Works matching AU Engkvist, Ola

Results: 64

Virtual laboratories: transforming research with AI.

Published in:

Data-Centric Engineering, 2024, v. 5, p. e19-1, doi. 10.1017/dce.2024.15

By:

Klami, Arto;
Damoulas, Theo;
Engkvist, Ola;
Rinke, Patrick;
Kaski, Samuel

Publication type:

Article

Extending in Silico Protein Target Prediction Models to Include Functional Effects.

Published in:

Frontiers in Pharmacology, 2018, p. 1, doi. 10.3389/fphar.2018.00613

By:

Mervin, Lewis H.;
Afzal, Avid M.;
Brive, Lars;
Engkvist, Ola;
Bender, Andreas

Publication type:

Article

On the Integration of In Silico Drug Design Methods for Drug Repurposing.

Published in:

Frontiers in Pharmacology, 2017, p. 1, doi. 10.3389/fphar.2017.00298

By:

March-Vila, Eric;
Pinzi, Luca;
Sturm, Noé;
Tinivella, Annachiara;
Engkvist, Ola;
Hongming Chen;
Rastelli, Giulio

Publication type:

Article

Exhaustive local chemical space exploration using a transformer model.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51672-4

By:

Tibo, Alessandro;
He, Jiazhen;
Janet, Jon Paul;
Nittinger, Eva;
Engkvist, Ola

Publication type:

Article

A data science roadmap for open science organizations engaged in early-stage drug discovery.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49777-x

By:

Edfeldt, Kristina;
Edwards, Aled M.;
Engkvist, Ola;
Günther, Judith;
Hartley, Matthew;
Hulcoop, David G.;
Leach, Andrew R.;
Marsden, Brian D.;
Menge, Amelie;
Misquitta, Leonie;
Müller, Susanne;
Owen, Dafydd R.;
Schütt, Kristof T.;
Skelton, Nicholas;
Steffen, Andreas;
Tropsha, Alexander;
Vernet, Erik;
Wang, Yanli;
Wellnitz, James;
Willson, Timothy M.

Publication type:

Article

Using Active Learning to Develop Machine Learning Models for Reaction Yield Prediction.

Published in:

Molecular Informatics, 2022, v. 41, n. 12, p. 1, doi. 10.1002/minf.202200043

By:

Viet Johansson, Simon;
Gummesson Svensson, Hampus;
Bjerrum, Esben;
Schliep, Alexander;
Haghir Chehreghani, Morteza;
Tyrchan, Christian;
Engkvist, Ola

Publication type:

Article

Prediction of the Chemical Context for Buchwald‐Hartwig Coupling Reactions.

Published in:

Molecular Informatics, 2022, v. 41, n. 8, p. 1, doi. 10.1002/minf.202100294

By:

Genheden, Samuel;
Mårdh, Agnes;
Lahti, Gustav;
Engkvist, Ola;
Olsson, Simon;
Kogej, Thierry

Publication type:

Article

Cheminformatics in Drug Discovery, an Industrial Perspective.

Published in:

Molecular Informatics, 2018, v. 37, n. 9/10, p. 1, doi. 10.1002/minf.201800041

By:

Chen, Hongming;
Kogej, Thierry;
Engkvist, Ola

Publication type:

Article

Application of Generative Autoencoder in <italic>De Novo</italic> Molecular Design.

Published in:

Molecular Informatics, 2018, v. 37, n. 1/2, p. 1, doi. 10.1002/minf.201700123

By:

Blaschke, Thomas;
Olivecrona, Marcus;
Engkvist, Ola;
Bajorath, Jürgen;
Chen, Hongming

Publication type:

Article

BIGCHEM: Challenges and Opportunities for Big Data Analysis in Chemistry.

Published in:

Molecular Informatics, 2016, v. 35, n. 11/12, p. 615, doi. 10.1002/minf.201600073

By:

Tetko, Igor V.;
Engkvist, Ola;
Koch, Uwe;
Reymond, Jean‐Louis;
Chen, Hongming

Publication type:

Article

Mining Molecular Pharmacological Effects from Biomedical Text: a Case Study for Eliciting Anti-Obesity/Diabetes Effects of Chemical Compounds.

Published in:

Molecular Informatics, 2014, v. 33, n. 5, p. 332, doi. 10.1002/minf.201300144

By:

Dura, Elzbieta;
Muresan, Sorel;
Engkvist, Ola;
Blomberg, Niklas;
Chen, Hongming

Publication type:

Article

An Investigation of the Relationship Between Molecular Topology and CYP3A4 Inhibition for Drug-like Compounds.

Published in:

Molecular Informatics, 2012, v. 31, n. 10, p. 719, doi. 10.1002/minf.201200054

By:

Oka, Rurika;
Engkvist, Ola;
Chen, Hongming

Publication type:

Article

Annotating Human P-Glycoprotein Bioassay Data.

Published in:

Molecular Informatics, 2012, v. 31, n. 8, p. 599, doi. 10.1002/minf.201200059

By:

Zdrazil, Barbara;
Pinto, Marta;
Vasanthanathan, Poongavanam;
Williams, Antony J.;
Balderud, Linda Zander;
Engkvist, Ola;
Chichester, Christine;
Hersey, Anne;
Overington, John P.;
Ecker, Gerhard F.

Publication type:

Article

Target prediction utilising negative bioactivity data covering large chemical space.

Published in:

Journal of Cheminformatics, 2015, v. 7, p. 1, doi. 10.1186/s13321-015-0098-y

By:

Mervin, Lewis H.;
Afzal, Avid M.;
Drakakis, Georgios;
Lewis, Richard;
Engkvist, Ola;
Bender, Andreas

Publication type:

Article

Hit series selection in noisy HTS data: clustering techniques, statistical tests and data visualisations.

Published in:

2014

By:

Müller, Christoph;
Ormsby, Daniel;
Feierberg, Isabella;
Engkvist, Ola;
Tyrchan, Christian;
Hartshorn, Michael J.

Publication type:

Abstract

Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules.

Published in:

Bioinformatics, 2022, v. 38, n. 21, p. 4951, doi. 10.1093/bioinformatics/btac614

By:

Moore, J Harry;
Bauer, Matthias R;
Guo, Jeff;
Patronov, Atanas;
Engkvist, Ola;
Margreitter, Christian

Publication type:

Article

A comparison between the NEMO intermolecular water potential and ab initio quantum chemical calculations for the water trimer tetramer.

Published in:

Molecular Physics, 1997, v. 90, n. 2, p. 277, doi. 10.1080/002689797172769

By:

Engkvist, Ola;
Forsberg, Niclas;
Schutz, Martin;
Karlstrom, Gunnar

Publication type:

Article

Metis: a python-based user interface to collect expert feedback for generative chemistry models.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00892-3

By:

Menke, Janosch;
Nahal, Yasmine;
Bjerrum, Esben Jannik;
Kabeshov, Mikhail;
Kaski, Samuel;
Engkvist, Ola

Publication type:

Article

Evaluation of reinforcement learning in transformer-based molecular design.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00887-0

By:

He, Jiazhen;
Tibo, Alessandro;
Janet, Jon Paul;
Nittinger, Eva;
Tyrchan, Christian;
Czechtizky, Werngard;
Engkvist, Ola

Publication type:

Article

AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application.

Published in:

Journal of Cheminformatics, 2024, v. 16, p. 1, doi. 10.1186/s13321-024-00860-x

By:

Saigiridharan, Lakshidaa;
Hassen, Alan Kai;
Lai, Helen;
Torren-Peraire, Paula;
Engkvist, Ola;
Genheden, Samuel

Publication type:

Article

Reinvent 4: Modern AI–driven generative molecule design.

Published in:

Journal of Cheminformatics, 2024, v. 16, p. 1, doi. 10.1186/s13321-024-00812-5

By:

Loeffler, Hannes H.;
He, Jiazhen;
Tibo, Alessandro;
Janet, Jon Paul;
Voronov, Alexey;
Mervin, Lewis H.;
Engkvist, Ola

Publication type:

Article

Human-in-the-loop assisted de novo molecular design.

Published in:

Journal of Cheminformatics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13321-022-00667-8

By:

Sundin, Iiris;
Voronov, Alexey;
Xiao, Haoping;
Papadopoulos, Kostas;
Bjerrum, Esben Jannik;
Heinonen, Markus;
Patronov, Atanas;
Kaski, Samuel;
Engkvist, Ola

Publication type:

Article

Transformer-based molecular optimization beyond matched molecular pairs.

