Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. - Jozica Dolenc; Sereina Riniker; Roberto Gaspari; Xavier Daura; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 2011)

Free enthalpies of replacing water molecules in protein binding pockets. - Sereina Riniker; Luzi J. Barandun; François Diederich; Oliver Krämer; Andreas Steffen; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 2012)

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. - Niels Hansen; Jozica Dolenc; Matthias Knecht; Sereina Riniker; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

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. - Bruno A. C. Horta; Zhixiong Lin; Wei Huang; Sereina Riniker; Wilfred F. van Gunsteren; Philippe H. Hünenberger (J. Comput. Chem., 2012)

New functionalities in the GROMOS biomolecular simulation software. - 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 (J. Comput. Chem., 2012)

Open-source platform to benchmark fingerprints for ligand-based virtual screening. - Sereina Riniker; Gregory A. Landrum (J. Cheminformatics, 2013)

Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. - Sereina Riniker; Gregory A. Landrum (J. Cheminformatics, 2013)

Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing. - Sereina Riniker; Nikolas Fechner; Gregory A. Landrum (J. Chem. Inf. Model., 2013)

Scents and sense: In silico perspectives on olfactory receptors. - Charleen G. Don; Sereina Riniker (J. Comput. Chem., 2014)

Using Information from Historical High-Throughput Screens to Predict Active Compounds. - Sereina Riniker; Yuan Wang; Jeremy L. Jenkins; Gregory A. Landrum (J. Chem. Inf. Model., 2014)

Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. - Sereina Riniker; Gregory A. Landrum (J. Chem. Inf. Model., 2015)

Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. - Jagna Witek; Bettina G. Keller; Marie-Claude Blatter; Axel Meissner; Trixie Wagner; Sereina Riniker (J. Chem. Inf. Model., 2016)

Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. - Sereina Riniker (J. Chem. Inf. Model., 2017)

Correction to Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. - Jagna Witek; Bettina G. Keller; Markus Blatter; Axel Meissner; Trixie Wagner; Sereina Riniker (J. Chem. Inf. Model., 2017)

Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. - Dominik Sidler; Marc Lehner; Simon Frasch; Michael Cristófol-Clough; Sereina Riniker (F1000Research, 2018)

Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations. - Patrick Bleiziffer; Kay Schaller; Sereina Riniker (J. Chem. Inf. Model., 2018)

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. - Sereina Riniker (J. Chem. Inf. Model., 2018)

Transition from Academia to Industry and Back. - Andrea Volkamer; Sereina Riniker (J. Chem. Inf. Model., 2018)

Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. - Lennard Böselt; Dominik Sidler; Tobias Kittelmann; Jürgen Stohner; Daniel Zindel; Trixie Wagner; Sereina Riniker (J. Chem. Inf. Model., 2019)

Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. - Jagna Witek; Shuzhe Wang; Benjamin Schroeder 002; Robin Lingwood; Andreas Dounas; Hans-Jörg Roth; Marianne Fouché; Markus Blatter; Oliver Lemke; Bettina G. Keller; Sereina Riniker (J. Chem. Inf. Model., 2019)

Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. - Shuzhe Wang; Sereina Riniker (J. Comput. Aided Mol. Des., 2020)

Novel Directions in Free Energy Methods and Applications. - Kira A. Armacost; Sereina Riniker; Zoe Cournia (J. Chem. Inf. Model., 2020)

Exploring Novel Directions in Free Energy Calculations. - Kira A. Armacost; Sereina Riniker; Zoe Cournia (J. Chem. Inf. Model., 2020)

Matched Molecular Series Analysis for ADME Property Prediction. - Mahendra Awale; Sereina Riniker; Christian Kramer (J. Chem. Inf. Model., 2020)

Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. - Carmen Esposito; Shuzhe Wang; Udo E. W. Lange; Frank Oellien; Sereina Riniker (J. Chem. Inf. Model., 2020)

Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients. - Julia Gebhardt; Matthias Kiesel; Sereina Riniker; Niels Hansen (J. Chem. Inf. Model., 2020)

An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. - Gerhard König; Nina Glaser; Benjamin Schroeder 002; Alzbeta Kubincová; Philippe H. Hünenberger; Sereina Riniker (J. Chem. Inf. Model., 2020)

Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. - Shuzhe Wang; Jagna Witek; Gregory A. Landrum; Sereina Riniker (J. Chem. Inf. Model., 2020)

The Playbooks of Medicinal Chemistry Design Moves. - Mahendra Awale; Jérôme Hert; Laura Guasch; Sereina Riniker; Christian Kramer (J. Chem. Inf. Model., 2021)

GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning. - Carmen Esposito; Gregory A. Landrum; Nadine Schneider; Nikolaus Stiefl; Sereina Riniker (J. Chem. Inf. Model., 2021)

Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations. - Benjamin Ries; Stephanie M. Linker; David F. Hahn; Gerhard König; Sereina Riniker (J. Chem. Inf. Model., 2021)

Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure. - Benjamin Ries; Karl Normak; R. Gregor Weiß; Salomé Rieder; Emília P. Barros; Candide Champion; Gerhard König; Sereina Riniker (J. Comput. Aided Mol. Des., 2022)

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. - Benjamin Ries; Salomé Rieder; Clemens Rhiner; Philippe H. Hünenberger; Sereina Riniker (J. Comput. Aided Mol. Des., 2022)

Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. - Salomé Rieder; Benjamin Ries; Kay Schaller; Candide Champion; Emília P. Barros; Philippe H. Hünenberger; Sereina Riniker (J. Chem. Inf. Model., 2022)

Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. - 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 (J. Chem. Inf. Model., 2022)

Anisotropic Message Passing: Graph Neural Networks with Directional and Long-Range Interactions. - Moritz Thürlemann; Sereina Riniker (ICLR, 2023)

Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. - Emília P. Barros; Benjamin Ries; Candide Champion; Salomé Rieder; Sereina Riniker (J. Chem. Inf. Model., 2023)

Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations". - Patrick Bleiziffer; Kay Schaller; Sereina Riniker (J. Chem. Inf. Model., 2023)

DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment. - Marc Lehner; Paul Katzberger; Niels Maeder; Carl C. G. Schiebroek; Jakob Teetz; Gregory A. Landrum; Sereina Riniker (J. Chem. Inf. Model., 2023)

Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. - Candide Champion; René Gall; Benjamin Ries; Salomé Rieder; Emília P. Barros; Sereina Riniker (J. Chem. Inf. Model., 2023)

SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches. - Gregory A. Landrum; Maximilian Beckers; Jessica Lanini; Nadine Schneider; Nikolaus Stiefl; Sereina Riniker (J. Cheminformatics, 2023)

Development of an open-source software for isomer enumeration. - Salomé Rieder; Marina P. Oliveira; Sereina Riniker; Philippe H. Hünenberger (J. Cheminformatics, 2023)

Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings. - Jessica Braun; Paul Katzberger; Gregory A. Landrum; Sereina Riniker (J. Chem. Inf. Model., 2024)

lwreg: A Lightweight System for Chemical Registration and Data Storage. - Gregory A. Landrum; Jessica Braun; Paul Katzberger; Marc Lehner; Sereina Riniker (J. Chem. Inf. Model., 2024)

Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents. - Franz Waibl; Fabio Casagrande; Fabian Dey; Sereina Riniker (J. Chem. Inf. Model., 2024)

Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise. - Gregory A. Landrum; Sereina Riniker (J. Chem. Inf. Model., 2024)

A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS. - Peter Poliak; Patrick Bleiziffer; Felix Pultar; Sereina Riniker; Chris Oostenbrink (J. Comput. Chem., 2025)