BIGCHEM: Challenges and Opportunities for Big Data Analysis in Chemistry

Spotting and designing promiscuous ligands for drug discovery

(2016) P. Schneider et al.   CHEMICAL COMMUNICATIONS

Leveraging big data to transform target selection and drug discovery

(2016) B Chen et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

A renaissance of neural networks in drug discovery

(2016) Igor I. Baskin et al.   Expert Opinion on Drug Discovery

Inverse QSPR/QSAR Analysis for Chemical Structure Generation (from y to x)

(2016) Tomoyuki Miyao et al.   Journal of Chemical Information and Modeling

De Novo Design at the Edge of Chaos

(2016) Petra Schneider et al.   JOURNAL OF MEDICINAL CHEMISTRY

Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists’ Bread and Butter

(2016) Nadine Schneider et al.   JOURNAL OF MEDICINAL CHEMISTRY

Feeling Nature’s PAINS: Natural Products, Natural Product Drugs, and Pan Assay Interference Compounds (PAINS)

(2016) Jonathan B. Baell   JOURNAL OF NATURAL PRODUCTS

The development of models to predict melting and pyrolysis point data associated with several hundred thousand compounds mined from PATENTS

(2016) Igor V. Tetko et al.   Journal of Cheminformatics

The Chemical Space Project

(2015) Jean-Louis Reymond   ACCOUNTS OF CHEMICAL RESEARCH

Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

(2015) Mahendra Awale et al.   Journal of Chemical Information and Modeling

Investigating Pharmacological Similarity by Charting Chemical Space

(2015) Rosa Buonfiglio et al.   Journal of Chemical Information and Modeling

Stargate GTM: Bridging Descriptor and Activity Spaces

(2015) Héléna A. Gaspar et al.   Journal of Chemical Information and Modeling

Activity, assay and target data curation and quality in the ChEMBL database

(2015) George Papadatos et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Promiscuous 2-Aminothiazoles (PrATs): A Frequent Hitting Scaffold

(2015) Shane M. Devine et al.   JOURNAL OF MEDICINAL CHEMISTRY

PAINS in the Assay: Chemical Mechanisms of Assay Interference and Promiscuous Enzymatic Inhibition Observed during a Sulfhydryl-Scavenging HTS

(2015) Jayme L. Dahlin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Deep Learning in Drug Discovery

(2015) Erik Gawehn et al.   Molecular Informatics

SureChEMBL: a large-scale, chemically annotated patent document database

(2015) George Papadatos et al.   NUCLEIC ACIDS RESEARCH

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Target prediction utilising negative bioactivity data covering large chemical space

(2015) Lewis H. Mervin et al.   Journal of Cheminformatics

Computational polypharmacology comes of age

(2015) Giulio Rastelli et al.   Frontiers in Pharmacology

Nonlinear Dimensionality Reduction for Visualizing Toxicity Data: Distance-Based Versus Topology-Based Approaches

(2014) Natalia V. Kireeva et al.   ChemMedChem

How Accurately Can We Predict the Melting Points of Drug-like Compounds?

(2014) Igor V. Tetko et al.   Journal of Chemical Information and Modeling

Polypharmacology: Challenges and Opportunities in Drug Discovery

(2014) Andrew Anighoro et al.   JOURNAL OF MEDICINAL CHEMISTRY

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Expanding the fragrance chemical space for virtual screening

(2014) Lars Ruddigkeit et al.   Journal of Cheminformatics

Evolving BioAssay Ontology (BAO): modularization, integration and applications

(2014) Saminda Abeyruwan et al.   Journal of Biomedical Semantics

Target deconvolution techniques in modern phenotypic profiling

(2013) Jiyoun Lee et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS)

(2013) Héléna A. Gaspar et al.   Journal of Chemical Information and Modeling

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

(2012) M. Gonen   BIOINFORMATICS

Big pharma screening collections: more of the same or unique libraries? The AstraZeneca–Bayer Pharma AG case

(2012) Thierry Kogej et al.   DRUG DISCOVERY TODAY

ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

(2012) Iurii Sushko et al.   Journal of Chemical Information and Modeling

Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis?

(2012) Alexandre Varnek et al.   Journal of Chemical Information and Modeling

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

(2012) Lars Ruddigkeit et al.   Journal of Chemical Information and Modeling

Visualization and Virtual Screening of the Chemical Universe Database GDB-17

(2012) Lars Ruddigkeit et al.   Journal of Chemical Information and Modeling

Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery

(2012) Michael Reutlinger et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

(2012) Markus Hartenfeller et al.   PLoS Computational Biology

Neighborhood-Preserving Visualization of Adaptive Structure-Activity Landscapes: Application to Drug Discovery

(2011) Michael Reutlinger et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Making every SAR point count: the development of Chemistry Connect for the large-scale integration of structure and bioactivity data

(2011) Sorel Muresan et al.   DRUG DISCOVERY TODAY

Reaction-drivende novodesign, synthesis and testing of potential type II kinase inhibitors

(2011) Gisbert Schneider et al.   Future Medicinal Chemistry

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

(2011) Iurii Sushko et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Applicability domain for in silico models to achieve accuracy of experimental measurements

(2010) Iurii Sushko et al.   JOURNAL OF CHEMOMETRICS

New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays

(2010) Jonathan B. Baell et al.   JOURNAL OF MEDICINAL CHEMISTRY

Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients

(2009) Alexandre Varnek et al.   Journal of Chemical Information and Modeling

A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem

(2009) William WL Wong et al.   Journal of Cheminformatics