Multi-model inference using mixed effects from a linear regression based genetic algorithm

por Van der Borght, Koen, Verbeke, Geert, van Vlijmen, Herman
Publicado 2014

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

por Pérez-Benito, Laura, Keränen, Henrik, van Vlijmen, Herman, Tresadern, Gary
Publicado 2018

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

por Voice, Angus T., Tresadern, Gary, Twidale, Rebecca M., van Vlijmen, Herman, Mulholland, Adrian J.
Publicado 2021

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

por Wan, Shunzhou, Tresadern, Gary, Pérez‐Benito, Laura, van Vlijmen, Herman, Coveney, Peter V.
Publicado 2019

Quantitative prediction of selectivity between the A(1) and A(2A) adenosine receptors

por Burggraaff, Lindsey, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.
Publicado 2020

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

por Wright, David W., Wan, Shunzhou, Meyer, Christophe, van Vlijmen, Herman, Tresadern, Gary, Coveney, Peter V.
Publicado 2019

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A(2A) receptor

por Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.
Publicado 2019

DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning

por Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.
Publicado 2023

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

por Wright, David W., Husseini, Fouad, Wan, Shunzhou, Meyer, Christophe, van Vlijmen, Herman, Tresadern, Gary, Coveney, Peter V.
Publicado 2019

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

por Gapsys, Vytautas, Pérez-Benito, Laura, Aldeghi, Matteo, Seeliger, Daniel, van Vlijmen, Herman, Tresadern, Gary, de Groot, Bert L.
Publicado 2019

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

por Van der Borght, Koen, Verheyen, Ann, Feyaerts, Maxim, Van Wesenbeeck, Liesbeth, Verlinden, Yvan, Van Craenenbroeck, Elke, van Vlijmen, Herman
Publicado 2013

Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data

por van Westen, Gerard J. P., Hendriks, Alwin, Wegner, Jörg K., IJzerman, Adriaan P., van Vlijmen, Herman W. T., Bender, Andreas
Publicado 2013

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets

por van Westen, Gerard JP, Swier, Remco F, Wegner, Jörg K, IJzerman, Adriaan P, van Vlijmen, Herman WT, Bender, Andreas
Publicado 2013

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

por Van der Borght, Koen, Thys, Kim, Wetzels, Yves, Clement, Lieven, Verbist, Bie, Reumers, Joke, van Vlijmen, Herman, Aerssens, Jeroen
Publicado 2015

In search of novel ligands using a structure-based approach: a case study on the adenosine A(2A) receptor

por Lenselink, Eelke B., Beuming, Thijs, van Veen, Corine, Massink, Arnault, Sherman, Woody, van Vlijmen, Herman W. T., IJzerman, Adriaan P.
Publicado 2016

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

por Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., Emmerich, Michael T. M., IJzerman, Adriaan P., van Westen, Gerard J. P.
Publicado 2021

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

por Wan, Shunzhou, Bhati, Agastya P., Wright, David W., Wade, Alexander D., Tresadern, Gary, van Vlijmen, Herman, Coveney, Peter V.
Publicado 2022

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

por Tresadern, Gary, Trabanco, Andres A., Pérez-Benito, Laura, Overington, John P., van Vlijmen, Herman W. T., van Westen, Gerard J. P.
Publicado 2017

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

por Burggraaff, Lindsey, van Veen, Amber, Lam, Chi Chung, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.
Publicado 2020

Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations

por Van der Borght, Koen, Van Craenenbroeck, Elke, Lecocq, Pierre, Van Houtte, Margriet, Van Kerckhove, Barbara, Bacheler, Lee, Verbeke, Geert, van Vlijmen, Herman
Publicado 2011