Published in:

Journal of Cheminformatics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13321-022-00599-3

By:

He, Jiazhen;
Nittinger, Eva;
Tyrchan, Christian;
Czechtizky, Werngard;
Patronov, Atanas;
Bjerrum, Esben Jannik;
Engkvist, Ola

Publication type:

Article

DockStream: a docking wrapper to enhance de novo molecular design.

Published in:

Journal of Cheminformatics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13321-021-00563-7

By:

Guo, Jeff;
Janet, Jon Paul;
Bauer, Matthias R.;
Nittinger, Eva;
Giblin, Kathryn A.;
Papadopoulos, Kostas;
Voronov, Alexey;
Patronov, Atanas;
Engkvist, Ola;
Margreitter, Christian

Publication type:

Article

Axl receptor tyrosine kinase is a regulator of apolipoprotein E.

Published in:

Molecular Brain, 2020, v. 13, n. 1, p. 1, doi. 10.1186/s13041-020-00609-1

By:

Zhao, Wenchen;
Fan, Jianjia;
Kulic, Iva;
Koh, Cheryl;
Clark, Amanda;
Meuller, Johan;
Engkvist, Ola;
Barichievy, Samantha;
Raynoschek, Carina;
Hicks, Ryan;
Maresca, Marcello;
Wang, Qi;
Brown, Dean G.;
Lok, Alvin;
Parro, Cameron;
Robert, Jerome;
Chou, Hsien-Ya;
Zuhl, Andrea M.;
Wood, Michael W.;
Brandon, Nicholas J.

Publication type:

Article

Theoretical study of intermolecular potential energy surface for HCl dimer: Example of nonspherical atom-atom exchange repulsion interaction.

Published in:

Journal of Computational Chemistry, 1998, v. 19, n. 16, p. 1816, doi. 10.1002/(SICI)1096-987X(199812)19:16<1816::AID-JCC3>3.0.CO;2-O

By:

Hermida-Ramón, Jose M.;
Engkvist, Ola;
Karlström, Gunnar

Publication type:

Article

Pluripotent Stem Cell-Derived Hepatocytes Phenotypic Screening Reveals Small Molecules Targeting the CDK2/4-C/EBPα/DGAT2 Pathway Preventing ER-Stress Induced Lipid Accumulation.

Published in:

International Journal of Molecular Sciences, 2020, v. 21, n. 24, p. 9557, doi. 10.3390/ijms21249557

By:

Parafati, Maddalena;
Bae, Sang Hyo;
Kirby, R. Jason;
Fitzek, Martina;
Iyer, Preeti;
Engkvist, Ola;
Smith, David M.;
Malany, Siobhan

Publication type:

Article

Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03132-2

By:

Bost, Jeremy P.;
Ojansivu, Miina;
Munson, Michael J.;
Wesén, Emelie;
Gallud, Audrey;
Gupta, Dhanu;
Gustafsson, Oskar;
Saher, Osama;
Rädler, Julia;
Higgins, Stuart G.;
Lehto, Taavi;
Holme, Margaret N.;
Dahlén, Anders;
Engkvist, Ola;
Strömstedt, Per-Erik;
Andersson, Shalini;
Edvard Smith, C. I.;
Stevens, Molly M.;
Esbjörner, Elin K.;
Collén, Anna

Publication type:

Article

review of biomedical datasets relating to drug discovery: a knowledge graph perspective.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 6, p. 1, doi. 10.1093/bib/bbac404

By:

Bonner, Stephen;
Barrett, Ian P;
Ye, Cheng;
Swiers, Rowan;
Engkvist, Ola;
Bender, Andreas;
Hoyt, Charles Tapley;
Hamilton, William L

Publication type:

Article

Implications of topological imbalance for representation learning on biomedical knowledge graphs.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac279

By:

Bonner, Stephen;
Kirik, Ufuk;
Engkvist, Ola;
Tang, Jian;
Barrett, Ian P

Publication type:

Article

Orthologue chemical space and its influence on target prediction.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 72, doi. 10.1093/bioinformatics/btx525

By:

Mervin, Lewis H;
Bulusu, Krishna C;
Kalash, Leen;
Afzal, Avid M;
Svensson, Fredrik;
Firth, Mike A;
Barrett, Ian;
Engkvist, Ola;
Bender, Andreas

Publication type:

Article

Automated relative binding free energy calculations from SMILES to ΔΔG.

