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Sereina Riniker
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2020 – today
- 2024
- [j41]Gregory A. Landrum
, Sereina Riniker
:
Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise. J. Chem. Inf. Model. 64(5): 1560-1567 (2024) - 2023
- [j40]Salomé Rieder
, Marina P. Oliveira, Sereina Riniker, Philippe H. Hünenberger:
Development of an open-source software for isomer enumeration. J. Cheminformatics 15(1): 10 (2023) - [j39]Gregory A. Landrum, Maximilian Beckers, Jessica Lanini, Nadine Schneider, Nikolaus Stiefl, Sereina Riniker:
SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches. J. Cheminformatics 15(1): 119 (2023) - [j38]Emília P. Barros
, Benjamin Ries
, Candide Champion
, Salomé Rieder
, Sereina Riniker
:
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. J. Chem. Inf. Model. 63(6): 1794-1805 (2023) - [j37]Patrick Bleiziffer, Kay Schaller
, Sereina Riniker
:
Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations". J. Chem. Inf. Model. 63(7): 2265 (2023) - [j36]Marc Lehner
, Paul Katzberger
, Niels Maeder, Carl C. G. Schiebroek
, Jakob Teetz, Gregory A. Landrum
, Sereina Riniker
:
DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment. J. Chem. Inf. Model. 63(19): 6014-6028 (2023) - [j35]Candide Champion
, René Gall, Benjamin Ries
, Salomé Rieder
, Emília P. Barros
, Sereina Riniker
:
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. J. Chem. Inf. Model. 63(22): 7133-7147 (2023) - [c1]Moritz Thürlemann, Sereina Riniker:
Anisotropic Message Passing: Graph Neural Networks with Directional and Long-Range Interactions. ICLR 2023 - 2022
- [j34]Benjamin Ries
, Karl Normak
, R. Gregor Weiß
, Salomé Rieder
, Emília P. Barros
, Candide Champion
, Gerhard König
, Sereina Riniker
:
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure. J. Comput. Aided Mol. Des. 36(2): 117-130 (2022) - [j33]Benjamin Ries
, Salomé Rieder
, Clemens Rhiner, Philippe H. Hünenberger
, Sereina Riniker
:
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. J. Comput. Aided Mol. Des. 36(3): 175-192 (2022) - [j32]Shuzhe Wang
, Kajo Krummenacher, Gregory A. Landrum
, Benjamin D. Sellers
, Paola Di Lello, Sarah J. Robinson, Bryan Martin, Jeffrey K. Holden, Jeffrey Y. K. Tom, Anastasia C. Murthy, Nataliya Popovych, Sereina Riniker
:
Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. J. Chem. Inf. Model. 62(3): 472-485 (2022) - [j31]Salomé Rieder
, Benjamin Ries
, Kay Schaller
, Candide Champion
, Emília P. Barros
, Philippe H. Hünenberger
, Sereina Riniker
:
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. J. Chem. Inf. Model. 62(12): 3043-3056 (2022) - 2021
- [j30]Benjamin Ries
, Stephanie M. Linker, David F. Hahn
, Gerhard König
, Sereina Riniker
:
Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations. J. Chem. Inf. Model. 61(2): 560-564 (2021) - [j29]Mahendra Awale
, Jérôme Hert
, Laura Guasch
, Sereina Riniker
, Christian Kramer:
The Playbooks of Medicinal Chemistry Design Moves. J. Chem. Inf. Model. 61(2): 729-742 (2021) - [j28]Carmen Esposito
, Gregory A. Landrum
, Nadine Schneider
, Nikolaus Stiefl
, Sereina Riniker
:
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning. J. Chem. Inf. Model. 61(6): 2623-2640 (2021) - 2020
- [j27]Shuzhe Wang
, Sereina Riniker
:
Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. J. Comput. Aided Mol. Des. 34(4): 393-403 (2020) - [j26]Kira A. Armacost
, Sereina Riniker
, Zoe Cournia
:
Novel Directions in Free Energy Methods and Applications. J. Chem. Inf. Model. 60(1): 1-5 (2020) - [j25]Shuzhe Wang
, Jagna Witek, Gregory A. Landrum
, Sereina Riniker
:
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. J. Chem. Inf. Model. 60(4): 2044-2058 (2020) - [j24]Mahendra Awale
, Sereina Riniker
, Christian Kramer:
Matched Molecular Series Analysis for ADME Property Prediction. J. Chem. Inf. Model. 60(6): 2903-2914 (2020) - [j23]Carmen Esposito
, Shuzhe Wang
, Udo E. W. Lange
, Frank Oellien
, Sereina Riniker
:
Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. J. Chem. Inf. Model. 60(10): 4730-4749 (2020) - [j22]Kira A. Armacost
, Sereina Riniker
, Zoe Cournia
:
Exploring Novel Directions in Free Energy Calculations. J. Chem. Inf. Model. 60(11): 5283-5286 (2020) - [j21]Julia Gebhardt, Matthias Kiesel, Sereina Riniker
