Sereina Riniker

48 papers A* 1Journal 47

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS. J. Comput. Chem. Peter Poliak, Patrick Bleiziffer, Felix Pultar, Sereina Riniker, Chris Oostenbrink
2025	J	`jnl`	Unraveling Torsional Preferences: Comparative Analysis of Torsion Motif Torsional-Angle Distributions across Different Environments. J. Chem. Inf. Model. Jessica Braun, Paul Katzberger, Gregory A. Landrum, Djahan Lamei, Sereina Riniker
2024	J	`jnl`	Combining IC J. Chem. Inf. Model. Gregory A. Landrum, Sereina Riniker
2024	J	`jnl`	Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings. J. Chem. Inf. Model. Jessica Braun, Paul Katzberger, Gregory A. Landrum, Sereina Riniker
2024	J	`jnl`	Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents. J. Chem. Inf. Model. Franz Waibl, Fabio Casagrande, Fabian Dey, Sereina Riniker
2024	J	`jnl`	lwreg: A Lightweight System for Chemical Registration and Data Storage. J. Chem. Inf. Model. Gregory A. Landrum, Jessica Braun, Paul Katzberger, Marc Lehner, Sereina Riniker
2023	J	`jnl`	Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. J. Chem. Inf. Model. Candide Champion, René Gall, Benjamin Ries, Salomé Rieder, Emília P. Barros, Sereina Riniker
2023	J	`jnl`	Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. J. Chem. Inf. Model. Emília P. Barros, Benjamin Ries, Candide Champion, Salomé Rieder, Sereina Riniker
2023	A*	`conf`	Anisotropic Message Passing: Graph Neural Networks with Directional and Long-Range Interactions. ICLR Moritz Thürlemann, Sereina Riniker
2023	J	`jnl`	Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations". J. Chem. Inf. Model. Patrick Bleiziffer, Kay Schaller, Sereina Riniker
2023	J	`jnl`	DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment. J. Chem. Inf. Model. Marc Lehner, Paul Katzberger, Niels Maeder, Carl C. G. Schiebroek, Jakob Teetz, Gregory A. Landrum, Sereina Riniker
2023	J	`jnl`	Development of an open-source software for isomer enumeration. J. Cheminformatics Salomé Rieder, Marina P. Oliveira, Sereina Riniker, Philippe H. Hünenberger
2023	J	`jnl`	SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches. J. Cheminformatics Gregory A. Landrum, Maximilian Beckers, Jessica Lanini, Nadine Schneider, Nikolaus Stiefl, Sereina Riniker
2022	J	`jnl`	Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. J. Chem. Inf. Model. 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
2022	J	`jnl`	Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure. J. Comput. Aided Mol. Des. Benjamin Ries, Karl Normak, R. Gregor Weiß, Salomé Rieder, Emília P. Barros, Candide Champion, Gerhard König, Sereina Riniker
2022	J	`jnl`	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. Salomé Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emília P. Barros, Philippe H. Hünenberger, Sereina Riniker
2022	J	`jnl`	RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. J. Comput. Aided Mol. Des. Benjamin Ries, Salomé Rieder, Clemens Rhiner, Philippe H. Hünenberger, Sereina Riniker
2021	J	`jnl`	Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations. J. Chem. Inf. Model. Benjamin Ries, Stephanie M. Linker, David F. Hahn, Gerhard König, Sereina Riniker
2021	J	`jnl`	GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning. J. Chem. Inf. Model. Carmen Esposito, Gregory A. Landrum, Nadine Schneider, Nikolaus Stiefl, Sereina Riniker
2021	J	`jnl`	The Playbooks of Medicinal Chemistry Design Moves. J. Chem. Inf. Model. Mahendra Awale, Jérôme Hert, Laura Guasch, Sereina Riniker, Christian Kramer
2020	J	`jnl`	An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. J. Chem. Inf. Model. Gerhard König, Nina Glaser, Benjamin Schroeder, Alzbeta Kubincová, Philippe H. Hünenberger, Sereina Riniker
2020	J	`jnl`	Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. J. Chem. Inf. Model. Carmen Esposito, Shuzhe Wang, Udo E. W. Lange, Frank Oellien, Sereina Riniker