Published in:

Communications Chemistry, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42004-023-00859-9

By:

Moore, J. Harry;
Margreitter, Christian;
Janet, Jon Paul;
Engkvist, Ola;
de Groot, Bert L.;
Gapsys, Vytautas

Publication type:

Article

Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity? Response from the MIABE group.

Published in:

Nature Reviews Drug Discovery, 2012, v. 11, n. 9, p. 730, doi. 10.1038/nrd3503-c2

By:

Orchard, Sandra;
Al-Lazikani, Bissan;
Bryant, Steve;
Clark, Dominic;
Calder, Elizabeth;
Dix, Ian;
Engkvist, Ola;
Forster, Mark;
Gaulton, Anna;
Gilson, Michael;
Glen, Robert;
Grigorov, Martin;
Hammond-Kosack, Kim;
Harland, Lee;
Hopkins, Andrew;
Larminie, Christopher;
Lynch, Nick;
Mann, Romeena K.;
Murray-Rust, Peter;
Piparo, Elena Lo

Publication type:

Article

Molecular modeling of the second extracellular loop of G-protein coupled receptors and its implication on structure-based virtual screening.

Published in:

Proteins, 2008, v. 71, n. 2, p. 599, doi. 10.1002/prot.21724

By:

de Graaf, Chris;
Foata, Nicolas;
Engkvist, Ola;
Rognan, Didier

Publication type:

Article

E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01014-3

By:

Palmacci, Vincenzo;
Nahal, Yasmine;
Welsch, Matthias;
Engkvist, Ola;
Kaski, Samuel;
Kirchmair, Johannes

Publication type:

Article

Publishing neural networks in drug discovery might compromise training data privacy.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00982-w

By:

Krüger, Fabian P.;
Östman, Johan;
Mervin, Lewis;
Tetko, Igor V.;
Engkvist, Ola

Publication type:

Article

Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00964-y

By:

Friesacher, Hannah Rosa;
Engkvist, Ola;
Mervin, Lewis;
Moreau, Yves;
Arany, Adam

Publication type:

Article

Human-in-the-loop active learning for goal-oriented molecule generation.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00924-y

By:

Nahal, Yasmine;
Menke, Janosch;
Martinelli, Julien;
Heinonen, Markus;
Kabeshov, Mikhail;
Janet, Jon Paul;
Nittinger, Eva;
Engkvist, Ola;
Kaski, Samuel

Publication type:

Article

Identification of Compounds That Interfere with High‐Throughput Screening Assay Technologies.

Published in:

ChemMedChem, 2019, v. 14, n. 20, p. 1795, doi. 10.1002/cmdc.201900395

By:

David, Laurianne;
Walsh, Jarrod;
Sturm, Noé;
Feierberg, Isabella;
Nissink, J. Willem M.;
Chen, Hongming;
Bajorath, Jürgen;
Engkvist, Ola

Publication type:

Article

Herzregeneration: Chancen und Aufgaben für die Wirkstoff-Forschung mit neuartigen chemischen und therapeutischen Methoden oder Agentien.

Published in:

Angewandte Chemie, 2014, v. 126, n. 16, p. 4138, doi. 10.1002/ange.201307034

By:

Plowright, Alleyn T.;
Engkvist, Ola;
Gill, Adrian;
Knerr, Laurent;
Wang, Qing ‐ Dong

Publication type:

Article

Utilizing reinforcement learning for de novo drug design.

Published in:

Machine Learning, 2024, v. 113, n. 7, p. 4811, doi. 10.1007/s10994-024-06519-w

By:

Gummesson Svensson, Hampus;
Tyrchan, Christian;
Engkvist, Ola;
Haghir Chehreghani, Morteza

Publication type:

Article

Minimum information about a bioactive entity (MIABE).