, Niels Hansen
:
Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients. J. Chem. Inf. Model. 60(11): 5319-5330 (2020) - [j20]Gerhard König
, Nina Glaser
, Benjamin Schroeder
, Alzbeta Kubincová
, Philippe H. Hünenberger
, Sereina Riniker
:
An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. J. Chem. Inf. Model. 60(11): 5407-5423 (2020)
2010 – 2019
- 2019
- [j19]Jagna Witek, Shuzhe Wang
, Benjamin Schroeder
, Robin Lingwood, Andreas Dounas
, Hans-Jörg Roth, Marianne Fouché, Markus Blatter, Oliver Lemke, Bettina G. Keller
, Sereina Riniker
:
Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J. Chem. Inf. Model. 59(1): 294-308 (2019) - [j18]Lennard Böselt, Dominik Sidler
, Tobias Kittelmann, Jürgen Stohner
, Daniel Zindel
, Trixie Wagner, Sereina Riniker
:
Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. J. Chem. Inf. Model. 59(5): 1826-1838 (2019) - 2018
- [j17]Sereina Riniker
:
Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. J. Chem. Inf. Model. 58(3): 565-578 (2018) - [j16]Patrick Bleiziffer, Kay Schaller
, Sereina Riniker
:
Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations. J. Chem. Inf. Model. 58(3): 579-590 (2018) - [j15]Andrea Volkamer
, Sereina Riniker
:
Transition from Academia to Industry and Back. J. Chem. Inf. Model. 58(8): 1469-1472 (2018) - [i1]Dominik Sidler
, Marc Lehner
, Simon Frasch, Michael Cristófol-Clough, Sereina Riniker
:
Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. F1000Research 7: 1745 (2018) - 2017
- [j14]Sereina Riniker
:
Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. J. Chem. Inf. Model. 57(4): 726-741 (2017) - [j13]Jagna Witek, Bettina G. Keller, Markus Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker
:
Correction to Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J. Chem. Inf. Model. 57(9): 2393 (2017) - 2016
- [j12]Jagna Witek, Bettina G. Keller
, Marie-Claude Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker
:
Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J. Chem. Inf. Model. 56(8): 1547-1562 (2016) - 2015
- [j11]Sereina Riniker
, Gregory A. Landrum
:
Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. J. Chem. Inf. Model. 55(12): 2562-2574 (2015) - 2014
- [j10]Charleen G. Don
, Sereina Riniker
:
Scents and sense: In silico perspectives on olfactory receptors. J. Comput. Chem. 35(32): 2279-2287 (2014) - [j9]Sereina Riniker
, Yuan Wang, Jeremy L. Jenkins, Gregory A. Landrum
:
Using Information from Historical High-Throughput Screens to Predict Active Compounds. J. Chem. Inf. Model. 54(7): 1880-1891 (2014) - 2013
- [j8]Sereina Riniker
, Gregory A. Landrum
:
Open-source platform to benchmark fingerprints for ligand-based virtual screening. J. Cheminformatics 5: 26 (2013) - [j7]Sereina Riniker
, Gregory A. Landrum:
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. J. Cheminformatics 5: 43 (2013) - [j6]Sereina Riniker
, Nikolas Fechner, Gregory A. Landrum
:
Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing. J. Chem. Inf. Model. 53(11): 2829-2836 (2013) - 2012
- [j5]Sereina Riniker
, Luzi J. Barandun, François Diederich, Oliver Krämer
, Andreas Steffen, Wilfred F. van Gunsteren:
Free enthalpies of replacing water molecules in protein binding pockets. J. Comput. Aided Mol. Des. 26(12): 1293-1309 (2012) - [j4]Anna-Pitschna E. Kunz, Jane R. Allison
, Daan P. Geerke
, Bruno A. C. Horta, Philippe H. Hünenberger
, Sereina Riniker
, Nathan Schmid, Wilfred F. van Gunsteren:
New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 33(3): 340-353 (2012) - [j3]Niels Hansen
, Jozica Dolenc
, Matthias Knecht, Sereina Riniker
, Wilfred F. van Gunsteren:
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. J. Comput. Chem. 33(6): 640-651 (2012) - [j2]Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker
, Wilfred F. van Gunsteren, Philippe H. Hünenberger
:
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol. J. Comput. Chem. 33(24): 1907-1917 (2012) - 2011
- [j1]Jozica Dolenc
, Sereina Riniker
, Roberto Gaspari, Xavier Daura
, Wilfred F. van Gunsteren:
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. J. Comput. Aided Mol. Des. 25(8): 709-716 (2011)
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