Shaping the interaction landscape of bioactive molecules

TargetHunter: An In Silico Target Identification Tool for Predicting Therapeutic Potential of Small Organic Molecules Based on Chemogenomic Database

(2013) Lirong Wang et al.   AAPS Journal

Target Identification for Small Bioactive Molecules: Finding the Needle in the Haystack

(2013) Slava Ziegler et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method

(2013) Jiayu Gong et al.   BIOINFORMATICS

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

(2013) M. Iskar et al.   Molecular Systems Biology

Systematic identification of proteins that elicit drug side effects

(2013) M. Kuhn et al.   Molecular Systems Biology

Challenges and opportunities of drug repositioning

(2013) Natalia Novac   TRENDS IN PHARMACOLOGICAL SCIENCES

Detecting Drug Promiscuity Using Gaussian Ensemble Screening

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

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

The Experimental Uncertainty of Heterogeneous Public Ki Data

(2012) Christian Kramer et al.   JOURNAL OF MEDICINAL CHEMISTRY

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach

(2012) Jui-Chih Wang et al.   NUCLEIC ACIDS RESEARCH

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

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

Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring

(2011) G. Madhavi Sastry et al.   Journal of Chemical Information and Modeling

Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension

(2011) M. Stuart Armstrong et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Chemical Structural Novelty: On-Targets and Off-Targets

(2011) Emmanuel R. Yera et al.   JOURNAL OF MEDICINAL CHEMISTRY

SwissDock, a protein-small molecule docking web service based on EADock DSS

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

ChEMBL: a large-scale bioactivity database for drug discovery

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

Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

(2010) Vishwesh Venkatraman et al.   Journal of Chemical Information and Modeling

ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics

(2010) M. Stuart Armstrong et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

A survey of yeast genomic assays for drug and target discovery

(2010) Andrew M. Smith et al.   PHARMACOLOGY & THERAPEUTICS

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Docking, virtual high throughput screening and in silico fragment-based drug design

(2009) Vincent Zoete et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology

(2009) Pedro J. Ballester et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

The Hallucinogen N,N-Dimethyltryptamine (DMT) Is an Endogenous Sigma-1 Receptor Regulator

(2009) D. Fontanilla et al.   SCIENCE

Small Molecule Subgraph Detector (SMSD) toolkit

(2009) Syed Rahman et al.   Journal of Cheminformatics

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

(2009) Jiao Li et al.   PLoS Computational Biology

Scaffold Topologies. 1. Exhaustive Enumeration up to Eight Rings

(2008) Sara N. Pollock et al.   Journal of Chemical Information and Modeling

Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics

(2008) Sebastian G. Rohrer et al.   Journal of Chemical Information and Modeling

SuperPred: drug classification and target prediction

(2008) M. Dunkel et al.   NUCLEIC ACIDS RESEARCH

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE