Stereochemistry of charged nitrogen-aromatic interactions and its involvement in ligand-receptor binding. - Marcel L. Verdonk; Gertjan J. Boks; Huub Kooijman; Jan A. Kanters; Jan Kroon (J. Comput. Aided Mol. Des., 1993)

ToBaD: A MEthod for the Estimation of Torsion Barriers from Crystal Structure Data; Conformational Analysis of N, N-Dimethylaniline and Derivatives. - Marcel L. Verdonk; R. W. Tjerkstra; I. S. Ridder; Jan A. Kanters; Jan Kroon; W. J. M. van der Kemp (J. Comput. Chem., 1994)

IsoStar: A library of information about nonbonded interactions. - Ian J. Bruno; Jason C. Cole; Jos P. M. Lommerse; R. Scott Rowland; Robin Taylor; Marcel L. Verdonk (J. Comput. Aided Mol. Des., 1997)

Superposition of molecules: Electron density fitting by application of fourier transforms. - J. Willem M. Nissink; Marcel L. Verdonk; Jan Kroon; Thomas Mietzner; Gerhard Klebe (J. Comput. Chem., 1997)

Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation. - J. Willem M. Nissink; Marcel L. Verdonk; Gerhard Klebe (J. Comput. Aided Mol. Des., 2000)

Calculating the knowledge-based similarity of functional groups using crystallographic data. - Paul Watson 002; Peter Willett 002; Valerie J. Gillet; Marcel L. Verdonk (J. Comput. Aided Mol. Des., 2001)

Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. - Louise Birch; Christopher W. Murray; Michael J. Hartshorn; Ian J. Tickle; Marcel L. Verdonk (J. Comput. Aided Mol. Des., 2002)

The consequences of translational and rotational entropy lost by small molecules on binding to proteins. - Christopher W. Murray; Marcel L. Verdonk (J. Comput. Aided Mol. Des., 2002)

Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment. - Marcel L. Verdonk; Valerio Berdini; Michael J. Hartshorn; Wijnand T. M. Mooij; Christopher W. Murray; Richard D. Taylor; Paul Watson 002 (J. Chem. Inf. Model., 2004)

Protein-Ligand Docking against Non-Native Protein Conformers. - Marcel L. Verdonk; Paul N. Mortenson; Richard J. Hall; Michael J. Hartshorn; Christopher W. Murray (J. Chem. Inf. Model., 2008)

Potential and Limitations of Ensemble Docking. - Oliver Korb; Tjelvar S. G. Olsson; Simon Bowden; Richard J. Hall; Marcel L. Verdonk; John W. Liebeschuetz; Jason C. Cole (J. Chem. Inf. Model., 2012)

ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields. - João Morado; Paul N. Mortenson; Marcel L. Verdonk; Richard A. Ward; Jonathan W. Essex; Chris-Kriton Skylaris (J. Chem. Inf. Model., 2021)

Meaningful machine learning models and machine-learned pharmacophores from fragment screening campaigns. - Carl Poelking; Gianni Chessari; Christopher W. Murray; Richard J. Hall; Lucy J. Colwell; Marcel L. Verdonk (CoRR, 2022)

3D pride without 2D prejudice: Bias-controlled multi-level generative models for structure-based ligand design. - Lucian Chan; Rajendra Kumar; Marcel L. Verdonk; Carl Poelking (CoRR, 2022)

A multilevel generative framework with hierarchical self-contrasting for bias control and transparency in structure-based ligand design. - Lucian Chan; Rajendra Kumar; Marcel L. Verdonk; Carl Poelking (Nat. Mac. Intell., 2022)

Embracing assay heterogeneity with neural processes for markedly improved bioactivity predictions. - Lucian Chan; Marcel L. Verdonk; Carl Poelking (CoRR, 2023)