benchmark fingerprints for ligand-based virtual screening Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-26  0.607
2013 Lin Z, Riniker S, Van Gunsteren WF. Free enthalpy differences between α-, π-, and 3 10-helices of an atomic level fine-grained alanine deca-peptide solvated in supramolecular coarse-grained water Journal of Chemical Theory and Computation. 9: 1328-1333. DOI: 10.1021/ct3010497  0.425
2012 Riniker S, Barandun LJ, Diederich F, Krämer O, Steffen A, van Gunsteren WF. Free enthalpies of replacing water molecules in protein binding pockets. Journal of Computer-Aided Molecular Design. 26: 1293-309. PMID 23247390 DOI: 10.1007/S10822-012-9620-8  0.53
2012 Riniker S, van Gunsteren WF. Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system. The Journal of Chemical Physics. 137: 044120. PMID 22852610 DOI: 10.1063/1.4739068  0.531
2012 Riniker S, Eichenberger AP, van Gunsteren WF. Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water. The Journal of Physical Chemistry. B. 116: 8873-9. PMID 22816513 DOI: 10.1021/Jp304188Z  0.542
2012 Riniker S, Eichenberger AP, van Gunsteren WF. Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations. European Biophysics Journal : Ebj. 41: 647-61. PMID 22797564 DOI: 10.1007/S00249-012-0837-1  0.56
2012 Riniker S, Allison JR, van Gunsteren WF. On developing coarse-grained models for biomolecular simulation: a review. Physical Chemistry Chemical Physics : Pccp. 14: 12423-30. PMID 22678152 DOI: 10.1039/C2Cp40934H  0.488
2012 Horta BA, Lin Z, Huang W, Riniker S, van Gunsteren WF, Hünenberger PH. 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. Journal of Computational Chemistry. 33: 1907-17. PMID 22648867 DOI: 10.1002/Jcc.23021  0.519
2012 Riniker S, Horta BA, Thijssen B, Gupta S, van Gunsteren WF, Hünenberger PH. Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: a molecular dynamics simulation study. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 13: 1182-90. PMID 22383366 DOI: 10.1002/Cphc.201100949  0.491
2012 Allison JR, Riniker S, van Gunsteren WF. Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol. The Journal of Chemical Physics. 136: 054505. PMID 22320749 DOI: 10.1063/1.3681140  0.558
2012 Hansen N, Dolenc J, Knecht M, Riniker S, van Gunsteren WF. Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. Journal of Computational Chemistry. 33: 640-51. PMID 22228455 DOI: 10.1002/Jcc.22879  0.498
2012 Kunz AP, Allison JR, Geerke DP, Horta BA, Hünenberger PH, Riniker S, Schmid N, van Gunsteren WF. New functionalities in the GROMOS biomolecular simulation software. Journal of Computational Chemistry. 33: 340-53. PMID 22076815 DOI: 10.1002/Jcc.21954  0.517
2011 Riniker S, Kunz AE, van Gunsteren WF. On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase. Journal of Chemical Theory and Computation. 7: 1469-1475. PMID 26610137 DOI: 10.1021/Ct100610V  0.542
2011 Lin Z, Liu H, Riniker S, van Gunsteren WF. 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. Journal of Chemical Theory and Computation. 7: 3884-97. PMID 26598335 DOI: 10.1021/Ct200623B  0.556
2011 Riniker S, Christ CD, Hansen HS, Hünenberger PH, Oostenbrink C, Steiner D, van Gunsteren WF. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software. The Journal of Physical Chemistry. B. 115: 13570-7. PMID 22039957 DOI: 10.1021/Jp204303A  0.666
2011 Riniker S, Christ CD, Hansen N, Mark AE, Nair PC, van Gunsteren WF. Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors. The Journal of Chemical Physics. 135: 024105. PMID 21766923 DOI: 10.1063/1.3604534  0.553
2011 Dolenc J, Riniker S, Gaspari R, Daura X, van Gunsteren WF. Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. Journal of Computer-Aided Molecular Design. 25: 709-16. PMID 21735261 DOI: 10.1007/S10822-011-9453-X  0.482
2011 Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE, van Gunsteren WF. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal : Ebj. 40: 843-56. PMID 21533652 DOI: 10.1007/S00249-011-0700-9  0.494
2011 Riniker S, van Gunsteren WF. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. The Journal of Chemical Physics. 134: 084110. PMID 21361530 DOI: 10.1063/1.3553378  0.544
2011 Lin Z, Liu H, Riniker S, Van Gunsteren WF. 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 Journal of Chemical Theory and Computation. 7: 3884-3897. DOI: 10.1021/ct200623b  0.439
2011 Riniker S, Kunz APE, Van Gunsteren WF. On the calculation of the dielectric permittivity and relaxation of molecular models in the liquid phase Journal of Chemical Theory and Computation. 7: 1469-1475. DOI: 10.1021/ct100610v  0.409
2010 Riniker S, Daura X, Van Gunsteren WF. α-cyclodextrin host-guest binding: A computational study of the different driving forces Helvetica Chimica Acta. 93: 2318-2325. DOI: 10.1002/Hlca.201000251  0.556
2009 Gattin Z, Riniker S, Hore PJ, Mok KH, van Gunsteren WF. Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations. Protein Science : a Publication of the Protein Society. 18: 2090-9. PMID 19693803 DOI: 10.1002/Pro.223  0.517
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