Using quantitative systems pharmacology for novel drug discovery

Systems biology approaches for advancing the discovery of effective drug combinations

(2015) Karen A Ryall et al.   Journal of Cheminformatics

A novel systems pharmacology model for herbal medicine injection: a case using reduning injection

(2014) Haixing Yang et al.   BMC Complementary and Alternative Medicine

Insights from systems pharmacology into cardiovascular drug discovery and therapy

(2014) Peng Li et al.   BMC Systems Biology

GES Polypharmacology Fingerprints: A Novel Approach for Drug Repositioning

(2014) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Polypharmacology: Challenges and Opportunities in Drug Discovery

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

DINIES: drug–target interaction network inference engine based on supervised analysis

(2014) Yoshihiro Yamanishi et al.   NUCLEIC ACIDS RESEARCH

Exploiting polypharmacology for drug target deconvolution

(2014) Taranjit Singh Gujral et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative versus qualitative data: The numerical dimensions of drug action

(2013) David B. Bylund et al.   BIOCHEMICAL PHARMACOLOGY

Systems pharmacology in drug discovery and therapeutic insight for herbal medicines

(2013) Chao Huang et al.   BRIEFINGS IN BIOINFORMATICS

Analysis of Chemical and Biological Features Yields Mechanistic Insights into Drug Side Effects

(2013) Miquel Duran-Frigola et al.   CHEMISTRY & BIOLOGY

Recent Trends and Future Prospects in Computational GPCR Drug Discovery: From Virtual Screening to Polypharmacology

(2013) Antonio Carrieri et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Computational Profiling of Bioactive Compounds Using a Target-Dependent Composite Workflow

(2013) Jamel Meslamani et al.   Journal of Chemical Information and Modeling

Prediction of Polypharmacological Profiles of Drugs by the Integration of Chemical, Side Effect, and Therapeutic Space

(2013) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Systems approaches and polypharmacology for drug discovery from herbal medicines: An example using licorice

(2013) Hui Liu et al.   JOURNAL OF ETHNOPHARMACOLOGY

Systems pharmacology strategies for drug discovery and combination with applications to cardiovascular diseases

(2013) Peng Li et al.   JOURNAL OF ETHNOPHARMACOLOGY

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments

(2013) Arnaud S. Karaboga et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

A pharmacological organization of G protein–coupled receptors

(2013) Henry Lin et al.   NATURE METHODS

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

(2012) Tiejun Cheng et al.   AAPS Journal

Relating drug-protein interaction network with drug side effects

(2012) S. Mizutani et al.   BIOINFORMATICS

Drug target prediction using adverse event report systems: a pharmacogenomic approach

(2012) M. Takarabe et al.   BIOINFORMATICS

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Relevance of systems pharmacology in drug discovery

(2012) Lourdes Cucurull-Sanchez et al.   DRUG DISCOVERY TODAY

Detecting Drug Promiscuity Using Gaussian Ensemble Screening

(2012) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling

(2012) Jamel Meslamani et al.   Journal of Chemical Information and Modeling

Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces

(2012) Yoshihiro Yamanishi et al.   Journal of Chemical Information and Modeling

Predicting cancer drug mechanisms of action using molecular network signatures

(2012) Justin R. Pritchard et al.   Molecular BioSystems

PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery

(2012) Maria C. Carrascosa et al.   Molecular Informatics

Automated design of ligands to polypharmacological profiles

(2012) Jérémy Besnard et al.   NATURE

NCATS launches drug repurposing program

(2012) Malorye Allison   NATURE BIOTECHNOLOGY

Pharmacogenomics and Patient Care: One Size Does Not Fit All

(2012) K. M. Giacomini et al.   Science Translational Medicine

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience

(2012) M. Krallinger et al.   Database-The Journal of Biological Databases and Curation

Text mining for the biocuration workflow

(2012) L. Hirschman et al.   Database-The Journal of Biological Databases and Curation

Multi-Scale In Vivo Systems Analysis Reveals the Influence of Immune Cells on TNF-α-Induced Apoptosis in the Intestinal Epithelium

(2012) Ken S. Lau et al.   PLOS BIOLOGY

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

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Accumulating evidence for the case of differential discounting

(2012) Maarten J Postma et al.   Expert Review of Clinical Pharmacology

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

(2011) Shan Zhao et al.   Annual Review of Pharmacology and Toxicology

Building the process-drug–side effect network to discover the relationship between biological Processes and side effects

(2011) Sejoon Lee et al.   BMC BIOINFORMATICS

Predicting drug side-effect profiles: a chemical fragment-based approach

(2011) Edouard Pauwels et al.   BMC BIOINFORMATICS

Identifying and characterizing promiscuous targets: Implications for virtual screening

(2011) Violeta I Pérez-Nueno et al.   Expert Opinion on Drug Discovery

Computational tools for polypharmacology and repurposing

(2011) Janosch Achenbach et al.   Future Medicinal Chemistry

SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening

(2011) Xiaofeng Liu et al.   Journal of Chemical Information and Modeling

ReverseScreen3D: A Structure-Based Ligand Matching Method To Identify Protein Targets

(2011) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

Drug Effect Prediction by Polypharmacology-Based Interaction Profiling

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

Network-Based Analysis and Characterization of Adverse Drug–Drug Interactions

(2011) Masataka Takarabe et al.   Journal of Chemical Information and Modeling

Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening

(2011) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach

(2011) Mohamed Diwan M. AbdulHameed et al.   Journal of Chemical Information and Modeling

An Algorithmic Framework for Predicting Side Effects of Drugs

(2011) Nir Atias et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

An inverse docking approach for identifying new potential anti-cancer targets

(2011) Sam Z. Grinter et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Analysis of multiple compound-protein interactions reveals novel bioactive molecules

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

Practical implications of gene-expression-based assays for breast oncologists

(2011) Aleix Prat et al.   Nature Reviews Clinical Oncology

Finding Promiscuous Old Drugs for New Uses

(2011) Sean Ekins et al.   PHARMACEUTICAL RESEARCH

Mining Significant Substructure Pairs for Interpreting Polypharmacology in Drug-Target Network

(2011) Ichigaku Takigawa et al.   PLoS One

Systematic Drug Repositioning Based on Clinical Side-Effects

(2011) Lun Yang et al.   PLoS One

Chronotherapeutics and Chronotherapeutic Drug Delivery Systems

(2011) J Sajan et al.   TROPICAL JOURNAL OF PHARMACEUTICAL RESEARCH

Predicting drug polypharmacology using a novel surface property similarity-based approach

(2011) Violeta I Perez-Nueno et al.   Journal of Cheminformatics

The Chemical Basis of Pharmacology

(2010) Michael J. Keiser et al.   BIOCHEMISTRY

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework

(2010) Y. Yamanishi et al.   BIOINFORMATICS

Multiscale Modeling in Drug Discovery and Development: Future Opportunities and Present Challenges

(2010) P Vicini   CLINICAL PHARMACOLOGY & THERAPEUTICS

Anticipating drug side effects by comparative pharmacology

(2010) Ricard Garcia-Serna et al.   Expert Opinion on Drug Metabolism & Toxicology

Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe

(2010) Francesca Milletti et al.   Journal of Chemical Information and Modeling

Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand−Target Space

(2010) Satoshi Niijima 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

Evaluation of various inverse docking schemes in multiple targets identification

(2010) Liu Hui-fang et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

In Silico Receptorome Screening of Antipsychotic Drugs

(2010) David Vidal et al.   Molecular Informatics

Systems Pharmacology

(2010) Aislyn D. W. Boran et al.   MOUNT SINAI JOURNAL OF MEDICINE

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach

(2010) Xiaofeng Liu et al.   NUCLEIC ACIDS RESEARCH

Network-Based Relating Pharmacological and Genomic Spaces for Drug Target Identification

(2010) Shiwen Zhao et al.   PLoS One

A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways

(2010) Izhar Wallach et al.   PLoS One

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)

(2009) Thomas C Wiegers et al.   BMC BIOINFORMATICS

Docking and chemoinformatic screens for new ligands and targets

(2009) Peter Kolb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Ligand Prediction for Orphan Targets Using Support Vector Machines and Various Target-Ligand Kernels Is Dominated by Nearest Neighbor Effects

(2009) Anne Mai Wassermann et al.   Journal of Chemical Information and Modeling

RED: A Set of Molecular Descriptors Based on Rényi Entropy

(2009) Laura Delgado-Soler et al.   Journal of Chemical Information and Modeling

Development and Validation of a Novel Protein−Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands

(2009) Nathanael Weill et al.   Journal of Chemical Information and Modeling

Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis

(2009) Josef Scheiber et al.   Journal of Chemical Information and Modeling

Mapping Adverse Drug Reactions in Chemical Space

(2009) Josef Scheiber et al.   JOURNAL OF MEDICINAL CHEMISTRY

The topology of drug–target interaction networks: implicit dependence on drug properties and target families

(2009) Jordi Mestres et al.   Molecular BioSystems

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 text mining into the MGI biocuration workflow

(2009) K.G. Dowell et al.   Database-The Journal of Biological Databases and Curation

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

(2009) Li Xie et al.   PLoS Computational Biology

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study

(2008) Allan P Davis et al.   BMC Medical Genomics

Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics

(2008) Florian Nigsch et al.   Journal of Chemical Information and Modeling

Clustering and Classifying Diverse HIV Entry Inhibitors Using a Novel Consensus Shape-Based Virtual Screening Approach: Further Evidence for Multiple Binding Sites within the CCR5 Extracellular Pocket

(2008) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Quantifying the Relationships among Drug Classes

(2008) Jérôme Hert et al.   Journal of Chemical Information and Modeling

γ-secretase inhibitors reverse glucocorticoid resistance in T cell acute lymphoblastic leukemia

(2008) Pedro J Real et al.   NATURE MEDICINE

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

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

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE