Progress in visual representations of chemical space

Extending kinome coverage by analysis of kinase inhibitor broad profiling data

(2015) Edgar Jacoby et al.   DRUG DISCOVERY TODAY

Designing novel building blocks is an overlooked strategy to improve compound quality

(2015) Frederick W. Goldberg et al.   DRUG DISCOVERY TODAY

DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis

(2015) Thomas Sander et al.   Journal of Chemical Information and Modeling

Visualization of bipartite relations between graphs and sets

(2015) Hong Zhou et al.   JOURNAL OF VISUALIZATION

Chemography of Natural Product Space

(2015) Tomoyuki Miyao et al.   PLANTA MEDICA

Chemical space is big. Really big

(2015) Derek Lowe   MedChemComm

Discovery of Potent Positive Allosteric Modulators of the α3β2 Nicotinic Acetylcholine Receptor by a Chemical Space Walk in ChEMBL

(2014) Justus J. Bürgi et al.   ACS Chemical Neuroscience

Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network

(2014) Helge G Roider et al.   BMC BIOINFORMATICS

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

(2014) Natalia V. Kireeva et al.   ChemMedChem

The Role of Big Data and Advanced Analytics in Drug Discovery, Development, and Commercialization

(2014) N Szlezák et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery

(2014) Christian Partl et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces

(2014) Philipp Thiel et al.   Journal of Chemical Information and Modeling

Chemical Data Visualization and Analysis with Incremental Generative Topographic Mapping: Big Data Challenge

(2014) Héléna A. Gaspar et al.   Journal of Chemical Information and Modeling

Euclidean chemical spaces from molecular fingerprints: Hamming distance and Hempel’s ravens

(2014) Eric Martin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Chemical space networks: a powerful new paradigm for the description of chemical space

(2014) Gerald M. Maggiora et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Chemoinformatic Analysis as a Tool for Prioritization of Trypanocidal Marine Derived Lead Compounds

(2014) Yunjiang Feng et al.   Marine Drugs

Revealing the macromolecular targets of complex natural products

(2014) Daniel Reker et al.   Nature Chemistry

Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process

(2014) Yurii Sushko et al.   Journal of Cheminformatics

The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

(2014) Antonino Fiannaca et al.   Journal of Cheminformatics

Expanding the fragrance chemical space for virtual screening

(2014) Lars Ruddigkeit et al.   Journal of Cheminformatics

CheS-Mapper 2.0 for visual validation of (Q)SAR models

(2014) Martin Gütlein et al.   Journal of Cheminformatics

Supervised extensions of chemography approaches: case studies of chemical liabilities assessment

(2014) Svetlana I Ovchinnikova et al.   Journal of Cheminformatics

Data-driven medicinal chemistry in the era of big data

(2013) Scott J. Lusher et al.   DRUG DISCOVERY TODAY

First principles view on chemical compound space: Gaining rigorous atomistic control of molecular properties

(2013) O. Anatole von Lilienfeld   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13

(2013) Mahendra Awale et al.   Journal of Chemical Information and Modeling

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

Estimation of the size of drug-like chemical space based on GDB-17 data

(2013) P. G. Polishchuk et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

(2013) Aaron M. Virshup et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Visual Analysis of Biological Activity Data with Scaffold Hunter

(2013) Karsten Klein et al.   Molecular Informatics

Progress in the Visualization and Mining of Chemical and Target Spaces

(2013) José L. Medina-Franco et al.   Molecular Informatics

The 'rule of three' for fragment-based drug discovery: where are we now?

(2013) Harren Jhoti et al.   NATURE REVIEWS DRUG DISCOVERY

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

(2013) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

Exploring the Chemical Space of Multitarget Ligands Using Aligned Self-Organizing Maps

(2013) Janosch Achenbach et al.   ACS Medicinal Chemistry Letters

Mining collections of compounds with Screening Assistant 2

(2013) Vincent Guilloux et al.   Journal of Cheminformatics

Druggable chemical space and enumerative combinatorics

(2013) Melvin J Yu   Journal of Cheminformatics

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

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

Using self-organizing maps to accelerate similarity search

(2012) Fanny Bonachera et al.   BIOORGANIC & MEDICINAL CHEMISTRY

HiTSEE KNIME: a visualization tool for hit selection and analysis in high-throughput screening experiments for the KNIME platform

(2012) Hendrik Strobelt et al.   BMC BIOINFORMATICS

Interrogating Novel Areas of Chemical Space for Drug Discovery using Chemoinformatics

(2012) José L. Medina-Franco   DRUG DEVELOPMENT RESEARCH

Modeling of activity landscapes for drug discovery

(2012) Jürgen Bajorath   Expert Opinion on Drug Discovery

Toward Navigating Chemical Space of Ionic Liquids: Prediction of Melting Points Using Generative Topographic Maps

