Active learning for computational chemogenomics

Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide

(2016) Gisbert Schneider et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Spotting and designing promiscuous ligands for drug discovery

(2016) P. Schneider et al.   CHEMICAL COMMUNICATIONS

In silico methods to address polypharmacology: current status, applications and future perspectives

(2016) Antonio Lavecchia et al.   DRUG DISCOVERY TODAY

Beware of Unreliable Q2! A Comparative Study of Regression Metrics for Predictivity Assessment of QSAR Models

(2016) Roberto Todeschini et al.   Journal of Chemical Information and Modeling

Feasibility of Active Machine Learning for Multiclass Compound Classification

(2016) Tobias Lang et al.   Journal of Chemical Information and Modeling

TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models

(2016) Zhi-Jiang Yao et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

De Novo Design at the Edge of Chaos

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

Multi-objective active machine learning rapidly improves structure–activity models and reveals new protein–protein interaction inhibitors

(2016) D. Reker et al.   Chemical Science

Active machine learning-driven experimentation to determine compound effects on protein patterns

(2016) Armaghan W Naik et al.   eLife

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations

(2015) Wallace K. B. Chan et al.   BIOINFORMATICS

Active-learning strategies in computer-assisted drug discovery

(2015) Daniel Reker et al.   DRUG DISCOVERY TODAY

Deep Learning in Drug Discovery

(2015) Erik Gawehn et al.   Molecular Informatics

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling

(2015) Isidro Cortes-Ciriano et al.   Journal of Cheminformatics

InChI, the IUPAC International Chemical Identifier

(2015) Stephen R Heller et al.   Journal of Cheminformatics

Accessing New Chemical Entities through Microfluidic Systems

(2014) Tiago Rodrigues et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Efficient discovery of responses of proteins to compounds using active learning

(2014) Joshua D Kangas et al.   BMC BIOINFORMATICS

Coping with Polypharmacology by Computational Medicinal Chemistry

(2014) Gisbert Schneider et al.   CHIMIA

REACH and in silico methods: an attractive opportunity for medicinal chemists

(2014) Orazio Nicolotti et al.   DRUG DISCOVERY TODAY

Computational chemogenomics: Is it more than inductive transfer?

(2014) J. B. Brown et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Revealing the macromolecular targets of complex natural products

(2014) Daniel Reker et al.   Nature Chemistry

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus

(2014) D. Reker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures

(2014) A. Y. Lee et al.   SCIENCE

Proteochemometric modeling in a Bayesian framework

(2014) Isidro Cortes-Ciriano et al.   Journal of Cheminformatics

Exhaustive Proteome Mining for Functional MHC-I Ligands

(2013) Christian P. Koch et al.   ACS Chemical Biology

Combining On-Chip Synthesis of a Focused Combinatorial Library with Computational Target Prediction Reveals Imidazopyridine GPCR Ligands

(2013) Michael Reutlinger et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The holistic integration of virtual screening in drug discovery

(2013) Yusuf Tanrikulu et al.   DRUG DISCOVERY TODAY

Predicting Potent Compounds via Model-Based Global Optimization

(2013) Mohsen Ahmadi et al.   Journal of Chemical Information and Modeling

Rapid Discovery of a Novel Series of Abl Kinase Inhibitors by Application of an Integrated Microfluidic Synthesis and Screening Platform

(2013) Bimbisar Desai et al.   JOURNAL OF MEDICINAL CHEMISTRY

CompoundProtein Interaction Prediction Within Chemogenomics: Theoretical Concepts, Practical Usage, and Future Directions

(2013) J. B. Brown et al.   Molecular Informatics

A Perspective on Computational Chemogenomics

(2013) Jürgen Bajorath   Molecular Informatics

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Efficient Modeling and Active Learning Discovery of Biological Responses

(2013) Armaghan W. Naik et al.   PLoS One

Chemotography for multi-target SAR analysis in the context of biological pathways

(2012) Eugen Lounkine et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Systems Biology and Systems Chemistry: New Directions for Drug Discovery

(2012) J.B. Brown et al.   CHEMISTRY & BIOLOGY

Automated design of ligands to polypharmacological profiles

(2012) Jérémy Besnard et al.   NATURE

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Comprehensive Analysis of Single- and Multi-Target Activity Cliffs Formed by Currently Available Bioactive Compounds

(2011) Anne M. Wassermann et al.   Chemical Biology & Drug Design

Integrating structure-based and ligand-based approaches for computational drug design

(2011) Gregory L Wilson et al.   Future Medicinal Chemistry

Computational tools for polypharmacology and repurposing

(2011) Janosch Achenbach et al.   Future Medicinal Chemistry

Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation

(2011) Fei Wang et al.   Journal of Chemical Information and Modeling

From in silico target prediction to multi-target drug design: Current databases, methods and applications

(2011) Alexios Koutsoukas et al.   Journal of Proteomics

Analysis of multiple compound-protein interactions reveals novel bioactive molecules

(2011) H. Yabuuchi et al.   Molecular Systems Biology

An active role for machine learning in drug development

(2011) Robert F Murphy   Nature Chemical Biology

Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development

(2011) Gerard J. P. van Westen et al.   PLoS One

Computational chemogenomics

(2011) Edgar Jacoby   Wiley Interdisciplinary Reviews-Computational Molecular Science

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation

(2010) Hanna Geppert et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

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

Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications

(2010) Peter Ripphausen et al.   JOURNAL OF MEDICINAL CHEMISTRY

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

(2010) Gerard J. P. van Westen et al.   MedChemComm

COMPOUND ANALYSIS VIA GRAPH KERNELS INCORPORATING CHIRALITY

(2010) J.B. BROWN et al.   Journal of Bioinformatics and Computational Biology

Network analyses in systems pharmacology

(2009) S. I. Berger et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Comparison of Structure- and Ligand-Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors

(2009) Dennis M. Krüger et al.   ChemMedChem

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

Integrating Structure- and Ligand-Based Virtual Screening: Comparison of Individual, Parallel, and Fused Molecular Docking and Similarity Search Calculations on Multiple Targets

(2008) Lu Tan et al.   ChemMedChem

Data completeness—the Achilles heel of drug-target networks

(2008) Jordi Mestres et al.   NATURE BIOTECHNOLOGY

Protein-protein interaction networks and biology—what's the connection?

(2008) Luke Hakes et al.   NATURE BIOTECHNOLOGY