Author details

Full Name

Marc van Dijk

Affiliation

ORCID

Career Start Year

2006

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37310542	OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.	J Comput Aided Mol Des	2023
32626725	Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations.	Frontiers in Molecular Biosciences	2020
31461271	A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.	Journal of Chemical Information and Modeling	2019
29318967	Inter-individual Variability in Activity of the Major Drug Metabolizing Enzymes in Liver Homogenates of 20 Individuals.	Current Drug Metabolism	2018
28889350	Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.	Journal of Computer-Aided Molecular Design	2018
29258884	Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine.	Toxicol In Vitro	2018
27802573	Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.	Proteins	2017
28776988	Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors.	Journal of Chemical Information and Modeling	2017
28730688	Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418).	Proteins	2017
29159598	eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.	Journal of Cheminformatics	2017
26410586	The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.	J Mol Biol	2016
25242457	Mass spec studio for integrative structural biology.	Structure	2014
24155158	Blind prediction of interfacial water positions in CAPRI.	Proteins	2014
23625455	Solvated protein-DNA docking using HADDOCK.	J Biomol NMR	2013
23913867	Defining the limits of homology modeling in information-driven protein docking.	Proteins	2013
23143278	Rapid prediction of multi-dimensional NMR data sets.	J Biomol NMR	2012
26592996	A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.	J Chem Theory Comput	2012
22483113	The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition.	Structure	2012
20466807	Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.	Nucleic Acids Res	2010
20718048	Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.	Proteins	2010
20431534	The HADDOCK web server for data-driven biomolecular docking.	Nat Protoc	2010
19417072	3D-DART: a DNA structure modelling server.	Nucleic Acids Res	2009
18583363	A protein-DNA docking benchmark.	Nucleic Acids Res	2008
17803234	HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets.	Proteins	2007
16820531	Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility.	Nucleic Acids Res	2006