(2012) Natalia Kireeva et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Using Novel Descriptor Accounting for Ligand–Receptor Interactions To Define and Visually Explore Biologically Relevant Chemical Space

(2012) Obdulia Rabal et al.   Journal of Chemical Information and Modeling

Biologically Relevant Chemical Space Navigator: From Patent and Structure–Activity Relationship Analysis to Library Acquisition and Design

(2012) Obdulia Rabal 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

About the concept of Chemical Space: a concerned reflection on some trends of modern scientific thought within theoretical chemical lore

(2012) Ramon Carbó-Dorca   JOURNAL OF MATHEMATICAL CHEMISTRY

Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery

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

Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, Structure-Activity Modeling and Dataset Comparison

(2012) N. Kireeva et al.   Molecular Informatics

In silico comparison of marine, terrestrial and synthetic compounds using ChemGPS-NP for navigating chemical space

(2012) Patrik Muigg et al.   PHYTOCHEMISTRY REVIEWS

Synthesis and Biological Evaluation of Phenanthrenes as Cytotoxic Agents with Pharmacophore Modeling and ChemGPS-NP Prediction as Topo II Inhibitors

(2012) Chia-Lin Lee et al.   PLoS One

CheS-Mapper - Chemical Space Mapping and Visualization in 3D

(2012) Martin Gütlein et al.   Journal of Cheminformatics

Rendezvous in chemical space? Comparing the small molecule compound libraries of Bayer and Schering

(2011) Jens Schamberger et al.   DRUG DISCOVERY TODAY

Evolution of the physicochemical properties of marketed drugs: can history foretell the future?

(2011) Bernard Faller et al.   DRUG DISCOVERY TODAY

Visualization of Molecular Fingerprints

(2011) John R. Owen et al.   Journal of Chemical Information and Modeling

Multitarget Structure–Activity Relationships Characterized by Activity-Difference Maps and Consensus Similarity Measure

(2011) José L. Medina-Franco et al.   Journal of Chemical Information and Modeling

Scaffold Diversity of Exemplified Medicinal Chemistry Space

(2011) Sarah R. Langdon et al.   Journal of Chemical Information and Modeling

Visual Characterization and Diversity Quantification of Chemical Libraries: 1. Creation of Delimited Reference Chemical Subspaces

(2011) Vincent Le Guilloux et al.   Journal of Chemical Information and Modeling

Mining for Bioactive Scaffolds with Scaffold Networks: Improved Compound Set Enrichment from Primary Screening Data

(2011) Thibault Varin et al.   Journal of Chemical Information and Modeling

SketchSort: Fast All Pairs Similarity Search for Large Databases of Molecular Fingerprints

(2011) Yasuo Tabei et al.   Molecular Informatics

Self-Organizing Maps for In Silico Screening and Data Visualization

(2011) Daniela Digles et al.   Molecular Informatics

The graphical representation of ADME-related molecule properties for medicinal chemists

(2010) Timothy J. Ritchie et al.   DRUG DISCOVERY TODAY

SARANEA: A Freely Available Program To Mine Structure−Activity and Structure−Selectivity Relationship Information in Compound Data Sets

(2010) Eugen Lounkine et al.   Journal of Chemical Information and Modeling

Scaffold Explorer: An Interactive Tool for Organizing and Mining Structure−Activity Data Spanning Multiple Chemotypes

(2010) Dimitris K. Agrafiotis et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular Shape and Medicinal Chemistry: A Perspective

(2010) Anthony Nicholls et al.   JOURNAL OF MEDICINAL CHEMISTRY

Stochastic Proximity Embedding: Methods and Applications

(2010) Dimitris K. Agrafiotis et al.   Molecular Informatics

Exploring the chemical space of γ-secretase modulators

(2010) Heiko Zettl et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Structure–activity relationships of benzimidazole derivatives as antiparasitic agents: Dual activity-difference (DAD) maps

(2010) Jaime Pérez-Villanueva et al.   MedChemComm

Using the Golden Triangle to optimize clearance and oral absorption

(2009) Ted W. Johnson et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Classification of Organic Molecules by Molecular Quantum Numbers

(2009) Kong T. Nguyen et al.   ChemMedChem

Novel Chemical Space Exploration via Natural Products

(2009) Josefin Rosén et al.   JOURNAL OF MEDICINAL CHEMISTRY

Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success

(2009) Frank Lovering et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Interactive exploration of chemical space with Scaffold Hunter

(2009) Stefan Wetzel et al.   Nature Chemical Biology

A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism

(2009) James Corey Adams et al.   PLoS Computational Biology

Visualization of the Chemical Space in Drug Discovery

(2008) Jose Medina-Franco et al.   Current Computer-Aided Drug Design

ChemGPS-NPWeb: chemical space navigation online

(2008) Josefin Rosén et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Merging chemical and biological space: Structural mapping of enzyme binding pocket space

(2008) Nils Weskamp et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS