Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case

Decoding the Structural Basis For Carbapenem Hydrolysis By Class A β-lactamases: Fishing For A Pharmacophore

(2016) Donatella Tondi et al.   CURRENT DRUG TARGETS

Histone demethylating agents as potential S-adenosyl-l-methionine-competitors

(2016) R. Navakauskienė et al.   MedChemComm

Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology

(2016) Thomas Hart et al.   Scientific Reports

Expanding the chemical space of human serine racemase inhibitors

(2015) Luca Dellafiora et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Drug discovery FAQs: workflows for answering multidomain drug discovery questions

(2015) Christine Chichester et al.   DRUG DISCOVERY TODAY

Evaluating the risk of phospholipidosis using a new multidisciplinary pipeline approach

(2015) Laura Goracci et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Repurposing Registered Drugs as Antagonists for Protease-Activated Receptor 2

(2015) Weijun Xu et al.   Journal of Chemical Information and Modeling

GESSE: Predicting Drug Side Effects from Drug–Target Relationships

(2015) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

(2015) Francesca Spyrakis et al.   Journal of Chemical Information and Modeling

Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets

(2015) Weijun Xu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

BioGPS: Navigating biological space to predict polypharmacology, off-targeting, and selectivity

(2015) Lydia Siragusa et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PPDMs--a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains

(2014) F. A. Kruger et al.   BIOINFORMATICS

The novel thymidylate synthase inhibitor trifluorothymidine (TFT) and TRAIL synergistically eradicate non-small cell lung cancer cells

(2014) Kaamar Azijli et al.   CANCER CHEMOTHERAPY AND PHARMACOLOGY

Targeting Cystalysin, a Virulence Factor ofTreponema denticola-Supported Periodontitis

(2014) Francesca Spyrakis et al.   ChemMedChem

The Inhibition of Extended Spectrum β-Lactamases: Hits and Leads

(2014) Davide Farina et al.   CURRENT MEDICINAL CHEMISTRY

BioGPS: The Music for the Chemo- and Bioinformatics Walzer

(2014) Lydia Siragusa et al.   Molecular Informatics

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

(2014) Yoshihiro Yamanishi et al.   NUCLEIC ACIDS RESEARCH

BioGPS Descriptors for Rational Engineering of Enzyme Promiscuity and Structure Based Bioinformatic Analysis

(2014) Valerio Ferrario et al.   PLoS One

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

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

Compound promiscuity: what can we learn from current data?

(2013) Ye Hu et al.   DRUG DISCOVERY TODAY

New linezolid-like 1,2,4-oxadiazoles active against Gram-positive multiresistant pathogens

(2013) Cosimo G. Fortuna et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Modeling Phospholipidosis Induction: Reliability and Warnings

(2013) Laura Goracci 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

The ChEMBL bioactivity database: an update

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

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

(2013) V. Joachim Haupt et al.   PLoS One

Isozyme-Specific Ligands for O-acetylserine sulfhydrylase, a Novel Antibiotic Target

(2013) Francesca Spyrakis et al.   PLoS One

Drug Repurposing: Far Beyond New Targets for Old Drugs

(2012) T. I. Oprea et al.   AAPS Journal

Human Cytomegalovirus Inhibitor AL18 Also Possesses Activity against Influenza A and B Viruses

(2012) Giulia Muratore et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Relating drug-protein interaction network with drug side effects

(2012) S. Mizutani et al.   BIOINFORMATICS

Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence

(2012) Shannan J. Ho Sui et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Inhibitor of Ovarian Cancer Cells Growth by Virtual Screening: A New Thiazole Derivative Targeting Human Thymidylate Synthase

(2012) Emanuele Carosati et al.   JOURNAL OF MEDICINAL CHEMISTRY

Reducing safety-related drug attrition: the use of in vitro pharmacological profiling

(2012) Joanne Bowes et al.   NATURE REVIEWS DRUG DISCOVERY

Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase

(2012) G. Muratore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polypharmacology: drug discovery for the future

(2012) A Srinivas Reddy et al.   Expert Review of Clinical Pharmacology

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

(2011) Edouard Pauwels et al.   BMC BIOINFORMATICS

Identify drug repurposing candidates by mining the Protein Data Bank

(2011) F. Moriaud et al.   BRIEFINGS IN BIOINFORMATICS

Drug Effect Prediction by Polypharmacology-Based Interaction Profiling

(2011) Zoltán Simon 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

Systematic Drug Repositioning Based on Clinical Side-Effects

(2011) Lun Yang et al.   PLoS One

Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

(2011) D. Cardinale et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding

(2011) Tianyun Liu et al.   PLoS Computational Biology

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

(2010) Janez Konc et al.   BIOINFORMATICS

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

(2010) Y. Yamanishi et al.   BIOINFORMATICS

Ligand-based virtual screening and ADME-tox guided approach to identify triazolo-quinoxalines as folate cycle inhibitors

(2010) Emanuele Carosati et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites

(2010) Nathanaël Weill et al.   Journal of Chemical Information and Modeling

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

(2010) Sarah L. Kinnings et al.   PLoS Computational Biology

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

PocketMatch: A new algorithm to compare binding sites in protein structures

(2009) Kalidas Yeturu et al.   BMC BIOINFORMATICS

Structural motifs recurring in different folds recognize the same ligand fragments

(2009) Gabriele Ausiello et al.   BMC BIOINFORMATICS

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

Predicting the multi-modal binding propensity of small molecules: towards an understanding of drug promiscuity

(2009) Keunwan Park et al.   Molecular BioSystems

Predicting promiscuity

(2009) Andrew L. Hopkins   NATURE

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding

(2009) R. Z. Cer et al.   NUCLEIC ACIDS RESEARCH

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE