| Year |
Citation |
Score |
| 2023 |
Landrum GA, Beckers M, Lanini J, Schneider N, Stiefl N, Riniker S. SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches. Journal of Cheminformatics. 15: 119. PMID 38082357 DOI: 10.1186/s13321-023-00787-9 |
0.527 |
|
| 2023 |
Thürlemann M, Böselt L, Riniker S. Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions. Journal of Chemical Theory and Computation. 19: 562-79. PMID 36633918 DOI: 10.1021/acs.jctc.2c00661 |
0.306 |
|
| 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 |
0.301 |
|
| 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 |
0.509 |
|
| 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 |
0.639 |
|
| 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 |
0.342 |
|
| 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 |
0.32 |
|
| 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 |
0.353 |
|
| 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 |
0.409 |
|
| 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 |
0.344 |
|
| 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 |
0.367 |
|
| 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 |
0.358 |
|
| 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 |
0.362 |
|
| 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 |
0.34 |
|
| 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 |
0.332 |
|
| 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 |
0.325 |
|
| 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 |
0.371 |
|
| 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 |
0.356 |
|
| 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 |
0.389 |
|
| 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 |
0.329 |
|
| 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 |
0.67 |
|
| 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 |
0.354 |
|
| 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 |
0.51 |
|
| 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 |
0.417 |
|
| 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 |
0.466 |
|
| 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 |
0.366 |
|
| 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 |
0.39 |
|
| 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 |
0.347 |
|
| 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 |
0.561 |
|
| 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 |
0.331 |
|
| 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 |
0.317 |
|
| 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 |
0.649 |
|
| 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 |
0.565 |
|
| 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 |
0.674 |
|
| 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 |
0.681 |
|
| 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 |
0.667 |
|
| 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 |
0.528 |
|
| 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 |
0.615 |
|
| 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 |
0.608 |
|
| 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 |
0.423 |
|
| 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 |
0.529 |
|
| 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 |
0.53 |
|
| 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 |
0.541 |
|
| 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 |
0.558 |
|
| 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 |
0.487 |
|
| 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 |
0.52 |
|
| 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 |
0.49 |
|
| 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 |
0.557 |
|
| 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 |
0.497 |
|
| 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 |
0.516 |
|
| 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 |
0.541 |
|
| 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 |
0.555 |
|
| 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 |
0.664 |
|
| 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 |
0.552 |
|
| 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 |
0.481 |
|
| 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 |
0.543 |
|
| 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 |
0.437 |
|
| 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 |
0.408 |
|
| 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 |
0.555 |
|
| 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 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2022 |
Rieder SR, Ries B, Schaller K, Champion C, Barros EP, Hünenberger PH, Riniker S. Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. Journal of Chemical Information and Modeling. 62: 3043-3056. PMID 35675713 DOI: 10.1021/acs.jcim.2c00383 |
0.296 |
|
| 2023 |
Champion C, Gall R, Ries B, Rieder SR, Barros EP, Riniker S. Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. Journal of Chemical Information and Modeling. 63: 7133-7147. PMID 37948537 DOI: 10.1021/acs.jcim.3c01469 |
0.296 |
|
| 2019 |
Smith AA, Ernst M, Riniker S, Meier BH. Localized and collective motions in HET-s(218-289) fibrils from combined NMR relaxation and MD simulation. Angewandte Chemie (International Ed. in English). PMID 31070275 DOI: 10.1002/Anie.201901929 |
0.291 |
|
| 2018 |
Song H, van der Velden NS, Shiran SL, Bleiziffer P, Zach C, Sieber R, Imani AS, Krausbeck F, Aebi M, Freeman MF, Riniker S, Künzler M, Naismith JH. A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds. Science Advances. 4: eaat2720. PMID 30151425 DOI: 10.1126/Sciadv.Aat2720 |
0.29 |
|
| 2017 |
Hentzen NB, Smeenk LEJ, Witek J, Riniker S, Wennemers H. Cross-Linked Collagen Triple Helices by Oxime Ligation. Journal of the American Chemical Society. PMID 28872857 DOI: 10.1021/Jacs.7B07498 |
0.289 |
|
| 2017 |
Witek J, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S. Correction to Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. Journal of Chemical Information and Modeling. PMID 28898064 DOI: 10.1021/Acs.Jcim.7B00502 |
0.285 |
|
| 2020 |
Boeselt L, Doetzer R, Steiner S, Stritzinger M, Salzmann S, Riniker S. Determining the Regio- and Relative Stereochemistry of Small and Drug-like Molecules Using an Alignment Algorithm for Infrared Spectra. Analytical Chemistry. PMID 32449349 DOI: 10.1021/Acs.Analchem.0C01399 |
0.284 |
|
| 2023 |
Katzberger P, Riniker S. Implicit solvent approach based on generalized Born and transferable graph neural networks for molecular dynamics simulations. The Journal of Chemical Physics. 158. PMID 37212404 DOI: 10.1063/5.0147027 |
0.284 |
|
| 2021 |
Böselt L, Thürlemann M, Riniker S. Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems. Journal of Chemical Theory and Computation. PMID 33818085 DOI: 10.1021/acs.jctc.0c01112 |
0.283 |
|
| 2022 |
Hofstetter A, Böselt L, Riniker S. Graph-convolutional neural networks for (QM)ML/MM molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. 24: 22497-22512. PMID 36106790 DOI: 10.1039/d2cp02931f |
0.282 |
|
| 2017 |
Riniker S, Landrum GA, Montanari F, Villalba SD, Maier J, Jansen JM, Walters WP, Shelat AA. Virtual-screening workflow tutorials and prospective results from the Teach-Discover-Treat competition 2014 against malaria. F1000research. 6: 1136. PMID 28928948 DOI: 10.12688/F1000Research.11905.2 |
0.281 |
|
| 2016 |
Renevey A, Riniker S. The importance of N-methylations for the stability of the [Formula: see text]-helical conformation of polytheonamide B. European Biophysics Journal : Ebj. PMID 27744521 DOI: 10.1007/S00249-016-1179-1 |
0.277 |
|
| 2020 |
Armacost KA, Riniker S, Cournia Z. Novel Directions in Free Energy Methods and Applications. Journal of Chemical Information and Modeling. 60: 1-5. PMID 31983210 DOI: 10.1021/Acs.Jcim.9B01174 |
0.275 |
|
| 2019 |
Sidler D, Bleiziffer P, Riniker S. Beyond Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutions. Journal of Chemical Theory and Computation. PMID 30802403 DOI: 10.1021/Acs.Jctc.8B01156 |
0.273 |
|
| 2022 |
Ries B, Normak K, Weiß RG, Rieder S, Barros EP, Champion C, König G, Riniker S. Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure. Journal of Computer-Aided Molecular Design. PMID 34978000 DOI: 10.1007/s10822-021-00436-z |
0.266 |
|
| 2022 |
Rieder SR, Ries B, Champion C, Barros EP, Hünenberger PH, Riniker S. Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS. Chimia. 76: 327-330. PMID 38069773 DOI: 10.2533/chimia.2022.327 |
