List of works - Ola Engkvist

"Ring Breaker": Neural Network Driven Synthesis Prediction of the Ring System Chemical Space

scientific article published on 30 April 2020

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

scientific article (publication date: April 2016)

A Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Ligand-Target Predictions

A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

scientific article published on 23 September 2019

A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective

preprint published on 02 April 2021

A de novo molecular generation method using latent vector based generative adversarial network

AI-assisted synthesis prediction

scientific article published on 01 December 2019

Accurate Hit Estimation for Iterative Screening Using Venn-ABERS Predictors

scientific article published on 22 February 2019

Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations.

scientific article

AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning

scientific article published on 17 November 2020

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

scientific article

Annotating Human P-Glycoprotein Bioassay Data

scientific article (publication date: August 2012)

Application of Bioactivity Profile Based Fingerprints For Building Machine Learning Models

scientific article published on 29 November 2018

Application of Bioactivity Profile Based Fingerprints for Building Machine Learning Models

scholarly article published 15 August 2018

Application of Generative Autoencoder in de Novo Molecular Design

scientific article published on 13 December 2017

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

scientific article published on 05 November 2019

Applying Mondrian Cross-Conformal Prediction To Estimate Prediction Confidence on Large Imbalanced Bioactivity Data Sets

scientific article published on 19 June 2017

Artificial applicability labels for improving policies in retrosynthesis prediction

scientific article published on 01 December 2020

Axl receptor tyrosine kinase is a regulator of apolipoprotein E

scientific article published on 04 May 2020

BIGCHEM: Challenges and Opportunities for Big Data Analysis in Chemistry

scientific article

Beyond size, ionization state, and lipophilicity: influence of molecular topology on absorption, distribution, metabolism, excretion, and toxicity for druglike compounds

scientific article published on 17 April 2012

Building Attention and Edge Convolution Neural Networks for Bioactivity and Physical-Chemical Property Prediction

scientific article published on 19 December 2019

Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature

scientific article published in 2022

Characterization of a conserved structural determinant controlling protein kinase sensitivity to selective inhibitors.

scientific article

Cheminformatics in Drug Discovery, an Industrial Perspective

scientific article published on 18 May 2018

Combinatorial library design from reagent pharmacophore fingerprints

scientific article

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold-hopping capability

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability

scientific article published on 08 August 2019

Comparison Between SMILES-Based Differential Neural Computer and Recurrent Neural Network Architectures for De Novo Molecule Design

scientific article published on 4 September 2019

Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Protein-Ligand Predictions

scientific article published on 21 September 2020

Comparison of molecular fingerprint methods on the basis of biological profile data

scientific article

Computational prediction of chemical reactions: current status and outlook

scientific article published on 3 March 2018

Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis

scientific article published on 03 April 2020

Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain

scientific article published on 05 November 2019

Direct Steering of de novo Molecular Generation using Descriptor Conditional Recurrent Neural Networks (cRNNs)

scholarly article published 25 November 2019

Does 'Big Data' exist in medicinal chemistry, and if so, how can it be harnessed?

scientific article

Erratum to: ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

scientific article published on 14 June 2017

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

scientific article (publication date: 7 March 2017)

Exploring in silico prediction of the unbound brain-to-plasma drug concentration ratio: model validation, renewal, and interpretation

scientific article published on 24 December 2014

Exploring the GDB-13 Chemical Space Using Deep Generative Models

Exploring the GDB-13 chemical space using deep generative models

article by Josep Arús-Pous et al published 12 March 2019 in Journal of Cheminformatics

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

scientific article published on 11 June 2018

From Big Data to Artificial Intelligence: chemoinformatics meets new challenges

scientific article published on 18 December 2020

HTS explorer.

scientific article published on 11 March 2014

Has Drug Design Augmented by Artificial Intelligence Become a Reality?

scientific article published on 16 October 2019

Heart regeneration: opportunities and challenges for drug discovery with novel chemical and therapeutic methods or agents

scientific article published on 27 January 2014

High-Throughput,In SilicoPrediction of Aqueous Solubility Based on One- and Two-Dimensional Descriptors

scientific article published on 01 September 2002

High-content phenotypic assay for proliferation of human iPSC-derived cardiomyocytes identifies L-type calcium channels as targets

scientific article published on 28 December 2018

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

scientific article published on 11 March 2014

Identification of Compounds That Interfere with High-Throughput Screening Assay Technologies

scientific article published on 19 September 2019

In silico prediction of unbound brain-to-plasma concentration ratio using machine learning algorithms

scientific article

Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published?

scientific article

Introduction to Pharmaceutical Bioinformatics

Third edition of the book originally published in 2010

Investigating Pharmacological Similarity by Charting Chemical Space

scientific article published on 20 October 2015

Investigation of the Relationship between Topology and Selectivity for Druglike Molecules

scientific article published on 01 November 2010

Investigation of the influence of molecular topology on ligand binding

scientific article published on 29 December 2012

Ligand-based target prediction with signature fingerprints

scientific article published on 3 October 2014

MAIP: A Prediction Platform for Predicting Blood-Stage Malaria Inhibitors

scientific article

MAIP: A web service for predicting blood-stage malaria inhibitors

scientific article

Memory-assisted reinforcement learning for diverse molecular de novo design

scientific article published on 10 November 2020

Methylated uracil dimers: potential energy and free energy surfaces

Minimum information about a bioactive entity (MIABE).

scientific article

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

scientific article published on 12 May 2014

Molecular de-novo design through deep reinforcement learning

scientific article published on 4 September 2017

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

scientific article

Molecular representations in AI-driven drug discovery: a review and practical guide

Molecular topology analysis of the differences between drugs, clinical candidate compounds, and bioactive molecules

scientific article published on 15 November 2010

Multi-Solvent Models for Solvation Free Energy Predictions Using 3D-RISM Hydration Thermodynamic Descriptors

Multi-Solvent Models for Solvation Free Energy Predictions using 3D-RISM Hydration Thermodynamic Descriptors

scientific article published on 20 April 2020

Multifingerprint Based Similarity Searches for Targeted Class Compound Selection

Multifingerprint based similarity searches for targeted class compound selection.

scientific article published in May 2006

Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides

scientific article published on 01 March 2022

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

scientific article published on 23 May 2017

On the Relationship between Molecular Hit Rates in High-Throughput Screening and Molecular Descriptors

scientific article published on 23 August 2013

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.

scientific article

Orthologue chemical space and its influence on target prediction

scientific article published on 26 August 2017

Phenotypic Screen for Cardiac Regeneration Identifies Molecules with Differential Activity in Human Epicardium-Derived Cells versus Cardiac Fibroblasts

scientific article

Physicochemical property profiles of marketed drugs, clinical candidates and bioactive compounds

scientific article published in December 2009

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

scientific article published on 15 December 2020

Prediction of CNS activity of compound libraries using substructure analysis

scientific article

ProSAR: a new methodology for combinatorial library design

scientific article

REINVENT 2.0: An AI Tool for De Novo Drug Design

scientific article published on 29 October 2020

Randomized SMILES Strings Improve the Quality of Molecular Generative Models

Randomized SMILES strings improve the quality of molecular generative models

article published in 2019

SMILES-Based Deep Generative Scaffold Decorator for De-Novo Drug Design

SMILES-based deep generative scaffold decorator for de-novo drug design

scientific article published on 29 May 2020

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

Small molecule inducers of ABCA1 and apoE that act through indirect activation of the LXR pathway

scientific article published on 21 March 2018

Systematic exploration of dual-acting modulators from a combined medicinal chemistry and biology perspective

scientific article

Target prediction utilising negative bioactivity data covering large chemical space

scientific article (publication date: 2015)

The Role of Historical Bioactivity Data in the Deconvolution of Phenotypic Screens.

scientific article

The convergence of artificial intelligence and chemistry for improved drug discovery

scientific article published on 30 November 2018

The rise of deep learning in drug discovery

scientific article published on 20 January 2018

Transporter assays and assay ontologies: useful tools for drug discovery

scientific article (publication date: June 2014)

Uncertainty quantification in drug design

scientific article published on 27 November 2020

Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection

scientific article

Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery

preprint published on 08 June 2021

Uracil Dimer: Potential Energy and Free Energy Surfaces. Ab Initio beyond Hartree−Fock and Empirical Potential Studies

article published in 1998

Using the BioAssay Ontology for analyzing high-throughput screening data

scientific article

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

scientific article published on 2 April 2018

List of works by Ola Engkvist

"Ring Breaker": Neural Network Driven Synthesis Prediction of the Ring System Chemical Space

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

A Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Ligand-Target Predictions

A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective

A de novo molecular generation method using latent vector based generative adversarial network

AI-assisted synthesis prediction

Accurate Hit Estimation for Iterative Screening Using Venn-ABERS Predictors

Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations.

AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning

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

Annotating Human P-Glycoprotein Bioassay Data

Application of Bioactivity Profile Based Fingerprints For Building Machine Learning Models

Application of Bioactivity Profile Based Fingerprints for Building Machine Learning Models

Application of Generative Autoencoder in de Novo Molecular Design

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

Applying Mondrian Cross-Conformal Prediction To Estimate Prediction Confidence on Large Imbalanced Bioactivity Data Sets

Artificial applicability labels for improving policies in retrosynthesis prediction

Axl receptor tyrosine kinase is a regulator of apolipoprotein E

BIGCHEM: Challenges and Opportunities for Big Data Analysis in Chemistry

Beyond size, ionization state, and lipophilicity: influence of molecular topology on absorption, distribution, metabolism, excretion, and toxicity for druglike compounds

Building Attention and Edge Convolution Neural Networks for Bioactivity and Physical-Chemical Property Prediction

Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature

Characterization of a conserved structural determinant controlling protein kinase sensitivity to selective inhibitors.

Cheminformatics in Drug Discovery, an Industrial Perspective

Combinatorial library design from reagent pharmacophore fingerprints

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold-hopping capability

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability

Comparison Between SMILES-Based Differential Neural Computer and Recurrent Neural Network Architectures for De Novo Molecule Design

Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Protein-Ligand Predictions

Comparison of molecular fingerprint methods on the basis of biological profile data

Computational prediction of chemical reactions: current status and outlook

Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis

Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain

Direct Steering of de novo Molecular Generation using Descriptor Conditional Recurrent Neural Networks (cRNNs)

Does 'Big Data' exist in medicinal chemistry, and if so, how can it be harnessed?

Erratum to: ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

Exploring in silico prediction of the unbound brain-to-plasma drug concentration ratio: model validation, renewal, and interpretation

Exploring the GDB-13 Chemical Space Using Deep Generative Models

Exploring the GDB-13 chemical space using deep generative models

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

From Big Data to Artificial Intelligence: chemoinformatics meets new challenges

HTS explorer.

Has Drug Design Augmented by Artificial Intelligence Become a Reality?

Heart regeneration: opportunities and challenges for drug discovery with novel chemical and therapeutic methods or agents

High-Throughput,In SilicoPrediction of Aqueous Solubility Based on One- and Two-Dimensional Descriptors

High-content phenotypic assay for proliferation of human iPSC-derived cardiomyocytes identifies L-type calcium channels as targets

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

Identification of Compounds That Interfere with High-Throughput Screening Assay Technologies

In silico prediction of unbound brain-to-plasma concentration ratio using machine learning algorithms

Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published?

Introduction to Pharmaceutical Bioinformatics

Investigating Pharmacological Similarity by Charting Chemical Space

Investigation of the Relationship between Topology and Selectivity for Druglike Molecules

Investigation of the influence of molecular topology on ligand binding

Ligand-based target prediction with signature fingerprints

MAIP: A Prediction Platform for Predicting Blood-Stage Malaria Inhibitors

MAIP: A web service for predicting blood-stage malaria inhibitors

Memory-assisted reinforcement learning for diverse molecular de novo design

Methylated uracil dimers: potential energy and free energy surfaces

Minimum information about a bioactive entity (MIABE).

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

Molecular de-novo design through deep reinforcement learning

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

Molecular representations in AI-driven drug discovery: a review and practical guide

Molecular topology analysis of the differences between drugs, clinical candidate compounds, and bioactive molecules

Multi-Solvent Models for Solvation Free Energy Predictions Using 3D-RISM Hydration Thermodynamic Descriptors

Multi-Solvent Models for Solvation Free Energy Predictions using 3D-RISM Hydration Thermodynamic Descriptors

Multifingerprint Based Similarity Searches for Targeted Class Compound Selection

Multifingerprint based similarity searches for targeted class compound selection.

Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides

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

On the Relationship between Molecular Hit Rates in High-Throughput Screening and Molecular Descriptors

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.

Orthologue chemical space and its influence on target prediction

Phenotypic Screen for Cardiac Regeneration Identifies Molecules with Differential Activity in Human Epicardium-Derived Cells versus Cardiac Fibroblasts

Physicochemical property profiles of marketed drugs, clinical candidates and bioactive compounds

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