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Author Details

Herman W T van Vlijmen
Leiden Academic Centre for Drug Research (LACDR), Leiden University
1988
90
34
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37423967Kinetic profiling of novel spirobenzo-oxazinepiperidinone derivatives as equilibrative nucleoside transporter 1 inhibitors.Purinergic Signal2024
36803659DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning.J Cheminform2023
37902715Alchemical Free Energy Calculations on Membrane-Associated Proteins.J Chem Theory Comput2023
35398021Corrigendum to "The European Lead Factory: An updated HTS compound library for innovative drug discovery" [Drug Discov. Today 26(10) (2021) 2406-2413].Drug Discov Today2023
37208467The FAIR Cookbook - the essential resource for and by FAIR doers.Sci Data2023
35061383The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions.J Chem Inf Model2022
35729177The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase.Sci Rep2022
36513718Pan-cancer functional analysis of somatic mutations in G protein-coupled receptors.Sci Rep2022
35041430Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery.J Chem Inf Model2022
34907316IMI European Lead Factory - democratizing access to high-throughput screening.Nat Rev Drug Discov2022
33995994Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations.Chem Sci2021
33892142The European Lead Factory: An updated HTS compound library for innovative drug discovery.Drug Discov Today2021
33753214Identification of novel inhibitors of rat Mrp3.Eur J Pharm Sci2021
34772471DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology.J Cheminform2021
32343143Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors.J Chem Inf Model2020
34527855Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica-Exchange.Adv Theory Simul2020
34553124Application of the ESMACS Binding Free Energy Protocol to a Multi-Binding Site Lactate Dehydogenase A Ligand Dataset.Adv Theory Simul2020
33431012Quantitative prediction of selectivity between the A<sub>1</sub> and A<sub>2A</sub> adenosine receptors.J Cheminform2020
32820916Assessment of the Fragment Docking Program SEED.J Chem Inf Model2020
32931270Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs.J Chem Inf Model2020
32539374Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation.J Chem Inf Model2020
30817146Advances and Challenges in Computational Target Prediction.J Chem Inf Model2019
34084371Large scale relative protein ligand binding affinities using non-equilibrium alchemy.Chem Sci2019
31498988Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors.J Chem Inf Model2019
31127405An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A<sub>2A</sub> receptor.J Cheminform2019
30776226Predicting Activity Cliffs with Free-Energy Perturbation.J Chem Theory Comput2019
30979914Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4.Sci Rep2019
30767155Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling.J Cheminform2019
29116686Protocols for the Design of Kinase-focused Compound Libraries.Mol Inform2018
29853330Chemical space screening around Phe<sup>3</sup> in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings.Bioorg Med Chem Lett2018
29981151Molecular Modeling of Drug-Transporter Interactions-An International Transporter Consortium Perspective.Clin Pharmacol Ther2018
30195888Corrigendum to "Chemical space screening around Phe<sup>3</sup> in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings" [Bioorg. Med. Chem. Lett. 28(13) (2018) 2320-2323].Bioorg Med Chem Lett2018
29617116Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces.J Chem Inf Model2018
29559702Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation.Sci Rep2018
27995515Computational chemistry at Janssen.J Comput Aided Mol Des2017
28103438Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study.J Chem Theory Comput2017
29086168Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set.J Cheminform2017
29172488Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.J Chem Inf Model2017
28951883Blood-based metabolic signatures in Alzheimer's disease.Alzheimers Dement (Amst)2017
27774140Open PHACTS computational protocols for <i>in silico</i> target validation of cellular phenotypic screens: knowing the knowns.Medchemcomm2016
30023478Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation.ACS Omega2016
26608890The ELF Honest Data Broker: informatics enabling public-private collaboration in a precompetitive arena.Drug Discov Today2016
28013427Collaborating to improve the use of free-energy and other quantitative methods in drug discovery.J Comput Aided Mol Des2016
27629350In search of novel ligands using a structure-based approach: a case study on the adenosine A<sub>2A</sub> receptor.J Comput Aided Mol Des2016
27626908Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening.J Chem Inf Model2016
25596550Extending kinome coverage by analysis of kinase inhibitor broad profiling data.Drug Discov Today2015
26554718QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles.BMC Bioinformatics2015
23994046Influence of canonical structure determining residues on antibody affinity and stability.J Struct Biol2014
24835542Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.J Chem Inf Model2014
24669828Multi-model inference using mixed effects from a linear regression based genetic algorithm.BMC Bioinformatics2014
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Collaborators

Martin Karplus
Harvard University
Co-authored papers 6
Kai Ye
Co-authored papers 4
Peter V Coveney
Co-authored papers 4
John P Overington
Institute of Cardiovascular Science, University College London
Co-authored papers 3
Chris T Evelo
Maastricht University
Co-authored papers 2
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 1
Elizabeth Potterton
University of York
Co-authored papers 1
Huib Ovaa
Leiden University Medical Center
Co-authored papers 1
Jason R Swedlow
University of Dundee
Co-authored papers 1
Salvador Capella-Gutierrez
Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
Co-authored papers 1
Serena Scollen
Pfizer Ltd
Co-authored papers 1
F Yuan
Co-authored papers 1
Susanna-Assunta Sansone
Oxford e-Research Centre, University of Oxford
Co-authored papers 1
Philippe Rocca-Serra
University of Oxford
Co-authored papers 1
Allyson L Lister
Oxford e-Research Centre, University of Oxford
Co-authored papers 1
Alasdair J G Gray
Heriot-Watt University
Co-authored papers 1
Nick Juty
University of Manchester
Co-authored papers 1
Ayse Demirkan
Co-authored papers 1
Avner Schlessinger
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai
Co-authored papers 1
Cornelia M van Duijn
University of Oxford
Co-authored papers 1
George Papadatos
European Molecular Biology Laboratory - European Bioinformatics Institute
Co-authored papers 1
Dorothy Reilly
Novartis Institutes for BioMedical Research, Novartis Pharma AG
Co-authored papers 1
Anna Gaulton
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 1
N??ria Queralt-Rosinach
Leiden University Medical Center
Co-authored papers 1
Laura I Furlong
Hospital del Mar Research Institute (IMIM), Pompeu Fabra University (UPF)
Co-authored papers 1
P??r Matsson
University of Gothenburg
Co-authored papers 1
Egon L Willighagen
Maastricht University
Co-authored papers 1
Tony Burdett
European Bioinformatics Institute
Co-authored papers 1
Mark A van de Wiel
Amsterdam University Medical Centers (Amsterdam UMC)
Co-authored papers 1
Robert W Shafer
Co-authored papers 1
Release 1.2