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Items: 1 to 50 of 61

1.

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

Smith AA, Ernst M, Riniker S, Meier BH.

Angew Chem Int Ed Engl. 2019 May 9. doi: 10.1002/anie.201901929. [Epub ahead of print]

PMID:
31070275
2.

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

Sidler D, Lehner M, Frasch S, Cristófol-Clough M, Riniker S.

Version 3. F1000Res. 2018 Nov 5 [revised 2019 Jan 1];7:1745. doi: 10.12688/f1000research.16715.3. eCollection 2018.

3.

Toward the elucidation of the mechanism for passive membrane permeability of cyclic peptides.

Riniker S.

Future Med Chem. 2019 Apr;11(7):637-639. doi: 10.4155/fmc-2018-0429. Epub 2019 Mar 28. No abstract available.

4.

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

Renevey A, Riniker S.

J Phys Chem B. 2019 Apr 11;123(14):3033-3042. doi: 10.1021/acs.jpcb.8b12149. Epub 2019 Mar 27.

PMID:
30916957
5.

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

Böselt L, Sidler D, Kittelmann T, Stohner J, Zindel D, Wagner T, Riniker S.

J Chem Inf Model. 2019 May 28;59(5):1826-1838. doi: 10.1021/acs.jcim.8b00789. Epub 2019 Mar 27.

PMID:
30916954
6.

Fast Nosé-Hoover thermostat: molecular dynamics in quasi-thermodynamic equilibrium.

Sidler D, Riniker S.

Phys Chem Chem Phys. 2019 Mar 13;21(11):6059-6070. doi: 10.1039/c8cp06800c.

PMID:
30810120
7.

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

Sidler D, Bleiziffer P, Riniker S.

J Chem Theory Comput. 2019 Apr 9;15(4):2492-2503. doi: 10.1021/acs.jctc.8b01156. Epub 2019 Mar 11.

PMID:
30802403
8.

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

Witek J, Wang S, Schroeder B, Lingwood R, Dounas A, Roth HJ, Fouché M, Blatter M, Lemke O, Keller B, Riniker S.

J Chem Inf Model. 2019 Jan 28;59(1):294-308. doi: 10.1021/acs.jcim.8b00485. Epub 2018 Dec 4.

PMID:
30457855
9.

11th Young Faculty Meeting, 5th June 2018.

Zoppe JO, Riniker S, Merz L.

Chimia (Aarau). 2018 Aug 22;72(7):550-552. doi: 10.2533/chimia.2018.550. No abstract available.

PMID:
30158021
10.

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

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.

Sci Adv. 2018 Aug 24;4(8):eaat2720. doi: 10.1126/sciadv.aat2720. eCollection 2018 Aug.

11.

Transition from Academia to Industry and Back.

Volkamer A, Riniker S.

J Chem Inf Model. 2018 Aug 27;58(8):1469-1472. doi: 10.1021/acs.jcim.8b00459. Epub 2018 Jul 30.

PMID:
30058337
12.

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

Sidler D, Frasch S, Cristòfol-Clough M, Riniker S.

J Chem Phys. 2018 Jun 21;148(23):234105. doi: 10.1063/1.5007132.

PMID:
29935522
13.

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

Riniker S, Landrum GA, Montanari F, Villalba SD, Maier J, Jansen JM, Walters WP, Shelat AA.

Version 2. F1000Res. 2017 Jul 17 [revised 2018 Jan 1];6:1136. doi: 10.12688/f1000research.11905.2. eCollection 2017.

14.

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

Riniker S.

J Chem Inf Model. 2018 Mar 26;58(3):565-578. doi: 10.1021/acs.jcim.8b00042. Epub 2018 Mar 13. Review.

PMID:
29510041
15.

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

Bleiziffer P, Schaller K, Riniker S.

J Chem Inf Model. 2018 Mar 26;58(3):579-590. doi: 10.1021/acs.jcim.7b00663. Epub 2018 Mar 7.

PMID:
29461814
16.

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

Witek J, Mühlbauer M, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S.

Chemphyschem. 2017 Dec 6;18(23):3309-3314. doi: 10.1002/cphc.201700995. Epub 2017 Nov 2.

PMID:
28921848
17.

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

Witek J, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S.

