M. Verdonk

发表

Improved protein–ligand docking using GOLD

Richard D. Taylor, C. Murray, M. Verdonk, 2003, Proteins.

Virtual Screening Using Protein—Ligand Docking: Avoiding Artificial Enrichment.

Richard D. Taylor, C. Murray, M. Verdonk, 2004 .

SuperStar: improved knowledge-based interaction fields for protein binding sites.

P. Willett, M. Verdonk, J. Cole, 2001, Journal of molecular biology.

Modeling water molecules in protein-ligand docking using GOLD.

Richard D. Taylor, C. Murray, Robin Taylor, 2005, Journal of medicinal chemistry.

3D pride without 2D prejudice: Bias-controlled multi-level generative models for structure-based ligand design

Lucian Chan, M. Verdonk, Rajendra Kumar, 2022, ArXiv.

Diverse, high-quality test set for the validation of protein-ligand docking performance.

Paul N. Mortenson, C. Murray, M. Verdonk, 2007, Journal of medicinal chemistry.

Structure-guided fragment screening for lead discovery.

M. Verdonk, M. Hartshorn, 2004, Current opinion in drug discovery & development.

SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

Robin Taylor, M. Verdonk, J. Cole, 1999, Journal of molecular biology.

Experiences in fragment-based drug discovery.

Christopher W Murray, Marcel L Verdonk, C. Murray, 2012, Trends in pharmacological sciences.

Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects.

G Klebe, M Hendlich, G. Klebe, 2001, Biopolymers.

Entropic Consequences of Linking Ligands

Christopher W. Murray, C. Murray, M. Verdonk, 2006 .

Predicting "Hot" and "Warm" Spots for Fragment Binding.

Christopher W Murray, Richard J. Hall, Marcel L Verdonk, 2017, Journal of medicinal chemistry.

SuperStar: comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions.

M. Verdonk, J. Cole, J. Kroon, 2001, Journal of molecular biology.

Group Efficiency: A Guideline for Hits‐to‐Leads Chemistry

Marcel L Verdonk, M. Verdonk, D. Rees, 2008, ChemMedChem.

Detection of secondary binding sites in proteins using fragment screening

Marcel L Verdonk, M. Verdonk, H. Jhoti, 2015, Proceedings of the National Academy of Sciences.

Fragment-based screening using X-ray crystallography and NMR spectroscopy.

Glyn Williams, M. Verdonk, H. Jhoti, 2007, Current opinion in chemical biology.

Docking performance of fragments and druglike compounds.

Richard J. Hall, Paul N. Mortenson, C. Murray, 2011, Journal of medicinal chemistry.

Melting behaviour of molecular mixed crystalline materials: measurement with adiabatic calorimetry and modelling using ULTRACAL

M. Verdonk, J. C. Miltenburg, H. Oonk, 2002 .

Crystal and molecular structure of 2,4,6-tri-O-benzoyl-3-O-benzyl-β-l-idopyranosyl fluoride

M. Verdonk, J. Kroon, R. Tjerkstra, 1996 .

On the bioactive conformation of R(+)-8-chloro-2,3,4,5-tetrahydro-3-methyl-5-phenyl-1H-3-benzazepin-7-ol

M. Verdonk, J. Kroon, F. B. Duijneveldt, 1994 .

On the estimation of thermodynamic excess properties of binary solid solutions

M. Verdonk, H. Oonk, P. V. D. Linde, 1993 .

Identification of inhibitors of protein kinase B using fragment-based lead discovery.

Marcel L Verdonk, Paul G Wyatt, Michelle D Garrett, 2007, Journal of medicinal chemistry.

Stereochemistry of charged nitrogen-aromatic interactions and its involvement in ligand-receptor binding

Jan Kroon, Marcel L. Verdonk, Jan A. Kanters, 1993, J. Comput. Aided Mol. Des..

Binary alkaline earth oxide mixtures: Estimation of the excess thermodynamic properties and calculation of the phase diagrams

M. Verdonk, H. Oonk, P. V. D. Linde, 1994 .

Isomorphism of 2-methylnaphthalene and 2-halonaphthalenes as a revealer of a special interaction between methyl and halogen

I. C. Kok, M. Verdonk, D. Mondieig, 1999 .

A multilevel generative framework with hierarchical self-contrasting for bias control and transparency in structure-based ligand design

Lucian Chan, M. Verdonk, C. Poelking, 2022, Nature Machine Intelligence.

A new test set for validating predictions of protein–ligand interaction

Robin Taylor, J Willem M Nissink, Jason C Cole, 2002, Proteins.

Directional preferences of intermolecular contacts to hydrophobic groups.

M. Verdonk, J. Cole, R. Taylor, 1998, Acta crystallographica. Section D, Biological crystallography.

A structural comparison of inhibitor binding to PKB, PKA and PKA-PKB chimera.

