Getting the most out of PubChem for virtual screening

Literature information in PubChem: associations between PubChem records and scientific articles

(2016) Sunghwan Kim et al.   Journal of Cheminformatics

The Cambridge Structural Database

(2016) Colin R. Groom et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

Computational investigations of hERG channel blockers: New insights and current predictive models

(2015) Bruno O. Villoutreix et al.   ADVANCED DRUG DELIVERY REVIEWS

Bayesian models trained with HTS data for predicting β-haematin inhibition and in vitro antimalarial activity

(2015) Kathryn J. Wicht et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Multiclass Comparative Virtual Screening to Identify Novel Hsp90 Inhibitors: A Therapeutic Breast Cancer Drug Target

(2015) Nageswara Dunna et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using Antioxidant Response Element Reporter Gene Assay Models and Big Data

(2015) Marlene Thai Kim et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Rule-Based Classification Models of Molecular Autofluorescence

(2015) Bo-Han Su et al.   Journal of Chemical Information and Modeling

Rule-Based Prediction Models of Cytochrome P450 Inhibition

(2015) Bo-Han Su et al.   Journal of Chemical Information and Modeling

Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data

(2015) Martin Lindh et al.   Journal of Chemical Information and Modeling

Dark chemical matter as a promising starting point for drug lead discovery

(2015) Anne Mai Wassermann et al.   Nature Chemical Biology

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

(2015) George Papadatos et al.   NUCLEIC ACIDS RESEARCH

PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem

(2015) Sunghwan Kim 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

The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

(2015) Christopher Southan et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

(2015) Gang Fu et al.   Journal of Cheminformatics

InChI, the IUPAC International Chemical Identifier

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

Classification of Cytochrome P450 Inhibitors and Noninhibitors Using Combined Classifiers

(2015) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Discovery of Novel-Scaffold Monoamine Transporter Ligands via in Silico Screening with the S1 Pocket of the Serotonin Transporter

(2014) Tammy L. Nolan et al.   ACS Chemical Neuroscience

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

The EBI RDF platform: linked open data for the life sciences

(2014) S. Jupp et al.   BIOINFORMATICS

Big Data in Chemical Toxicity Research: The Use of High-Throughput Screening Assays To Identify Potential Toxicants

(2014) Hao Zhu et al.   CHEMICAL RESEARCH IN TOXICOLOGY

QSAR Modeling of Imbalanced High-Throughput Screening Data in PubChem

(2014) Alexey V. Zakharov et al.   Journal of Chemical Information and Modeling

An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs

(2014) Jie Xia et al.   Journal of Chemical Information and Modeling

The National Library of Medicine’s (NLM) Hazardous Substances Data Bank (HSDB): Background, recent enhancements and future plans

(2014) George Charles Fonger et al.   TOXICOLOGY

Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study

(2014) Hemanth Naick Banavath et al.   Scientific Reports

An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data

(2013) Ming Hao et al.   ANALYTICA CHIMICA ACTA

Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets

(2013) Matthias R. Bauer et al.   Journal of Chemical Information and Modeling

Oversampling to Overcome Overfitting: Exploring the Relationship between Data Set Composition, Molecular Descriptors, and Predictive Modeling Methods

(2013) Chia-Yun Chang et al.   Journal of Chemical Information and Modeling

Integrated One-Against-One Classifiers as Tools for Virtual Screening of Compound Databases: A Case Study with CNS Inhibitors

(2013) Mehdi Jalali-Heravi et al.   Molecular Informatics

Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

(2013) Mariusz Butkiewicz et al.   MOLECULES

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

MMDB and VAST+: tracking structural similarities between macromolecular complexes

(2013) Thomas Madej et al.   NUCLEIC ACIDS RESEARCH

PubChem BioAssay: 2014 update

(2013) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

The ChEMBL bioactivity database: an update

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

Exploring Chemical Space for Drug Discovery Using the Chemical Universe Database

(2012) Jean-Louis Reymond et al.   ACS Chemical Neuroscience

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

(2012) Christopher A. Lipinski et al.   ADVANCED DRUG DELIVERY REVIEWS

Improvement of Catalytic Efficiency, Thermo-stability and Dye Decolorization Capability of Pleurotus ostreatus IBL-02 laccase by Hydrophobic Sol Gel Entrapment

(2012) Muhammad Asgher et al.   Chemistry Central Journal

Novel Inhibitor Discovery through Virtual Screening against Multiple Protein Conformations Generated via Ligand-Directed Modeling: A Maternal Embryonic Leucine Zipper Kinase Example

(2012) Kiran V. Mahasenan et al.   Journal of Chemical Information and Modeling

Recognizing Pitfalls in Virtual Screening: A Critical Review

(2012) Thomas Scior 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

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

ADMET Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage

(2012) Sichao Wang et al.   MOLECULAR PHARMACEUTICS

In silico classification and virtual screening of maleimide derivatives using projection to latent structures discriminant analysis (PLS-DA) and hybrid docking

