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ORCIDSamuel Genheden
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2020 – today
- 2024
[j25]Peter B. R. Hartog, Fabian Krüger, Samuel Genheden, Igor V. Tetko:
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition. J. Cheminformatics 16(1): 39 (2024)- [j24]Lakshidaa Saigiridharan, Alan Kai Hassen, Helen Lai, Paula Torren-Peraire, Ola Engkvist, Samuel Genheden:
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application. J. Cheminformatics 16(1): 57 (2024) - [j23]Varvara Voinarovska
, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V. Tetko:
When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. J. Chem. Inf. Model. 64(1): 42-56 (2024) - [j22]Annie M. Westerlund, Siva Manohar Koki, Supriya Kancharla, Alessandro Tibo, Lakshidaa Saigiridharan, Mikhail Kabeshov, Rocío Mercado, Samuel Genheden:
Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis. J. Chem. Inf. Model. 64(8): 3021-3033 (2024) - [j21]Olaf Wiest, Christoph Alexander Bauer, Paul Helquist, Per-Ola Norrby, Samuel Genheden:
Finding Relevant Retrosynthetic Disconnections for Stereocontrolled Reactions. J. Chem. Inf. Model. 64(15): 5796-5805 (2024) - [c1]Peter B. R. Hartog, Emma Svensson, Lewis H. Mervin, Samuel Genheden, Ola Engkvist, Igor V. Tetko:
Registries in Machine Learning-Based Drug Discovery: A Shortcut to Code Reuse. AIDD@ICANN 2024: 98-115 - 2023
- [j20]Samuel Genheden, Per-Ola Norrby, Ola Engkvist:
AiZynthTrain: Robust, Reproducible, and Extensible Pipelines for Training Synthesis Prediction Models. J. Chem. Inf. Model. 63(7): 1841-1846 (2023) - [i2]Paula Torren-Peraire, Alan Kai Hassen, Samuel Genheden, Jonas Verhoeven, Djork-Arné Clevert, Mike Preuss, Igor V. Tetko:
Models Matter: The Impact of Single-Step Retrosynthesis on Synthesis Planning. CoRR abs/2308.05522 (2023) - 2022
- [j19]Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum:
Fast prediction of distances between synthetic routes with deep learning. Mach. Learn. Sci. Technol. 3(1): 15018 (2022) - [i1]Alan Kai Hassen, Paula Torren-Peraire, Samuel Genheden, Jonas Verhoeven, Mike Preuss, Igor V. Tetko:
Mind the Retrosynthesis Gap: Bridging the divide between Single-step and Multi-step Retrosynthesis Prediction. CoRR abs/2212.11809 (2022) - 2021
- [j18]Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum:
Clustering of Synthetic Routes Using Tree Edit Distance. J. Chem. Inf. Model. 61(8): 3899-3907 (2021) - 2020
- [j17]Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist, Esben Jannik Bjerrum:
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. J. Cheminformatics 12(1): 70 (2020)
2010 – 2019
- 2017
- [j16]Samuel Genheden:
Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models. J. Comput. Aided Mol. Des. 31(10): 867-876 (2017) - [j15]Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde:
Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? J. Chem. Inf. Model. 57(11): 2865-2873 (2017) - 2016
- [j14]Samuel Genheden, Jonathan W. Essex:
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. J. Comput. Aided Mol. Des. 30(11): 969-976 (2016) - 2015
- [j13]Samuel Genheden, Ulf Ryde, Pär Söderhjelm:
Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. J. Comput. Chem. 36(28): 2114-2124 (2015) - 2014
- [j12]Samuel Genheden, Ana I. Cabedo Martinez, Michael P. Criddle, Jonathan W. Essex:
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge. J. Comput. Aided Mol. Des. 28(3): 187-200 (2014) - [j11]Paulius Mikulskis, Daniela Cioloboc, Milica Andrejic, Sakshi Khare, Joakim Brorsson, Samuel Genheden, Ricardo A. Mata, Pär Söderhjelm, Ulf Ryde:
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. J. Comput. Aided Mol. Des. 28(4): 375-400 (2014) - [j10]Paulius Mikulskis, Samuel Genheden, Ulf Ryde:
A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities. J. Chem. Inf. Model. 54(10): 2794-2806 (2014) - 2012
- [j9]Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde:
Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. J. Comput. Aided Mol. Des. 26(5): 527-541 (2012) - [j8]Paulius Mikulskis, Samuel Genheden, Karin Wichmann, Ulf Ryde:
A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections. J. Comput. Chem. 33(12): 1179-1189 (2012) - [j7]Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde:
The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. J. Chem. Inf. Model. 52(8): 2079-2088 (2012) - [j6]Samuel Genheden:
Are Homology Models Sufficiently Good for Free-Energy Simulations? J. Chem. Inf. Model. 52(11): 3013-3021 (2012) - 2011
- [j5]Antonella Ciancetta, Samuel Genheden, Ulf Ryde:
A QM/MM study of the binding of RAPTA ligands to cathepsin B. J. Comput. Aided Mol. Des. 25(8): 729-742 (2011) - [j4]Samuel Genheden:
MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model. J. Comput. Aided Mol. Des. 25(11): 1085-1093 (2011) - [j3]Samuel Genheden, Ulf Ryde:
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. J. Comput. Chem. 32(2): 187-195 (2011) - [j2]Samuel Genheden, Ingemar Nilsson, Ulf Ryde:
Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA. J. Chem. Inf. Model. 51(4): 947-958 (2011) - 2010
- [j1]Samuel Genheden, Ulf Ryde:
How to obtain statistically converged MM/GBSA results. J. Comput. Chem. 31(4): 837-846 (2010)
Coauthor Index
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