Marcel L. Verdonk

Publication Activity (10 Years)

Years Active: 1993-2023
Publications (10 Years): 5

Top Topics

Discriminative Models

Hierarchical Hidden Markov Models

Generative Model

Top Venues

Nat. Mac. Intell.

J. Chem. Inf. Model.

Publications

Lucian Chan, Marcel L. Verdonk, Carl Poelking
Embracing assay heterogeneity with neural processes for markedly improved bioactivity predictions. CoRR (2023)
Lucian Chan, Rajendra Kumar, Marcel L. Verdonk, Carl Poelking
A multilevel generative framework with hierarchical self-contrasting for bias control and transparency in structure-based ligand design. Nat. Mac. Intell. 4 (12) (2022)
Lucian Chan, Rajendra Kumar, Marcel L. Verdonk, Carl Poelking
3D pride without 2D prejudice: Bias-controlled multi-level generative models for structure-based ligand design. CoRR (2022)
Carl Poelking, Gianni Chessari, Christopher W. Murray, Richard J. Hall, Lucy Colwell, Marcel L. Verdonk
Meaningful machine learning models and machine-learned pharmacophores from fragment screening campaigns. CoRR (2022)
João Morado, Paul N. Mortenson, Marcel L. Verdonk, Richard A. Ward, Jonathan W. Essex, Chris-Kriton Skylaris
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields. J. Chem. Inf. Model. 61 (4) (2021)
Oliver Korb, Tjelvar S. G. Olsson, Simon Bowden, Richard J. Hall, Marcel L. Verdonk, John W. Liebeschuetz, Jason C. Cole
Potential and Limitations of Ensemble Docking. J. Chem. Inf. Model. 52 (5) (2012)
Marcel L. Verdonk, Paul N. Mortenson, Richard J. Hall, Michael J. Hartshorn, Christopher W. Murray
Protein-Ligand Docking against Non-Native Protein Conformers. J. Chem. Inf. Model. 48 (11) (2008)
Marcel L. Verdonk, Valerio Berdini, Michael J. Hartshorn, Wijnand T. M. Mooij, Christopher W. Murray, Richard D. Taylor, Paul Watson
Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment. J. Chem. Inf. Model. 44 (3) (2004)
Louise Birch, Christopher W. Murray, Michael J. Hartshorn, Ian J. Tickle, Marcel L. Verdonk
Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. J. Comput. Aided Mol. Des. 16 (12) (2002)
Christopher W. Murray, Marcel L. Verdonk
The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J. Comput. Aided Mol. Des. 16 (10) (2002)
Paul Watson, Peter Willett, Valerie J. Gillet, Marcel L. Verdonk
Calculating the knowledge-based similarity of functional groups using crystallographic data. J. Comput. Aided Mol. Des. 15 (9) (2001)
J. Willem M. Nissink, Marcel L. Verdonk, Gerhard Klebe
Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation. J. Comput. Aided Mol. Des. 14 (8) (2000)
Ian J. Bruno, Jason C. Cole, Jos P. M. Lommerse, R. Scott Rowland, Robin Taylor, Marcel L. Verdonk
IsoStar: A library of information about nonbonded interactions. J. Comput. Aided Mol. Des. 12 (6) (1998)
J. Willem M. Nissink, Marcel L. Verdonk, Jan Kroon, Thomas Mietzner, Gerhard Klebe
Superposition of molecules: Electron density fitting by application of fourier transforms. J. Comput. Chem. 18 (5) (1997)
Ian J. Bruno, Jason C. Cole, Jos P. M. Lommerse, R. Scott Rowland, Robin Taylor, Marcel L. Verdonk
IsoStar: A library of information about nonbonded interactions. J. Comput. Aided Mol. Des. 11 (6) (1997)
Marcel L. Verdonk, R. W. Tjerkstra, I. S. Ridder, Jan A. Kanters, Jan Kroon, W. J. M. van der Kemp
ToBaD: A MEthod for the Estimation of Torsion Barriers from Crystal Structure Data; Conformational Analysis of N, N-Dimethylaniline and Derivatives. J. Comput. Chem. 15 (12) (1994)
Marcel L. Verdonk, Gertjan J. Boks, Huub Kooijman, Jan A. Kanters, Jan Kroon
Stereochemistry of charged nitrogen-aromatic interactions and its involvement in ligand-receptor binding. J. Comput. Aided Mol. Des. 7 (2) (1993)