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Papers matching “binding prediction” 18

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Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding
2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access

Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M. Rangwala, Jessica B. White, +10 more

3

citations
Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site
2025 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

David Alencar Araripe, Alejandro Díaz‐Holguín, Antti Poso, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez‐de‐Terán, +1 more

0

citations
Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-objective molecular optimization
2025 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

David F. Nippa, Kenneth Atz, Yannick Stenzhorn, Alex T. Müller, Andreas Tosstorff, Jörg Benz, +17 more

1

citations
Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-objective molecular optimization
2025 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

David F. Nippa, Kenneth Atz, Yannick Stenzhorn, Alex T. Müller, Andreas Tosstorff, Jörg Benz, +17 more

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
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
QligFEP-2: an automated workflow for small molecule free energy calculations in Q
2025 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

David Alencar Araripe, Alejandro Díaz‐Holguín, Antti Poso, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez‐de‐Terán, +1 more

0

citations
QligFEP-2: an automated workflow for small molecule free energy calculations in Q
2025 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

David Alencar Araripe, Alejandro Díaz‐Holguín, Antti Poso, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez‐de‐Terán, +1 more

0

citations
Assessing the performance of implicit ensembling of neural networks for proteochemometric modeling with RandomNets
2026 ChemRxiv preprint Computer Science Computational Drug Discovery Methods

Chiel Jespers, Olivier J. M. Béquignon, Mike Preuß, Gerard J. P. van Westen

0

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 blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics
2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access

Jonas Goßen, Simone Albani, Anton Hanke, Benjamin Philipp Joseph, Cathrine C. Bergh, Maria Kuzikov, +14 more

5

citations
MULTIMAP TARGETED FREE ENERGY ESTIMATION: A MECHANICAL EMBEDDING QM/MM SCHEME FOR PROTEIN-LIGAND AFFINITIES
2026 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Jacques Gay, Andrea Rizzi, Shina Caroline Lynn Kamerlin, Davide Mandelli, Paolo Carloni

0

citations
Learning to Ground Existentially Quantified Goals
2024 arXiv (Cornell University) preprint Computer Science AI-based Problem Solving and Planning Open access

Martin Funkquist, Simon Ståhlberg, Héctor Geffner

0

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
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
Large-scale modelling of sparse kinase activitydata
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Sohvi Luukkonen, Erik Meijer, Giovanni A. Tricarico, Johan Hofmans, Pieter F. W. Stouten, Gerard J. P. van Westen, +1 more

0

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

0

citations

18 results