0.265 |
|
| 2020 |
Kubincová A, Riniker S, Hünenberger PH. Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff. Physical Chemistry Chemical Physics : Pccp. PMID 33180085 DOI: 10.1039/d0cp03835k |
0.26 |
|
| 2021 |
Ries B, Linker SM, Hahn DF, König G, Riniker S. Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations. Journal of Chemical Information and Modeling. PMID 33512157 DOI: 10.1021/acs.jcim.0c01283 |
0.259 |
|
| 2016 |
Fuchs SW, Lackner G, Morinaka BI, Morishita Y, Asai T, Riniker S, Piel J. A Lanthipeptide-like N-Terminal Leader Region Guides Peptide Epimerization by Radical SAM Epimerases: Implications for RiPP Evolution. Angewandte Chemie (International Ed. in English). PMID 27584723 DOI: 10.1002/Anie.201602863 |
0.255 |
|
| 2021 |
Barros EP, Ries B, Böselt L, Champion C, Riniker S. Recent developments in multiscale free energy simulations. Current Opinion in Structural Biology. 72: 55-62. PMID 34534706 DOI: 10.1016/j.sbi.2021.08.003 |
0.255 |
|
| 2022 |
Ries B, Rieder S, Rhiner C, Hünenberger PH, Riniker S. RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. Journal of Computer-Aided Molecular Design. 36: 175-192. PMID 35314898 DOI: 10.1007/s10822-022-00445-6 |
0.251 |
|
| 2020 |
Wang Q, Riniker S, Kraft P, Liu J, Hürlimann V, Emter R, Natsch A, Esposito C, Linker SM, Zou Y, Zhou L. A New Family of Rigid Dienone Musks Challenges the Perceptive Range of the Human Olfactory Receptor OR5AN1 Synlett. 31: 972-976. DOI: 10.1055/S-0040-1708009 |
0.25 |
|
| 2022 |
Wang S, Krummenacher K, Landrum GA, Sellers BD, Di Lello P, Robinson SJ, Martin B, Holden JK, Tom JYK, Murthy AC, Popovych N, Riniker S. Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. Journal of Chemical Information and Modeling. PMID 35029985 DOI: 10.1021/acs.jcim.1c01165 |
0.242 |
|
| 2021 |
Kubincová A, Riniker S, Hünenberger PH. Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme. The Journal of Chemical Physics. 155: 094107. PMID 34496576 DOI: 10.1063/5.0057384 |
0.237 |
|
| 2021 |
König G, Ries B, Hünenberger PH, Riniker S. Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling. Journal of Chemical Theory and Computation. PMID 34476947 DOI: 10.1021/acs.jctc.1c00418 |
0.234 |
|
| 2022 |
Thürlemann M, Böselt L, Riniker S. Learning Atomic Multipoles: Prediction of the Electrostatic Potential with Equivariant Graph Neural Networks. Journal of Chemical Theory and Computation. PMID 35112866 DOI: 10.1021/acs.jctc.1c01021 |
0.231 |
|
| 2023 |
Thürlemann M, Riniker S. Hybrid classical/machine-learning force fields for the accurate description of molecular condensed-phase systems. Chemical Science. 14: 12661-12675. PMID 38020395 DOI: 10.1039/d3sc04317g |
0.23 |
|
| 2020 |
Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. Journal of Chemical Theory and Computation. PMID 33231449 DOI: 10.1021/acs.jctc.0c00683 |
0.228 |
|
| 2013 |
Meier K, Choutko A, Dolenc J, Eichenberger AP, Riniker S, van Gunsteren WF. Biomolekulare Simulationen mit mehreren Auflösungsniveaus: ein Überblick über methodische Aspekte Angewandte Chemie. 125: 2888-2904. DOI: 10.1002/Ange.201205408 |
0.226 |
|
| 2021 |
Weiß RG, Losfeld ME, Aebi M, Riniker S. N-Glycosylation Enhances Conformational Flexibility of Protein Disulfide Isomerase Revealed by Microsecond Molecular Dynamics and Markov State Modeling. The Journal of Physical Chemistry. B. PMID 34379416 DOI: 10.1021/acs.jpcb.1c04279 |
0.221 |
|
| 2023 |
Barros EP, Ries B, Champion C, Rieder SR, Riniker S. Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. Journal of Chemical Information and Modeling. 63: 1794-1805. PMID 36917685 DOI: 10.1021/acs.jcim.2c01610 |
0.221 |
|
| 2024 |
Isert C, Atz K, Riniker S, Schneider G. Exploring protein-ligand binding affinity prediction with electron density-based geometric deep learning. Rsc Advances. 14: 4492-4502. PMID 38312732 DOI: 10.1039/d3ra08650j |
0.221 |
|
| 2020 |
König G, Riniker S. On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces. Interface Focus. 10: 20190121. PMID 33184586 DOI: 10.1098/rsfs.2019.0121 |
0.216 |
|
| 2020 |