Ian Collins, Paul Workman, Brent Graham, 2007, Journal of molecular biology.

Potential and Limitations of Ensemble Docking

Oliver Korb, Jason C. Cole, Tjelvar S. G. Olsson, 2012, J. Chem. Inf. Model..

General and targeted statistical potentials for protein–ligand interactions

Marcel L Verdonk, Wijnand T M Mooij, M. Verdonk, 2005, Proteins.

IsoStar: A library of information about nonbonded interactions

Robin Taylor, Jason C. Cole, Marcel L. Verdonk, 1997, J. Comput. Aided Mol. Des..

Identification of 4-(4-aminopiperidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidines as selective inhibitors of protein kinase B through fragment elaboration.

Ian Collins, Paul Workman, Michelle D Garrett, 2008, Journal of medicinal chemistry.

The consequences of translational and rotational entropy lost by small molecules on binding to proteins

Marcel L. Verdonk, Christopher W. Murray, C. Murray, 2002, J. Comput. Aided Mol. Des..

Practical High-Quality Electrostatic Potential Surfaces for Drug Discovery Using a Graph-Convolutional Deep Neural Network.

M. Verdonk, R. Ludlow, P. C. Rathi, 2019, Journal of medicinal chemistry.

Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment

Paul Watson, Marcel L. Verdonk, Christopher W. Murray, 2004, J. Chem. Inf. Model..

Superposition of molecules: Electron density fitting by application of fourier transforms

Gerhard Klebe, Jan Kroon, Marcel L. Verdonk, 1997, J. Comput. Chem..

Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?

Julien Michel, Jonathan W Essex, Marcel L Verdonk, 2006, Journal of medicinal chemistry.

Prediction of binding modes for ligands in the cytochromes P450 and other heme‐containing proteins

Stewart B Kirton, Richard D. Taylor, Christopher W Murray, 2005, Proteins.

Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase

Marcel L. Verdonk, Christopher W. Murray, Michael J. Hartshorn, 2002, J. Comput. Aided Mol. Des..

COSMIC-3D provides structural perspectives on cancer genetics for drug discovery

Marcel L Verdonk, S. Forbes, M. Verdonk, 2018, Nature Genetics.

A web-based platform for virtual screening.

Paul Watson, Marcel Verdonk, Michael J Hartshorn, 2003, Journal of molecular graphics & modelling.

ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields

Jonathan W. Essex, Marcel L. Verdonk, Chris-Kriton Skylaris, 2021, J. Chem. Inf. Model..

The Fragment Network: A Chemistry Recommendation Engine Built Using a Graph Database.

Christopher W Murray, Richard J. Hall, Marcel L Verdonk, 2017, Journal of medicinal chemistry.

Fragment-Guided Discovery of Pyrazole Carboxylic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2 Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction.

M. Verdonk, W. Rumsey, H. Willems, 2021, Journal of medicinal chemistry.

Generation of Quantum Configurational Ensembles Using Approximate Potentials.

Paul N. Mortenson, M. Verdonk, J. Essex, 2021, Journal of chemical theory and computation.

Meaningful machine learning models and machine-learned pharmacophores from fragment screening campaigns

Lucy J. Colwell, Richard J. Hall, C. Murray, 2022, ArXiv.

Illustration of Current Challenges in Molecular Docking

Gianni Chessari, Christopher William Murray, Marcel L. Verdonk, 2007 .

Protein-Ligand Complexes: Computation of the Relative Free Energy of Different Scaffolds and Binding Modes.

Julien Michel, Jonathan W Essex, Marcel L Verdonk, 2007, Journal of chemical theory and computation.

Automated Protein–Ligand Crystallography for Structure‐Based Drug Design

Marcel L Verdonk, Michael J Hartshorn, Wijnand T M Mooij, 2006, ChemMedChem.

Embracing assay heterogeneity with neural processes for markedly improved bioactivity predictions

Lucian Chan, M. Verdonk, C. Poelking, 2023, ArXiv.

A comparison of physicochemical property profiles of marketed oral drugs and orally bioavailable anti-cancer protein kinase inhibitors in clinical development.

M. Verdonk, A. Gill, Adrian L Gill, 2007, Current topics in medicinal chemistry.

Calculating the knowledge-based similarity of functional groups using crystallographic data

Paul Watson, Peter Willett, Valerie J. Gillet, 2001, J. Comput. Aided Mol. Des..

ParaMol: A Package for Parametrization of Molecular Mechanics Force Fields

Paul N. Mortenson, M. Verdonk, J. Essex, 2021 .

Protein-Ligand Docking against Non-Native Protein Conformers

Marcel L. Verdonk, Michael J. Hartshorn, Richard J. Hall, 2008, J. Chem. Inf. Model..