Publications by authors named "Samuel Genheden"

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SMARTS-RX: a SMARTS-based representation of chemical functions for reactivity analysis.
Thierry Kogej, Christos Kannas, Samuel Genheden, Eike Caldeweyher, Mikhail Kabeshov

J Cheminform· December 2025

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From concept to chemistry: integrating protection group strategy and reaction feasibility into non-natural amino acid synthesis planning.
Gökçe Geylan, Mikhail Kabeshov, Samuel Genheden, Christos Kannas, Thierry Kogej

Chem Sci· October 2025

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Measuring the efficiency of synthetic routes and transformations using vectors derived from similarity and complexity.
Samuel Genheden, Gareth P Howell

Chem Sci· September 2025

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Precedent Finder: Locating Pareto-Optimal Reactions.
Christoph A Bauer, Thierry Kogej, Samuel Genheden, Per-Ola Norrby

J Chem Inf Model· September 2025

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Human-guided synthesis planning prompting.
Annie M Westerlund, Lakshidaa Saigiridharan, Samuel Genheden

Chem Sci· August 2025

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Network Analysis of the Organic Chemistry in Patents, Literature, and Pharmaceutical Industry.
Emma Svensson, Emma Granqvist, Tomas Bastys, Christos Kannas, Mikhail Kabeshov, Samuel Genheden

Mol Inform· July 2025

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Investigations into the Efficiency of Computer-Aided Synthesis Planning.
Peter B R Hartog, Annie M Westerlund, Igor V Tetko, Samuel Genheden

J Chem Inf Model· February 2025

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Finding Relevant Retrosynthetic Disconnections for Stereocontrolled Reactions.
Olaf Wiest, Christoph Bauer, Paul Helquist, Per-Ola Norrby, Samuel Genheden

J Chem Inf Model· August 2024

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AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application.
Lakshidaa Saigiridharan, Alan Kai Hassen, Helen Lai, Paula Torren-Peraire, Ola Engkvist, Samuel Genheden

J Cheminform· May 2024

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Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition.
Peter B R Hartog, Fabian Krüger, Samuel Genheden, Igor V Tetko

J Cheminform· April 2024

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Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis.
Annie M Westerlund, Siva Manohar Koki, Supriya Kancharla, Alessandro Tibo, Lakshidaa Saigiridharan, Samuel Genheden

J Chem Inf Model· April 2024

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When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges.
Varvara Voinarovska, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V Tetko

J Chem Inf Model· January 2024

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Data-driven approaches for identifying hyperparameters in multi-step retrosynthesis.
Annie M Westerlund, Bente Barge, Lewis Mervin, Samuel Genheden

Mol Inform· November 2023

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Negative Data in Data Sets for Machine Learning Training.
Michael P Maloney, Connor W Coley, Samuel Genheden, Nessa Carson, Paul Helquist

J Org Chem· May 2023

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Negative Data in Data Sets for Machine Learning Training.
Michael P Maloney, Connor W Coley, Samuel Genheden, Nessa Carson, Paul Helquist

Org Lett· May 2023

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AiZynthTrain: Robust, Reproducible, and Extensible Pipelines for Training Synthesis Prediction Models.
Samuel Genheden, Per-Ola Norrby, Ola Engkvist

J Chem Inf Model· April 2023

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Prediction of the Chemical Context for Buchwald-Hartwig Coupling Reactions.
Samuel Genheden, Agnes Mårdh, Gustav Lahti, Ola Engkvist, Simon Olsson

Mol Inform· August 2022

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Clustering of Synthetic Routes Using Tree Edit Distance.
Samuel Genheden, Ola Engkvist, Esben Bjerrum

J Chem Inf Model· August 2021

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Molecular-dynamics-simulation-guided membrane engineering allows the increase of membrane fatty acid chain length in Saccharomyces cerevisiae.
Jeroen M Maertens, Simone Scrima, Matteo Lambrughi, Samuel Genheden, Cecilia Trivellin

Sci Rep· August 2021

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AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning.
Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist

J Cheminform· November 2020

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AI-assisted synthesis prediction.
Simon Johansson, Amol Thakkar, Thierry Kogej, Esben Bjerrum, Samuel Genheden

Drug Discov Today Technol· December 2019

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Mechanism of Trehalose-Induced Protein Stabilization from Neutron Scattering and Modeling.
Christoffer Olsson, Samuel Genheden, Victoria García Sakai, Jan Swenson

J Phys Chem B· May 2019

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Alcohols enhance the rate of acetic acid diffusion in : biophysical mechanisms and implications for acetic acid tolerance.
Lina Lindahl, Samuel Genheden, Fábio Faria-Oliveira, Stefan Allard, Leif A Eriksson

Microb Cell· December 2017

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Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?
Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde

J Chem Inf Model· November 2017

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Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.
Samuel Genheden

J Comput Aided Mol Des· October 2017

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