König G, Riniker S. On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces Interface Focus. 10: 20190121. DOI: 10.1098/rsfs.2019.0121 |
0.216 |
|
| 2022 |
Stenström O, Champion C, Lehner M, Bouvignies G, Riniker S, Ferrage F. How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation. Current Opinion in Structural Biology. 77: 102459. PMID 36148743 DOI: 10.1016/j.sbi.2022.102459 |
0.214 |
|
| 2019 |
Riniker S. Toward the elucidation of the mechanism for passive membrane permeability of cyclic peptides. Future Medicinal Chemistry. PMID 30920310 DOI: 10.4155/Fmc-2018-0429 |
0.213 |
|
| 2023 |
Kubincová A, Riniker S, Hünenberger PH. Simulation of aqueous solutes using the adaptive solvent-scaling (AdSoS) scheme. The Journal of Chemical Physics. 159. PMID 38099543 DOI: 10.1063/5.0174839 |
0.212 |
|
| 2023 |
Lehner MT, Katzberger P, Maeder N, Schiebroek CCG, Teetz J, Landrum GA, Riniker S. DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment. Journal of Chemical Information and Modeling. 63: 6014-6028. PMID 37738206 DOI: 10.1021/acs.jcim.3c00800 |
0.211 |
|
| 2022 |
Kamenik AS, Linker SM, Riniker S. Enhanced sampling without borders: on global biasing functions and how to reweight them. Physical Chemistry Chemical Physics : Pccp. 24: 1225-1236. PMID 34935813 DOI: 10.1039/d1cp04809k |
0.206 |
|
| 2018 |
Volkamer A, Riniker S. Transition from Academia to Industry and Back. Journal of Chemical Information and Modeling. PMID 30058337 DOI: 10.1021/Acs.Jcim.8B00459 |
0.201 |
|
| 2020 |
Linker SM, Weiß RG, Riniker S. Connecting dynamic reweighting Algorithms: Derivation of the dynamic reweighting family tree. The Journal of Chemical Physics. 153: 234106. PMID 33353335 DOI: 10.1063/5.0019687 |
0.201 |
|
| 2021 |
Wang S, König G, Roth HJ, Fouché M, Rodde S, Riniker S. Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides. Journal of Medicinal Chemistry. PMID 34406766 DOI: 10.1021/acs.jmedchem.1c00775 |
0.199 |
|
| 2022 |
Stadelmann T, Balmer C, Riniker S, Ebert MO. Impact of solvent interactions on H and C chemical shifts investigated using DFT and a reference dataset recorded in CDCl and CCl. Physical Chemistry Chemical Physics : Pccp. 24: 23551-23560. PMID 36129319 DOI: 10.1039/d2cp03205h |
0.193 |
|
| 2021 |
Linker SM, Wang S, Ries B, Stadelmann T, Riniker S. Passing the Barrier - How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides. Chimia. 75: 518-521. PMID 34233816 DOI: 10.2533/chimia.2021.518 |
0.192 |
|
| 2021 |
Linker SM, Wang S, Ries B, Stadelmann T, Riniker S. Passing the Barrier - How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides. Chimia. 75: 518-521. PMID 34233816 DOI: 10.2533/chimia.2021.518 |
0.192 |
|
| 2021 |
Weiß RG, Ries B, Wang S, Riniker S. Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy. The Journal of Chemical Physics. 154: 084106. PMID 33639726 DOI: 10.1063/5.0025797 |
0.189 |
|
| 2022 |
Linker SM, Schellhaas C, Ries B, Roth HJ, Fouché M, Rodde S, Riniker S. Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability. Rsc Advances. 12: 5782-5796. PMID 35424539 DOI: 10.1039/d1ra09025a |
0.183 |
|
| 2022 |
Fiala T, Barros EP, Ebert MO, Ruijsenaars E, Riniker S, Wennemers H. Frame Shifts Affect the Stability of Collagen Triple Helices. Journal of the American Chemical Society. 144: 18642-18649. PMID 36179150 DOI: 10.1021/jacs.2c08727 |
0.18 |
|
| 2023 |
Metternich JB, Katzberger P, Kamenik AS, Tiwari P, Wu R, Riniker S, Zenobi R. Influence of the Fluorophore Mobility on Distance Measurements by Gas-Phase FRET. The Journal of Physical Chemistry. A. 127: 5620-5628. PMID 37403246 DOI: 10.1021/acs.jpca.3c01509 |
0.18 |
|
| 2018 |
Zoppe JO, Riniker S, Merz L. 11 Young Faculty Meeting, 5 June 2018. Chimia. 72: 550-552. PMID 30158021 DOI: 10.2533/Chimia.2018.550 |
0.177 |
|
| 2021 |
Comeau C, Ries B, Stadelmann T, Tremblay J, Poulet S, Fröhlich U, Côté J, Boudreault PL, Derbali RM, Sarret P, Grandbois M, Leclair G, Riniker S, Marsault É. Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties. Journal of Medicinal Chemistry. PMID 33750117 DOI: 10.1021/acs.jmedchem.0c02036 |
0.167 |
|
| 2021 |
