H. V. van Vlijmen

发表

Evaluation of comparative protein modeling by MODELLER

M. Karplus, A. Sali, Liz Potterton, 1995, Proteins.

Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development

H. V. van Vlijmen, A. Bender, G. V. van Westen, 2011, PloS one.

Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data.

H. V. van Vlijmen, A. Bender, G. V. van Westen, 2012, Journal of medicinal chemistry.

PDB-based protein loop prediction: parameters for selection and methods for optimization.

M. Karplus, H. V. van Vlijmen, H. Vlijmen, 1997, Journal of molecular biology.

A knowledge‐based forcefield for protein–protein interface design

L. A. Clark, H. V. van Vlijmen, 2007, Proteins.

Improving the accuracy of protein pKa calculations: Conformational averaging versus the average structure

M Karplus, M. Karplus, H. V. van Vlijmen, 1998, Proteins.

Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space.

John P. Overington, Julio E. Peironcely, H. V. van Vlijmen, 2011, Current topics in medicinal chemistry.

Structure-based site of metabolism prediction for cytochrome P450 2D6.

Arnout Ceulemans, Maxwell D Cummings, Samuel L. C. Moors, 2011, Journal of medicinal chemistry.

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

P. Coveney, H. V. van Vlijmen, G. Tresadern, 2018, Scientific Reports.

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica‐Exchange

P. Coveney, H. V. van Vlijmen, G. Tresadern, 2019, Advanced theory and simulations.

Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset

Fouad S. Husseini, P. Coveney, H. V. van Vlijmen, 2019, Advanced theory and simulations.

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling

John P. Overington, H. V. van Vlijmen, G. V. van Westen, 2017, J. Chem. Inf. Model..

An antibody loop replacement design feasibility study and a loop-swapped dimer structure.

L. A. Clark, H. V. van Vlijmen, J. Eldredge, 2008, Protein engineering, design & selection : PEDS.

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study.

Laura Pérez-Benito, Herman W T van Vlijmen, Myriam Ciordia, 2017, Journal of chemical theory and computation.

Influence of canonical structure determining residues on antibody affinity and stability.

L. A. Clark, H. V. van Vlijmen, J. Eldredge, 2014, Journal of structural biology.

Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype

Thomas Lengauer, Yardena Peres, Rolf Kaiser, 2008, Antiviral therapy.

Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation

H. V. van Vlijmen, G. Tresadern, Henrik Keränen, 2018, Scientific Reports.

DrugEx v2: De Novo Design of Drug Molecule by Pareto-based Multi-Objective Reinforcement Learning in Polypharmacology

H. V. van Vlijmen, M. Emmerich, A. IJzerman, 2021 .

Extending kinome coverage by analysis of kinase inhibitor broad profiling data.

Edgar Jacoby, Jean-Marc Neefs, Dmitrii Rassokhin, 2015, Drug discovery today.

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Agastya P. Bhati, P. Coveney, H. V. van Vlijmen, 2022, Scientific Reports.

Mutations of the anti-mullerian hormone gene in patients with persistent mullerian duct syndrome: biosynthesis, secretion, and processing of the abnormal proteins and analysis using a three-dimensional model.

H. V. van Vlijmen, J. Picard, C. Belville, 2004, Molecular endocrinology.

Mining protein dynamics from sets of crystal structures using “consensus structures”

Andreas Bender, Jörg K Wegner, Gerard J P van Westen, 2010, Protein science : a publication of the Protein Society.

The CRIPTO/FRL-1/CRYPTIC (CFC) domain of human Cripto. Functional and structural insights through disulfide structure analysis.

H. V. van Vlijmen, Juswinder Singh, H. Adkins, 2003, European journal of biochemistry.

Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations

Rebecca M. Twidale, H. V. van Vlijmen, G. Tresadern, 2020, Chemical science.

The ELF Honest Data Broker: informatics enabling public-private collaboration in a precompetitive arena.

Philip S. Jones, H. V. van Vlijmen, G. Paillard, 2016, Drug discovery today.

DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology

Michael T. M. Emmerich, Adriaan P. IJzerman, Herman W. T. van Vlijmen, 2021, Journal of Cheminformatics.

Pan-cancer functional analysis of somatic mutations in G protein-coupled receptors

H. V. van Vlijmen, G. V. van Westen, A. IJzerman, 2022, Scientific reports.

The European Lead Factory: an updated HTS compound library for innovative drug discovery.

H. V. van Vlijmen, J. Ortholand, Volkhart M-J Li, 2021, Drug discovery today.

Novel bicyclic piperazine derivatives of triazolotriazine and triazolopyrimidines as highly potent and selective adenosine A2A receptor antagonists.

H. V. van Vlijmen, T. Engber, T. Bohnert, 2004, Journal of medicinal chemistry.

Structure-activity relationship of ortho- and meta-phenol based LFA-1 ICAM inhibitors.

H. V. van Vlijmen, K. Guckian, D. Chin, 2008, Bioorganic & medicinal chemistry letters.

Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.

M. Karplus, H. V. van Vlijmen, S. Curry, 1998, Journal of molecular biology.

Advances and Challenges in Computational Target Prediction

Andrea Volkamer, Adriaan P IJzerman, Gerard J P van Westen, 2019, J. Chem. Inf. Model..

A study of model energetics and conformational properties of polynucleotide triplexes

H. V. van Vlijmen, B. Pettitt, Graciela L. Rameé, 1990, Biopolymers.

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

Woody Sherman, Adriaan P. IJzerman, Robert Abel, 2016, ACS omega.

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

George Papadatos, Gerard J. P. van Westen, Adriaan P. IJzerman, 2017, bioRxiv.

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Jeroen Aerssens, Koen Van der Borght, Herman van Vlijmen, 2015, BMC Bioinformatics.

Pan-cancer in silico analysis of somatic mutations in G-protein coupled receptors: The effect of evolutionary conservation and natural variance

H. V. van Vlijmen, G. V. van Westen, A. IJzerman, 2021, bioRxiv.

Structure activity relationships of monocyte chemoattractant proteins in complex with a blocking antibody.

H. V. van Vlijmen, T. Cachero, Fang Qian, 2006, Protein engineering, design & selection : PEDS.

Identification of a New Murine Tumor Necrosis Factor Receptor Locus That Contains Two Novel Murine Receptors for Tumor Necrosis Factor-related Apoptosis-inducing Ligand (TRAIL)*

H. V. van Vlijmen, J. Tschopp, K. Hofmann, 2003, The Journal of Biological Chemistry.

Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs

Adriaan P IJzerman, Gerard J P van Westen, Chi Chung Lam, 2020, J. Chem. Inf. Model..

Trends in Antibody Sequence Changes during the Somatic Hypermutation Process

Herman W. T. van Vlijmen, L. A. Clark, H. V. van Vlijmen, 2006, The Journal of Immunology.

Affinity enhancement of an in vivo matured therapeutic antibody using structure‐based computational design

Woody Sherman, Kenneth Simon, L. A. Clark, 2006, Protein science : a publication of the Protein Society.

Identification of novel inhibitors of rat Mrp3.

H. V. van Vlijmen, Bing Qi, Christophe Buyck, 2021, European Journal of Pharmaceutical Sciences.

Blood-based metabolic signatures in Alzheimer's disease

Philip Scheltens, Thomas Hankemeier, Mark A. van de Wiel, 2017, Alzheimer's & dementia.

Antibody humanization by redesign of complementarity-determining region residues proximate to the acceptor framework.

Herman W T van Vlijmen, Alexey Lugovskoy, Ling Ling Chen, 2014, Methods.

Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein

H. V. van Vlijmen, Peggy Geluykens, M. Cummings, 2009, Proceedings of the National Academy of Sciences.

A model for the antagonist binding site on the adenosine A1 receptor, based on steric, electrostatic, and hydrophobic properties.

H. V. van Vlijmen, A. IJzerman, P. van Galen, 1990, Journal of medicinal chemistry.

Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry.

Martin Karplus, Herman W T van Vlijmen, M. Karplus, 2005, Journal of molecular biology.

Chemical space screening around Phe3 in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings.

H. V. van Vlijmen, L. Gendron, P. Schiller, 2018, Bioorganic & Medicinal Chemistry Letters.

IMI European Lead Factory — democratizing access to high-throughput screening

Stuart P. McElroy, Philip S. Jones, H. V. van Vlijmen, 2021, Nature reviews. Drug discovery.

Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation

H. V. van Vlijmen, G. Tresadern, Henrik Keränen, 2018, Scientific Reports.

The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions

H. V. van Vlijmen, G. Tresadern, H. Geys, 2022, J. Chem. Inf. Model..

Predicting Activity Cliffs with Free-Energy Perturbation.

Mireia Jiménez-Rosés, Laura Pérez-Benito, Gary Tresadern, 2019, Journal of chemical theory and computation.

DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology

Michael T. M. Emmerich, Adriaan P. IJzerman, Herman Van Vlijmen, 2021, Journal of Cheminformatics.

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor

Gerard J. P. van Westen, Adriaan P. IJzerman, Xuhan Liu, 2018, Journal of Cheminformatics.

Electrostatic contributions to molecular free energies in solution.

M. Karplus, H. V. van Vlijmen, M. Schaefer, 1998, Advances in protein chemistry.

A novel database of disulfide patterns and its application to the discovery of distantly related homologs.

Herman W T van Vlijmen, Juswinder Singh, H. V. van Vlijmen, 2004, Journal of molecular biology.

Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors

Adriaan P IJzerman, Gerard J P van Westen, Lindsey Burggraaff, 2020, J. Chem. Inf. Model..

The FAIR Cookbook - the essential resource for and by FAIR doers

Allyson L. Lister, M. Thurston, H. V. van Vlijmen, 2023, Scientific data.

Quantitative prediction of selectivity between the A1 and A2A adenosine receptors

Gerard J. P. van Westen, Adriaan P. IJzerman, Herman W. T. van Vlijmen, 2020, Journal of Cheminformatics.

Mining protein dynamics from sets of crystal structures using “consensus structures”

H. V. van Vlijmen, A. Bender, G. V. van Westen, 2010, Protein Science.

Quantitative prediction of integrase inhibitor resistance from genotype through consensus linear regression modeling

H. V. van Vlijmen, Y. Verlinden, L. Van Wesenbeeck, 2013, Virology Journal.

Alchemical Free Energy Calculations on Membrane-Associated Proteins

H. V. van Vlijmen, P. Matricon, G. Tresadern, 2023, Journal of chemical theory and computation.

Structure-based site of metabolism prediction for cytochrome P450 2D6.

Samuel L. C. Moors, H. V. van Vlijmen, M. Cummings, 2011, Journal of medicinal chemistry.

Kinetic profiling of novel spirobenzo-oxazinepiperidinone derivatives as equilibrative nucleoside transporter 1 inhibitors

H. V. van Vlijmen, A. IJzerman, L. Heitman, 2023, Purinergic signalling.