Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze

CANDO and the infinite drug discovery frontier

(2014) Mark Minie et al.   DRUG DISCOVERY TODAY

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

(2014) K. Khafizov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drug–target interaction prediction through domain-tuned network-based inference

(2013) Salvatore Alaimo et al.   BIOINFORMATICS

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Phase 2 study of azacytidine plus sorafenib in patients with acute myeloid leukemia and FLT-3 internal tandem duplication mutation

(2013) F. Ravandi et al.   BLOOD

Network-Based Approaches in Drug Discovery and Early Development

(2013) J M Harrold et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Trendspotting in the Protein Data Bank

(2013) Helen M. Berman et al.   FEBS LETTERS

Project ranks billions of drug interactions

(2013) Sara Reardon   NATURE

The why and how of phenotypic small-molecule screens

(2013) Ulrike S Eggert   Nature Chemical Biology

Beyond magic bullets: true innovation in health care

(2013) Vaibhav A. Narayan et al.   NATURE REVIEWS DRUG DISCOVERY

ModBase, a database of annotated comparative protein structure models and associated resources

(2013) Ursula Pieper et al.   NUCLEIC ACIDS RESEARCH

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile

(2013) Twan van Laarhoven et al.   PLoS One

Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach

(2013) Dorothea Emig et al.   PLoS One

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

(2013) Francisco Martínez-Jiménez et al.   PLoS Computational Biology

Biological network inference for drug discovery

(2012) Paola Lecca et al.   DRUG DISCOVERY TODAY

Drug–target interaction prediction by random walk on the heterogeneous network

(2012) Xing Chen et al.   Molecular BioSystems

Chemical genetic discovery of targets and anti-targets for cancer polypharmacology

(2012) Arvin C. Dar et al.   NATURE

Quantifying the chemical beauty of drugs

(2012) G. Richard Bickerton et al.   Nature Chemistry

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

Analysis of multiple compound-protein interactions reveals novel bioactive molecules

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

Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs

(2011) Olga V. Kalinina et al.   PLoS Computational Biology

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

(2010) Y. Yamanishi et al.   BIOINFORMATICS

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

(2010) Brice Hoffmann et al.   BMC BIOINFORMATICS

Sorafenib induces growth inhibition and apoptosis in human synovial sarcoma cells via inhibiting the RAF/MEK/ERK signaling pathway

(2010) Chang-Liang Peng et al.   CANCER BIOLOGY & THERAPY

Phase I/II Study of Combination Therapy With Sorafenib, Idarubicin, and Cytarabine in Younger Patients With Acute Myeloid Leukemia

(2010) Farhad Ravandi et al.   JOURNAL OF CLINICAL ONCOLOGY

Thousands of chemical starting points for antimalarial lead identification

(2010) Francisco-Javier Gamo et al.   NATURE

ProBiS: a web server for detection of structurally similar protein binding sites

(2010) J. Konc et al.   NUCLEIC ACIDS RESEARCH

ModBase, a database of annotated comparative protein structure models, and associated resources

(2010) U. Pieper et al.   NUCLEIC ACIDS RESEARCH

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

A Kernel for Open Source Drug Discovery in Tropical Diseases

(2009) Leticia Ortí et al.   PLoS Neglected Tropical Diseases

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

(2008) R. Najmanovich et al.   BIOINFORMATICS

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

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

(2002) Angel R. Ortiz et al.   PROTEIN SCIENCE