Samuel Genheden

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 14

Top Topics

Tree Edit Distance

Protein Sequences

Prediction Model

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Cheminformatics

Publications

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) (2024)
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) (2024)
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) (2024)
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) (2024)
Samuel Genheden, Per-Ola Norrby, Ola Engkvist
AiZynthTrain: Robust, Reproducible, and Extensible Pipelines for Training Synthesis Prediction Models. J. Chem. Inf. Model. 63 (7) (2023)
Paula Torren-Peraire, Alan Kai Hassen, Samuel Genheden, Jonas Verhoeven, Djork-Arne Clevert, Mike Preuss, Igor V. Tetko
Models Matter: The Impact of Single-Step Retrosynthesis on Synthesis Planning. CoRR (2023)
Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum
Fast prediction of distances between synthetic routes with deep learning. Mach. Learn. Sci. Technol. 3 (1) (2022)
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 (2022)
Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum
Clustering of Synthetic Routes Using Tree Edit Distance. J. Chem. Inf. Model. 61 (8) (2021)
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) (2020)
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) (2017)
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) (2017)
Samuel Genheden, Jonathan W. Essex
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. J. Comput. Aided Mol. Des. 30 (11) (2016)
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) (2015)
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) (2014)
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) (2014)
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) (2014)
Samuel Genheden
Are Homology Models Sufficiently Good for Free-Energy Simulations? J. Chem. Inf. Model. 52 (11) (2012)
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) (2012)
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) (2012)
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) (2012)
Samuel Genheden, Ulf Ryde
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. J. Comput. Chem. 32 (2) (2011)
Samuel Genheden
MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model. J. Comput. Aided Mol. Des. 25 (11) (2011)
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) (2011)
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) (2011)
Samuel Genheden, Ulf Ryde
How to obtain statistically converged MM/GBSA results. J. Comput. Chem. 31 (4) (2010)