List of works - Ola Engkvist

Molecular de-novo design through deep reinforcement learning

scientific article published on 4 September 2017

The rise of deep learning in drug discovery

scientific article published on 20 January 2018

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

scientific article

Target prediction utilising negative bioactivity data covering large chemical space

scientific article (publication date: 2015)

Minimum information about a bioactive entity (MIABE).

scientific article

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

scientific article

Application of Generative Autoencoder in de Novo Molecular Design

scientific article published on 13 December 2017

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

scientific article (publication date: 7 March 2017)

Annotating Human P-Glycoprotein Bioassay Data

scientific article (publication date: August 2012)

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

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

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

scientific article

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

scientific article published on 23 May 2017

Ligand-based target prediction with signature fingerprints

scientific article published on 3 October 2014

Computational prediction of chemical reactions: current status and outlook

scientific article published on 3 March 2018

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

scientific article

BIGCHEM: Challenges and Opportunities for Big Data Analysis in Chemistry

scientific article

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

scientific article published in December 2009

Benzene trimer and benzene tetramer: Structures and properties determined by the nonempirical model (NEMO) potential calibrated from the CCSD(T) benzene dimer energies

article

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

Multifingerprint based similarity searches for targeted class compound selection

scientific article published in May 2006

Prediction of CNS activity of compound libraries using substructure analysis

scientific article

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

article published in 1998

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

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

Building attention and edge message passing neural networks for bioactivity and physical–chemical property prediction

scientific article published on 8 January 2020

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

scientific article

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

Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection

scientific article

Randomized SMILES strings improve the quality of molecular generative models

article published in 2019

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

scientific article published on 21 March 2018

Using the BioAssay Ontology for analyzing high-throughput screening data

scientific article

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

scientific article published on 19 June 2017

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

scientific article published on 15 November 2010

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

scientific article published on June 14, 2017

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

scientific article

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

scientific article

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

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

scientific article

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

scientific article

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

scientific article published on 17 November 2020

REINVENT 2.0: An AI Tool for De Novo Drug Design

scientific article published on 29 October 2020

Has Drug Design Augmented by Artificial Intelligence Become a Reality?

scientific article published on 16 October 2019

Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis

scientific article published on 03 April 2020

ProSAR: a new methodology for combinatorial library design

scientific article

Orthologue chemical space and its influence on target prediction

scientific article published on 26 August 2017

Memory-assisted reinforcement learning for diverse molecular de novo design

scientific article published on 10 November 2020

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

scientific article published on 23 August 2013

List of works by Ola Engkvist

Molecular de-novo design through deep reinforcement learning

The rise of deep learning in drug discovery

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

Target prediction utilising negative bioactivity data covering large chemical space

Minimum information about a bioactive entity (MIABE).

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

Application of Generative Autoencoder in de Novo Molecular Design

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

Annotating Human P-Glycoprotein Bioassay Data

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

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

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

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

Ligand-based target prediction with signature fingerprints

Computational prediction of chemical reactions: current status and outlook

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

BIGCHEM: Challenges and Opportunities for Big Data Analysis in Chemistry

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

Benzene trimer and benzene tetramer: Structures and properties determined by the nonempirical model (NEMO) potential calibrated from the CCSD(T) benzene dimer energies

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

Multifingerprint based similarity searches for targeted class compound selection

Prediction of CNS activity of compound libraries using substructure analysis

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

Exploring the GDB-13 chemical space using deep generative models

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

Building attention and edge message passing neural networks for bioactivity and physical–chemical property prediction

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

Investigating Pharmacological Similarity by Charting Chemical Space

Investigation of the Relationship between Topology and Selectivity for Druglike Molecules

Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection

Randomized SMILES strings improve the quality of molecular generative models

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

Using the BioAssay Ontology for analyzing high-throughput screening data

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

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

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

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

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

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

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

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

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

REINVENT 2.0: An AI Tool for De Novo Drug Design

Has Drug Design Augmented by Artificial Intelligence Become a Reality?

Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis

ProSAR: a new methodology for combinatorial library design

Orthologue chemical space and its influence on target prediction

Memory-assisted reinforcement learning for diverse molecular de novo design

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