Sereina Riniker

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 32

Top Topics

Generalized Belief Propagation

Molecular Dynamics

Sampling Procedure

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Cheminformatics

J. Comput. Chem.

Publications

Gregory A. Landrum, Sereina Riniker
Values from Different Sources Is a Source of Significant Noise. J. Chem. Inf. Model. 64 (5) (2024)
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) (2023)
Moritz Thürlemann, Sereina Riniker
Anisotropic Message Passing: Graph Neural Networks with Directional and Long-Range Interactions. ICLR (2023)
Salomé Rieder, Marina P. Oliveira, Sereina Riniker, Philippe H. Hünenberger
Development of an open-source software for isomer enumeration. J. Cheminformatics 15 (1) (2023)
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) (2023)
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) (2023)
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) (2023)
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) (2023)
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) (2022)
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) (2022)
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) (2022)
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) (2022)
Mahendra Awale, Jérôme Hert, Laura Guasch, Sereina Riniker, Christian Kramer
The Playbooks of Medicinal Chemistry Design Moves. J. Chem. Inf. Model. 61 (2) (2021)
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) (2021)
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) (2021)
Kira A. Armacost, Sereina Riniker, Zoe Cournia
Novel Directions in Free Energy Methods and Applications. J. Chem. Inf. Model. 60 (1) (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
Mahendra Awale, Sereina Riniker, Christian Kramer
Matched Molecular Series Analysis for ADME Property Prediction. J. Chem. Inf. Model. 60 (6) (2020)
Kira A. Armacost, Sereina Riniker, Zoe Cournia
Exploring Novel Directions in Free Energy Calculations. J. Chem. Inf. Model. 60 (11) (2020)
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) (2020)
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) (2019)
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) (2019)
Andrea Volkamer, Sereina Riniker
Transition from Academia to Industry and Back. J. Chem. Inf. Model. 58 (8) (2018)
Patrick Bleiziffer, Kay Schaller, Sereina Riniker
Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations. J. Chem. Inf. Model. 58 (3) (2018)
Sereina Riniker
Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. J. Chem. Inf. Model. 58 (3) (2018)
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 (2018)
Sereina Riniker
Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. J. Chem. Inf. Model. 57 (4) (2017)
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) (2017)
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) (2016)
Sereina Riniker, Gregory A. Landrum
Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. J. Chem. Inf. Model. 55 (12) (2015)
Charleen G. Don, Sereina Riniker
perspectives on olfactory receptors. J. Comput. Chem. 35 (32) (2014)
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) (2014)
Sereina Riniker, Gregory A. Landrum
Open-source platform to benchmark fingerprints for ligand-based virtual screening. J. Cheminformatics 5 (2013)
Sereina Riniker, Gregory A. Landrum
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. J. Cheminformatics 5 (2013)
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) (2013)
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) (2012)
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) (2012)
Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren, Philippe H. Hünenberger
-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol. J. Comput. Chem. 33 (24) (2012)
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) (2012)
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) (2011)