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Papers in Computational Drug Discovery Methods 50

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DrugEx v3: Scaffold-Constrained Drug Design with Graph Transformer-based Reinforcement Learning
2021 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Xuhan Liu, Kai Ye, Herman van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen

11

citations
Papyrus - A large scale curated dataset aimed at bioactivity predictions
2021 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Olivier J. M. Béquignon, Brandon J. Bongers, Willem Jespers, Adriaan P. IJzerman, Bob van de Water, Gerard J. P. van Westen

8

citations
Excuse me, there is a mutant in my bioactivity soup!A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Marina Gorostiola González, Olivier J. M. Béquignon, Emma J. Manners, Anna Gaulton, Prudence Mutowo, Elisabeth Dawson, +5 more

3

citations
MolBar: A Molecular Identifier for Inorganic and Organic Molecules with Full Support of Stereoisomerism
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Nils van Staalduinen, Christoph Bannwarth

3

citations
MolBar: A Molecular Identifier for Inorganic and Organic Molecules with Full Support of Stereoisomerism
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Nils van Staalduinen, Christoph Bannwarth

3

citations
UnCorrupt SMILES: a novel approach to de novo design
2022 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Linde Schoenmaker, Olivier J. M. Béquignon, Willem Jespers, Gerard J. P. van Westen

3

citations
UnCorrupt SMILES: a novel approach to de novo design
2022 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Linde Schoenmaker, Olivier J. M. Béquignon, Willem Jespers, Gerard J. P. van Westen

3

citations
Generate What You Can Make: Achieving in-house synthesizability with readily available resources in de novo drug design
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Alan Kai Hassen, Martin Šícho, Yorick J. van Aalst, Mirjam C. W. Huizenga, Darcy N. R. Reynolds, Sohvi Luukkonen, +5 more

3

citations
Identifying Novel Inhibitors for Hepatic Organic Ani-on Transporting Polypeptides by Machine-learning based Virtual Screening
2021 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Alzbeta Tuerkova, Brandon J. Bongers, Ulf Norinder, Orsolya Ungvári, Virág Székely, Andrey Tarnovskiy, +4 more

2

citations
Towards assay-aware bioactivity model(er)s: getting a grip on biological context
2025 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Linde Schoenmaker, Enzo G. Sastrokarijo, Laura H. Heitman, Joost B. Beltman, Willem Jespers, Gerard J. P. van Westen

1

citations
Predictions of the poses and affinity of a ligand over the entire surface of a NEET protein: the case of human mitoNEET
2022 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Ke Zuo, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni

1

citations
A community effort to discover small molecule SARS-CoV-2 inhibitors
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, Frank Noé, +93 more

1

citations
3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Marina Gorostiola González, Remco L. van den Broek, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, +1 more

1

citations
QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Helle W. van den Maagdenberg, Martin Šícho, David Alencar Araripe, Sohvi Luukkonen, Linde Schoenmaker, Michiel Jespers, +7 more

1

citations
DrugEx v2: De Novo Design of Drug Molecule by Pareto-based Multi-Objective Reinforcement Learning in Polypharmacology
2021 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Xuhan Liu, Herman van Vlijmen, Michael Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen

1

citations
DrugEx v2: De Novo Design of Drug Molecule by Pareto-based Multi-Objective Reinforcement Learning in Polypharmacology
2021 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Xuhan Liu, Kai Ye, Herman van Vlijmen, Michael Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen

1

citations
Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets
2022 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Agastya P. Bhati, Art Hoti, Andrew Potterton, Peter V. Coveney

1

citations
DrugEx: Deep Learning Models and Tools for Exploration of Drug-like Chemical Space
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Martin Šícho, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier J. M. Béquignon, Gerard J. P. van Westen

1

citations
DrugEx: Deep Learning Models and Tools for Exploration of Drug-like Chemical Space
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Martin Šícho, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier J. M. Béquignon, Gerard J. P. van Westen

1

citations
Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Agastya P. Bhati, Art Hoti, Andrew Potterton, M. Bieniek, Peter V. Coveney

1

citations
MetalDock: an open access docking tool for easy and reproducible docking of metal complexes
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Matthijs L. A. Hakkennes, Francesco Buda, Sylvestre A. Bonnet

1

citations
Docking-informed machine learning for kinome wide affinity prediction
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Jordy Schifferstein, Andrius Bernatavicius, Antonius P. A. Janssen

1

citations
AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative models
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Andrius Bernatavicius, Martin Šícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuß, Gerard J. P. van Westen

1

citations
MULTI-OBJECTIVE SYNTHESIS PLANNING BY MEANS OF MONTE CARLO TREE SEARCH
2024 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Helen Lai, Christos C. Kannas, Alan Kai Hassen, Emma Rydholm, Annie M. Westerlund, Djork-Arné Clevert, +2 more

1

citations
Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design
2025 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Helle W. van den Maagdenberg, Jikke de Mol van Otterloo, J. G. Coen van Hasselt, Piet H. van der Graaf, Gerard J. P. van Westen

1

citations