Egli J, Esposito C, Müri M, Riniker S, Wennemers H. Influence of Lipidation on the Folding and Stability of Collagen Triple Helices-An Experimental and Theoretical Study. Journal of the American Chemical Society. 143: 5937-5942. PMID 33830753 DOI: 10.1021/jacs.1c01512 |
0.166 |
|
| 2022 |
Fiala T, Barros EP, Heeb R, Riniker S, Wennemers H. Predicting Collagen Triple Helix Stability through Additive Effects of Terminal Residues and Caps. Angewandte Chemie (International Ed. in English). PMID 36409045 DOI: 10.1002/anie.202214728 |
0.159 |
|
| 2021 |
Mathew C, Weiß RG, Giese C, Lin CW, Losfeld ME, Glockshuber R, Riniker S, Aebi M. Glycan-protein interactions determine kinetics of -glycan remodeling. Rsc Chemical Biology. 2: 917-931. PMID 34212152 DOI: 10.1039/d1cb00019e |
0.156 |
|
| 2014 |
Riniker S. Crossing the boundaries within computational chemistry: From molecular dynamics to cheminformatics and back Chimia. 68: 620-623. DOI: 10.2533/chimia.2014.620 |
0.15 |
|
| 2023 |
Linker SM, Schellhaas C, Kamenik AS, Veldhuizen MM, Waibl F, Roth HJ, Fouché M, Rodde S, Riniker S. Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes. Journal of Medicinal Chemistry. PMID 36762908 DOI: 10.1021/acs.jmedchem.2c01837 |
0.147 |
|
| 2023 |
Thürlemann M, Riniker S. Energy-based clustering: Fast and robust clustering of data with known likelihood functions. The Journal of Chemical Physics. 159. PMID 37428043 DOI: 10.1063/5.0148735 |
0.146 |
|
| 2021 |
Awale M, Hert J, Guasch L, Riniker S, Kramer C. The Playbooks of Medicinal Chemistry Design Moves. Journal of Chemical Information and Modeling. PMID 33522806 DOI: 10.1021/acs.jcim.0c01143 |
0.143 |
|
| 2020 |
Armacost KA, Riniker S, Cournia Z. Exploring Novel Directions in Free Energy Calculations. Journal of Chemical Information and Modeling. 60: 5283-5286. PMID 33222441 DOI: 10.1021/acs.jcim.0c01266 |
0.14 |
|
| 2022 |
Böselt L, Aerts R, Herrebout W, Riniker S. Improving the IR spectra alignment algorithm with spectra deconvolution and combination with Raman or VCD spectroscopy. Physical Chemistry Chemical Physics : Pccp. PMID 36546852 DOI: 10.1039/d2cp04907d |
0.137 |
|
| 2023 |
Rieder SR, Oliveira MP, Riniker S, Hünenberger PH. Development of an open-source software for isomer enumeration. Journal of Cheminformatics. 15: 10. PMID 36683047 DOI: 10.1186/s13321-022-00677-6 |
0.132 |
|
| 2023 |
Wu R, Metternich JB, Kamenik AS, Tiwari P, Harrison JA, Kessen D, Akay H, Benzenberg LR, Chan TD, Riniker S, Zenobi R. Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data. Nature Communications. 14: 2913. PMID 37217470 DOI: 10.1038/s41467-023-38463-z |
0.131 |
|
| 2023 |
Bleiziffer P, Schaller K, Riniker S. Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations". Journal of Chemical Information and Modeling. 63: 2265. PMID 36940093 DOI: 10.1021/acs.jcim.3c00351 |
0.128 |
|
| 2024 |
Landrum GA, Riniker S. Combining IC or Values from Different Sources Is a Source of Significant Noise. Journal of Chemical Information and Modeling. PMID 38394344 DOI: 10.1021/acs.jcim.4c00049 |
0.12 |
|
| 2021 |
Pultar F, Hansen ME, Wolfrum S, Böselt L, Fróis-Martins R, Bloch S, Kravina AG, Pehlivanoglu D, Schäffer C, LeibundGut-Landmann S, Riniker S, Carreira EM. Mutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluation. Journal of the American Chemical Society. 143: 10389-10402. PMID 34212720 DOI: 10.1021/jacs.1c04825 |
0.106 |
|
| 2024 |
Cotter E, Pultar F, Riniker S, Altmann KH. Experimental and Theoretical Studies on the Reactions of Aliphatic Imines with Isocyanates. Chemistry (Weinheim An Der Bergstrasse, Germany). e202304272. PMID 38226702 DOI: 10.1002/chem.202304272 |
0.106 |
|
| 2012 |
Hitz F, Klingbiel D, Omlin A, Riniker S, Zerz A, Cerny T. Athrombogenic coating of long-term venous catheter for cancer patients: a prospective, randomised, double-blind trial. Annals of Hematology. 91: 613-20. PMID 21956636 DOI: 10.1007/s00277-011-1343-8 |
0.039 |
|
| 2012 |
Hitz F, Klingbiel D, Omlin A, Riniker S, Zerz A, Cerny T. Athrombogenic coating of long-term venous catheter for cancer patients: A prospective, randomised, double-blind trial Annals of Hematology. 91: 613-620. DOI: 10.1007/s00277-011-1343-8 |
0.013 |
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