Samuel Genheden

32 papers Journal 31Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Exploring Modularity of Agentic Systems for Drug Discovery. CoRR Laura van Weesep, Samuel Genheden, Ola Engkvist, Jens Sjölund
2025	J	`jnl`	Investigations into the Efficiency of Computer-Aided Synthesis Planning. J. Chem. Inf. Model. Peter B. R. Hartog, Annie M. Westerlund, Igor V. Tetko, Samuel Genheden
2025	J	`jnl`	Precedent Finder: Locating Pareto-Optimal Reactions. J. Chem. Inf. Model. Christoph Alexander Bauer, Thierry Kogej, Samuel Genheden, Per-Ola Norrby
2025	J	`jnl`	SMARTS-RX: a SMARTS-based representation of chemical functions for reactivity analysis. J. Cheminformatics Thierry Kogej, Christos Kannas, Samuel Genheden, Eike Caldeweyher, Mikhail Kabeshov
2024	J	`jnl`	AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application. J. Cheminformatics Lakshidaa Saigiridharan, Alan Kai Hassen, Helen Lai, Paula Torren-Peraire, Ola Engkvist, Samuel Genheden
2024	J	`jnl`	Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis. J. Chem. Inf. Model. Annie M. Westerlund, Siva Manohar Koki, Supriya Kancharla, Alessandro Tibo, Lakshidaa Saigiridharan, Mikhail Kabeshov, Rocío Mercado, Samuel Genheden
2024	J	`jnl`	Finding Relevant Retrosynthetic Disconnections for Stereocontrolled Reactions. J. Chem. Inf. Model. Olaf Wiest, Christoph Alexander Bauer, Paul Helquist, Per-Ola Norrby, Samuel Genheden
2024	—	`conf`	Registries in Machine Learning-Based Drug Discovery: A Shortcut to Code Reuse. AIDD@ICANN Peter B. R. Hartog, Emma Svensson, Lewis H. Mervin, Samuel Genheden, Ola Engkvist, Igor V. Tetko
2024	J	`jnl`	Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition. J. Cheminformatics Peter B. R. Hartog, Fabian Krüger, Samuel Genheden, Igor V. Tetko
2024	J	`jnl`	When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. J. Chem. Inf. Model. Varvara Voinarovska, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V. Tetko
2023	J	`jnl`	AiZynthTrain: Robust, Reproducible, and Extensible Pipelines for Training Synthesis Prediction Models. J. Chem. Inf. Model. Samuel Genheden, Per-Ola Norrby, Ola Engkvist
2023	J	`jnl`	Models Matter: The Impact of Single-Step Retrosynthesis on Synthesis Planning. CoRR Paula Torren-Peraire, Alan Kai Hassen, Samuel Genheden, Jonas Verhoeven, Djork-Arné Clevert, Mike Preuss, Igor V. Tetko
2022	J	`jnl`	Fast prediction of distances between synthetic routes with deep learning. Mach. Learn. Sci. Technol. Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum
2022	J	`jnl`	Mind the Retrosynthesis Gap: Bridging the divide between Single-step and Multi-step Retrosynthesis Prediction. CoRR Alan Kai Hassen, Paula Torren-Peraire, Samuel Genheden, Jonas Verhoeven, Mike Preuss, Igor V. Tetko
2021	J	`jnl`	Clustering of Synthetic Routes Using Tree Edit Distance. J. Chem. Inf. Model. Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum
2020	J	`jnl`	AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. J. Cheminformatics Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist, Esben Jannik Bjerrum
2017	J	`jnl`	Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? J. Chem. Inf. Model. Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde
2017	J	`jnl`	Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models. J. Comput. Aided Mol. Des. Samuel Genheden
2016	J	`jnl`	All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. J. Comput. Aided Mol. Des. Samuel Genheden, Jonathan W. Essex
2015	J	`jnl`	Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. J. Comput. Chem. Samuel Genheden, Ulf Ryde, Pär Söderhjelm
2014	J	`jnl`	A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities. J. Chem. Inf. Model. Paulius Mikulskis, Samuel Genheden, Ulf Ryde
2014	J	`jnl`	Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge. J. Comput. Aided Mol. Des. Samuel Genheden, Ana I. Cabedo Martinez, Michael P. Criddle, Jonathan W. Essex
2014	J	`jnl`	Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. J. Comput. Aided Mol. Des. Paulius Mikulskis, Daniela Cioloboc, Milica Andrejic, Sakshi Khare, Joakim Brorsson, Samuel Genheden, Ricardo A. Mata, Pär Söderhjelm, Ulf Ryde
2012	J	`jnl`	A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections. J. Comput. Chem. Paulius Mikulskis, Samuel Genheden, Karin Wichmann, Ulf Ryde
2012	J	`jnl`	Are Homology Models Sufficiently Good for Free-Energy Simulations? J. Chem. Inf. Model. Samuel Genheden
2012	J	`jnl`	Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. J. Comput. Aided Mol. Des. Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde
2012	J	`jnl`	The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. J. Chem. Inf. Model. Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde
2011	J	`jnl`	A QM/MM study of the binding of RAPTA ligands to cathepsin B. J. Comput. Aided Mol. Des. Antonella Ciancetta, Samuel Genheden, Ulf Ryde
2011	J	`jnl`	A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. J. Comput. Chem. Samuel Genheden, Ulf Ryde
2011	J	`jnl`	Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA. J. Chem. Inf. Model. Samuel Genheden, Ingemar Nilsson, Ulf Ryde
2011	J	`jnl`	MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model. J. Comput. Aided Mol. Des. Samuel Genheden
2010	J	`jnl`	How to obtain statistically converged MM/GBSA results. J. Comput. Chem. Samuel Genheden, Ulf Ryde