(2012) Liliana Pacureanu et al.   MONATSHEFTE FUR CHEMIE

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Pharmacophore-based database mining for probing fragmental drug-likeness of diketo acid analogues

(2012) A. Bak et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance

(2011) Varun Khanna et al.   BMC BIOINFORMATICS

A Comprehensive Support Vector Machine Binary hERG Classification Model Based on Extensive but Biased End Point hERG Data Sets

(2011) Meng-yu Shen et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Predicting Adverse Drug Reactions Using Publicly Available PubChem BioAssay Data

(2011) Y Pouliot et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Activity-Aware Clustering of High Throughput Screening Data and Elucidation of Orthogonal Structure–Activity Relationships

(2011) Eugen Lounkine et al.   Journal of Chemical Information and Modeling

Discovery of Novel Pim-1 Kinase Inhibitors by a Hierarchical Multistage Virtual Screening Approach Based on SVM Model, Pharmacophore, and Molecular Docking

(2011) Ji-Xia Ren et al.   Journal of Chemical Information and Modeling

A New Protocol for Predicting Novel GSK-3β ATP Competitive Inhibitors

(2011) Jiansong Fang et al.   Journal of Chemical Information and Modeling

A comparison of different QSAR approaches to modeling CYP450 1A2 inhibition

(2011) Sergii Novotarskyi et al.   Journal of Chemical Information and Modeling

DEKOIS: Demanding Evaluation Kits for Objectivein SilicoScreening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions

(2011) Simon M. Vogel et al.   Journal of Chemical Information and Modeling

Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors

(2011) Edgar A. Gatica et al.   Journal of Chemical Information and Modeling

Virtual Decoy Sets for Molecular Docking Benchmarks

(2011) Izhar Wallach et al.   Journal of Chemical Information and Modeling

Visualisation and subsets of the chemical universe database GDB-13 for virtual screening

(2011) Lorenz C. Blum et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

(2011) A. R. Kinjo et al.   NUCLEIC ACIDS RESEARCH

SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents

(2011) A. Heifets et al.   NUCLEIC ACIDS RESEARCH

Predicting Adverse Drug Events Using Pharmacological Network Models

(2011) A. Cami et al.   Science Translational Medicine

FlaME: Flash Molecular Editor - a 2D structure input tool for the web

(2011) Pavel Dallakian et al.   Journal of Cheminformatics

Use of in Vitro HTS-Derived Concentration–Response Data as Biological Descriptors Improves the Accuracy of QSAR Models of in Vivo Toxicity

(2010) Alexander Sedykh et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

In Silico Binary Classification QSAR Models Based on 4D-Fingerprints and MOE Descriptors for Prediction of hERG Blockage

(2010) Bo-Han Su et al.   Journal of Chemical Information and Modeling

Trainable structure–activity relationship model for virtual screening of CYP3A4 inhibition

(2010) Remigijus Didziapetris et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Identifying Novel Type ZBGs and Nonhydroxamate HDAC Inhibitors Through a SVM Based Virtual Screening Approach

(2010) X. H. Liu et al.   Molecular Informatics

Virtual Screening of Selective Multitarget Kinase Inhibitors by Combinatorial Support Vector Machines

(2010) X. H. Ma et al.   MOLECULAR PHARMACEUTICS

Cheminformatics-Based Drug Design Approach for Identification of Inhibitors Targeting the Characteristic Residues of MMP-13 Hemopexin Domain

(2010) Roopa Kothapalli et al.   PLoS One

A novel method for mining highly imbalanced high-throughput screening data in PubChem

(2009) Qingliang Li et al.   BIOINFORMATICS

PubChem as a Source of Polypharmacology

(2009) Bin Chen et al.   Journal of Chemical Information and Modeling

Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data

(2009) Sebastian G. Rohrer et al.   Journal of Chemical Information and Modeling

Identification of small molecule aggregators from large compound libraries by support vector machines

(2009) Hanbing Rao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Combinatorial chemistry: oh what a decade or two can do

(2009) Walter H. Moos et al.   MOLECULAR DIVERSITY

Virtual screening of bioassay data

(2009) Amanda C Schierz   Journal of Cheminformatics

Use of Cell Viability Assay Data Improves the Prediction Accuracy of Conventional Quantitative Structure–Activity Relationship Models of Animal Carcinogenicity

(2008) Hao Zhu et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

SVMs Modeling for Highly Imbalanced Classification

(2008) Yuchun Tang et al.   IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS

A group center overlap based approach for “3D QSAR” studies on TIBO derivatives

(2008) Nitin S. Sapre et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening

(2008) Jui-Hua Hsieh et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Utilizing high throughput screening data for predictive toxicology models: protocols and application to MLSCN assays

(2008) Rajarshi Guha et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor

(2008) L.Y. Han et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors

(2008) Qiyuan Li et al.   MOLECULAR PHARMACEUTICS