J Chem Inf Model. 2017 Sep 25;57(9):2393. doi: 10.1021/acs.jcim.7b00502. Epub 2017 Sep 12. No abstract available.

PMID:
28898064
18.

Cross-Linked Collagen Triple Helices by Oxime Ligation.

Hentzen NB, Smeenk LEJ, Witek J, Riniker S, Wennemers H.

J Am Chem Soc. 2017 Sep 13;139(36):12815-12820. doi: 10.1021/jacs.7b07498. Epub 2017 Sep 5.

PMID:
28872857
19.

Phase I trial of the androgen receptor modulator CR1447 in breast cancer patients.

Zweifel M, Thürlimann B, Riniker S, Weder P, von Moos R, Pagani O, Bigler M, Rothgiesser KM, Pilop C, Hawle H, Brauchli P, Tapia C, Schoenfeld W, Sessa C; Swiss Group for Clinical Cancer Research (SAKK).

Endocr Connect. 2017 Oct;6(7):549-556. doi: 10.1530/EC-17-0174. Epub 2017 Aug 16.

20.

Validation of Molecular Simulation: An Overview of Issues.

van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ.

Angew Chem Int Ed Engl. 2018 Jan 22;57(4):884-902. doi: 10.1002/anie.201702945. Epub 2017 Dec 27. Review.

PMID:
28682472
21.

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

Sidler D, Cristòfol-Clough M, Riniker S.

J Chem Theory Comput. 2017 Jun 13;13(6):3020-3030. doi: 10.1021/acs.jctc.7b00286. Epub 2017 May 26.

PMID:
28510459
22.

Erratum: "Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system" [J. Chem. Phys. 137, 044120 (2012)].

Riniker S, van Gunsteren WF.

J Chem Phys. 2017 Mar 28;146(12):129901. doi: 10.1063/1.4979127. No abstract available.

PMID:
28388170
23.

Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions.

Renevey A, Riniker S.

J Chem Phys. 2017 Mar 28;146(12):124131. doi: 10.1063/1.4979128.

PMID:
28388132
24.

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

Riniker S.

J Chem Inf Model. 2017 Apr 24;57(4):726-741. doi: 10.1021/acs.jcim.6b00778. Epub 2017 Apr 12.

PMID:
28368113
25.
26.

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

Renevey A, Riniker S.

Eur Biophys J. 2017 May;46(4):363-374. doi: 10.1007/s00249-016-1179-1. Epub 2016 Oct 15.

PMID:
27744521
27.

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

Fuchs SW, Lackner G, Morinaka BI, Morishita Y, Asai T, Riniker S, Piel J.

Angew Chem Int Ed Engl. 2016 Sep 26;55(40):12330-3. doi: 10.1002/anie.201602863. Epub 2016 Sep 1.

PMID:
27584723
28.

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

Witek J, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S.

J Chem Inf Model. 2016 Aug 22;56(8):1547-62. doi: 10.1021/acs.jcim.6b00251. Epub 2016 Jul 19. Erratum in: J Chem Inf Model. 2017 Sep 25;57(9):2393.

PMID:
27387150
29.

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

Horta BA, Merz PT, Fuchs PF, Dolenc J, Riniker S, Hünenberger PH.

J Chem Theory Comput. 2016 Aug 9;12(8):3825-50. doi: 10.1021/acs.jctc.6b00187. Epub 2016 Jul 8.

PMID:
27248705
30.

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

Eichenberger AP, Huang W, Riniker S, van Gunsteren WF.

J Chem Theory Comput. 2015 Jul 14;11(7):2925-37. doi: 10.1021/acs.jctc.5b00295. Epub 2015 Jun 23.

PMID:
26575730
31.

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

Riniker S, Landrum GA.

J Chem Inf Model. 2015 Dec 28;55(12):2562-74. doi: 10.1021/acs.jcim.5b00654. Epub 2015 Nov 30.

PMID:
26575315
32.

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

Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G.

Drug Discov Today. 2015 Jun;20(6):686-702. doi: 10.1016/j.drudis.2015.01.003. Epub 2015 Jan 20. Review.

PMID:
25615716
33.

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

Riniker S.

Chimia (Aarau). 2014 Sep;68(9):620-3. doi: 10.2533/chimia.2014.620.

PMID:
25437781
34.

Scents and sense: in silico perspectives on olfactory receptors.