2020	J	`jnl`	Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients. J. Chem. Inf. Model. Julia Gebhardt, Matthias Kiesel, Sereina Riniker, Niels Hansen
2020	J	`jnl`	Exploring Novel Directions in Free Energy Calculations. J. Chem. Inf. Model. Kira A. Armacost, Sereina Riniker, Zoe Cournia
2020	J	`jnl`	Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. J. Chem. Inf. Model. Shuzhe Wang, Jagna Witek, Gregory A. Landrum, Sereina Riniker
2020	J	`jnl`	Matched Molecular Series Analysis for ADME Property Prediction. J. Chem. Inf. Model. Mahendra Awale, Sereina Riniker, Christian Kramer
2020	J	`jnl`	Novel Directions in Free Energy Methods and Applications. J. Chem. Inf. Model. Kira A. Armacost, Sereina Riniker, Zoe Cournia
2020	J	`jnl`	Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. J. Comput. Aided Mol. Des. Shuzhe Wang, Sereina Riniker
2019	J	`jnl`	Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. J. Chem. Inf. Model. Lennard Böselt, Dominik Sidler, Tobias Kittelmann, Jürgen Stohner, Daniel Zindel, Trixie Wagner, Sereina Riniker
2019	J	`jnl`	Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J. Chem. Inf. Model. Jagna Witek, Shuzhe Wang, Benjamin Schroeder, Robin Lingwood, Andreas Dounas, Hans-Jörg Roth, Marianne Fouché, Markus Blatter, Oliver Lemke, Bettina G. Keller, Sereina Riniker
2018	J	`jnl`	Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. F1000Research Dominik Sidler, Marc Lehner, Simon Frasch, Michael Cristófol-Clough, Sereina Riniker
2018	J	`jnl`	Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. J. Chem. Inf. Model. Sereina Riniker
2018	J	`jnl`	Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations. J. Chem. Inf. Model. Patrick Bleiziffer, Kay Schaller, Sereina Riniker
2018	J	`jnl`	Transition from Academia to Industry and Back. J. Chem. Inf. Model. Andrea Volkamer, Sereina Riniker
2017	J	`jnl`	Correction to Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J. Chem. Inf. Model. Jagna Witek, Bettina G. Keller, Markus Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker
2017	J	`jnl`	Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. J. Chem. Inf. Model. Sereina Riniker
2016	J	`jnl`	Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J. Chem. Inf. Model. Jagna Witek, Bettina G. Keller, Marie-Claude Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker
2015	J	`jnl`	Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. J. Chem. Inf. Model. Sereina Riniker, Gregory A. Landrum
2014	J	`jnl`	Scents and sense: J. Comput. Chem. Charleen G. Don, Sereina Riniker
2014	J	`jnl`	Using Information from Historical High-Throughput Screens to Predict Active Compounds. J. Chem. Inf. Model. Sereina Riniker, Yuan Wang, Jeremy L. Jenkins, Gregory A. Landrum
2013	J	`jnl`	Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing. J. Chem. Inf. Model. Sereina Riniker, Nikolas Fechner, Gregory A. Landrum
2013	J	`jnl`	Open-source platform to benchmark fingerprints for ligand-based virtual screening. J. Cheminformatics Sereina Riniker, Gregory A. Landrum
2013	J	`jnl`	Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. J. Cheminformatics Sereina Riniker, Gregory A. Landrum
2012	J	`jnl`	Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. J. Comput. Chem. Niels Hansen, Jozica Dolenc, Matthias Knecht, Sereina Riniker, Wilfred F. van Gunsteren
2012	J	`jnl`	Free enthalpies of replacing water molecules in protein binding pockets. J. Comput. Aided Mol. Des. Sereina Riniker, Luzi J. Barandun, François Diederich, Oliver Krämer, Andreas Steffen, Wilfred F. van Gunsteren
2012	J	`jnl`	New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 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
2012	J	`jnl`	Reoptimized interaction parameters for the peptide-backbone model compound J. Comput. Chem. Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren, Philippe H. Hünenberger
2011	J	`jnl`	Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. J. Comput. Aided Mol. Des. Jozica Dolenc, Sereina Riniker, Roberto Gaspari, Xavier Daura, Wilfred F. van Gunsteren