Published in:

2011

By:

Orchard, Sandra;
Al-Lazikani, Bissan;
Bryant, Steve;
Clark, Dominic;
Calder, Elizabeth;
Dix, Ian;
Engkvist, Ola;
Forster, Mark;
Gaulton, Anna;
Gilson, Michael;
Glen, Robert;
Grigorov, Martin;
Hammond-Kosack, Kim;
Harland, Lee;
Hopkins, Andrew;
Larminie, Christopher;
Lynch, Nick;
Mann, Romeena K.;
Murray-Rust, Peter;
Lo Piparo, Elena

Publication type:

journal article

Author Correction: DrugnomeAI is an ensemble machine-learning framework for predicting druggability of candidate drug targets.

Published in:

2023

By:

Raies, Arwa;
Tulodziecka, Ewa;
Stainer, James;
Middleton, Lawrence;
Dhindsa, Ryan S.;
Hill, Pamela;
Engkvist, Ola;
Harper, Andrew R.;
Petrovski, Slavé;
Vitsios, Dimitrios

Publication type:

Correction Notice

DrugnomeAI is an ensemble machine-learning framework for predicting druggability of candidate drug targets.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-04245-4

By:

Raies, Arwa;
Tulodziecka, Ewa;
Stainer, James;
Middleton, Lawrence;
Dhindsa, Ryan S.;
Hill, Pamela;
Engkvist, Ola;
Harper, Andrew R.;
Petrovski, Slavé;
Vitsios, Dimitrios

Publication type:

Article

Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research.

Published in:

Frontiers in Pharmacology, 2019, v. 10, p. 1, doi. 10.3389/fphar.2019.01303

By:

David, Laurianne;
Arús-Pous, Josep;
Karlsson, Johan;
Engkvist, Ola;
Bjerrum, Esben Jannik;
Kogej, Thierry;
Kriegl, Jan M.;
Beck, Bernd;
Chen, Hongming

Publication type:

Article

Heart Regeneration: Opportunities and Challenges for Drug Discovery with Novel Chemical and Therapeutic Methods or Agents.

Published in:

Angewandte Chemie International Edition, 2014, v. 53, n. 16, p. 4056, doi. 10.1002/anie.201307034

By:

Plowright, Alleyn T.;
Engkvist, Ola;
Gill, Adrian;
Knerr, Laurent;
Wang, Qing‐Dong

Publication type:

Article

Utility of Resazurin, Horseradish Peroxidase, and NMR Assays to Identify Redox-Related False-Positive Behavior in High-Throughput Screens.

Published in:

Assay & Drug Development Technologies, 2018, v. 16, n. 3, p. 171, doi. 10.1089/adt.2017.838

By:

Tarnowski, Matthew;
Barozet, Amélie;
Johansson, Carina;
Eriksson, Per-Olof;
Engkvist, Ola;
Walsh, Jarrod;
Nissink, J. Willem M.

Publication type:

Article

Understanding Intracellular Biology to Improve mRNA Delivery by Lipid Nanoparticles.

Published in:

Small Methods, 2023, v. 7, n. 9, p. 1, doi. 10.1002/smtd.202201695

By:

Hunter, Morag Rose;
Cui, Lili;
Porebski, Benjamin Thomas;
Pereira, Sara;
Sonzini, Silvia;
Odunze, Uchechukwu;
Iyer, Preeti;
Engkvist, Ola;
Lloyd, Rebecca Louise;
Peel, Samantha;
Sabirsh, Alan;
Ross‐Thriepland, Douglas;
Jones, Arwyn Tomos;
Desai, Arpan Shailesh

Publication type:

Article

Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty.

Published in:

Journal of Cheminformatics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13321-021-00539-7

By:

Mervin, Lewis H.;
Trapotsi, Maria-Anna;
Afzal, Avid M.;
Barrett, Ian P.;
Bender, Andreas;
Engkvist, Ola

Publication type:

Article

MAIP: a web service for predicting blood‐stage malaria inhibitors.

Published in:

Journal of Cheminformatics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13321-021-00487-2

By:

Bosc, Nicolas;
Felix, Eloy;
Arcila, Ricardo;
Mendez, David;
Saunders, Martin R.;
Green, Darren V. S.;
Ochoada, Jason;
Shelat, Anang A.;
Martin, Eric J.;
Iyer, Preeti;
Engkvist, Ola;
Verras, Andreas;
Duffy, James;
Burrows, Jeremy;
Gardner, J. Mark F.;
Leach, Andrew R.

Publication type:

Article