Don CG, Riniker S.

J Comput Chem. 2014 Dec 15;35(32):2279-87. doi: 10.1002/jcc.23757. Epub 2014 Oct 18. Review.

PMID:
25327850
35.

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

Eichenberger AP, van Gunsteren WF, Riniker S, von Ziegler L, Hansen N.

Biochim Biophys Acta. 2015 May;1850(5):983-995. doi: 10.1016/j.bbagen.2014.09.014. Epub 2014 Sep 18.

PMID:
25239199
36.

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

Riniker S, Wang Y, Jenkins JL, Landrum GA.

J Chem Inf Model. 2014 Jul 28;54(7):1880-91. doi: 10.1021/ci500190p. Epub 2014 Jun 26.

PMID:
24933016
37.

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

Huang W, Riniker S, van Gunsteren WF.

J Chem Theory Comput. 2014 Jun 10;10(6):2213-23. doi: 10.1021/ct500048c.

PMID:
26580745
38.

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

Riniker S, Fechner N, Landrum GA.

J Chem Inf Model. 2013 Nov 25;53(11):2829-36. doi: 10.1021/ci400466r. Epub 2013 Nov 14.

PMID:
24171408
39.

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

Riniker S, Landrum GA.

J Cheminform. 2013 Sep 24;5(1):43. doi: 10.1186/1758-2946-5-43.

40.

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

Riniker S, Landrum GA.

J Cheminform. 2013 May 30;5(1):26. doi: 10.1186/1758-2946-5-26.

41.

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

Lin Z, Riniker S, van Gunsteren WF.

J Chem Theory Comput. 2013 Mar 12;9(3):1328-33. doi: 10.1021/ct3010497. Epub 2013 Feb 6.

PMID:
26587595
42.

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

Meier K, Choutko A, Dolenc J, Eichenberger AP, Riniker S, van Gunsteren WF.

Angew Chem Int Ed Engl. 2013 Mar 4;52(10):2820-34. doi: 10.1002/anie.201205408. Epub 2013 Feb 18. Review.

PMID:
23417997
43.

Free enthalpies of replacing water molecules in protein binding pockets.

Riniker S, Barandun LJ, Diederich F, Krämer O, Steffen A, van Gunsteren WF.

J Comput Aided Mol Des. 2012 Dec;26(12):1293-309. doi: 10.1007/s10822-012-9620-8. Epub 2012 Dec 18.

PMID:
23247390
44.

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

Riniker S, van Gunsteren WF.

J Chem Phys. 2012 Jul 28;137(4):044120. doi: 10.1063/1.4739068. Erratum in: J Chem Phys. 2017 Mar 28;146(12):129901.

PMID:
22852610
45.

Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water.

Riniker S, Eichenberger AP, van Gunsteren WF.

J Phys Chem B. 2012 Aug 2;116(30):8873-9. doi: 10.1021/jp304188z. Epub 2012 Jul 20.

PMID:
22816513
46.

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

Riniker S, Eichenberger AP, van Gunsteren WF.

Eur Biophys J. 2012 Aug;41(8):647-61. doi: 10.1007/s00249-012-0837-1. Epub 2012 Jul 14.

PMID:
22797564
47.

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

Riniker S, Allison JR, van Gunsteren WF.

Phys Chem Chem Phys. 2012 Sep 28;14(36):12423-30. doi: 10.1039/c2cp40934h. Epub 2012 Jun 8. Review.

PMID:
22678152
48.

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.

Horta BA, Lin Z, Huang W, Riniker S, van Gunsteren WF, Hünenberger PH.

J Comput Chem. 2012 Sep 15;33(24):1907-17. doi: 10.1002/jcc.23021. Epub 2012 May 30.

PMID:
22648867
49.

Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: a molecular dynamics simulation study.

Riniker S, Horta BA, Thijssen B, Gupta S, van Gunsteren WF, Hünenberger PH.

Chemphyschem. 2012 Apr 10;13(5):1182-90. doi: 10.1002/cphc.201100949. Epub 2012 Mar 1.

PMID:
22383366
50.

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

Allison JR, Riniker S, van Gunsteren WF.

J Chem Phys. 2012 Feb 7;136(5):054505. doi: 10.1063/1.3681140.

PMID:
22320749

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