Published in PLoS One on August 23, 2010
Open Babel: An open chemical toolbox. J Cheminform (2011) 11.12
Systematic drug repositioning based on clinical side-effects. PLoS One (2011) 1.56
Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study. PLoS Comput Biol (2011) 1.26
Relating drug-protein interaction network with drug side effects. Bioinformatics (2012) 1.10
DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. Nucleic Acids Res (2014) 0.89
Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. J Chem Inf Model (2015) 0.86
From laptop to benchtop to bedside: structure-based drug design on protein targets. Curr Pharm Des (2012) 0.85
Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines. PLoS One (2014) 0.82
Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms. Wiley Interdiscip Rev Syst Biol Med (2015) 0.78
3D pharmacophoric similarity improves multi adverse drug event identification in pharmacovigilance. Sci Rep (2015) 0.78
Systematic Analysis of the Associations between Adverse Drug Reactions and Pathways. Biomed Res Int (2015) 0.75
Ensemble-based docking: From hit discovery to metabolism and toxicity predictions. Bioorg Med Chem (2016) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett (1999) 25.40
Liver fibrosis. J Clin Invest (2005) 17.27
How many drug targets are there? Nat Rev Drug Discov (2006) 14.22
DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res (2007) 13.94
Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics (2009) 12.21
Predicting new molecular targets for known drugs. Nature (2009) 9.71
Drug target identification using side-effect similarity. Science (2008) 9.24
Pharmacogenomics--drug disposition, drug targets, and side effects. N Engl J Med (2003) 7.23
Parkinson's disease: clinical features and diagnosis. J Neurol Neurosurg Psychiatry (2008) 7.20
Practice guidelines in acute pancreatitis. Am J Gastroenterol (2006) 7.05
A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol (2010) 6.75
Relating protein pharmacology by ligand chemistry. Nat Biotechnol (2007) 6.61
Benchmarking sets for molecular docking. J Med Chem (2006) 5.57
The Blue Obelisk-interoperability in chemical informatics. J Chem Inf Model (2006) 4.88
Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nat Rev Drug Discov (2004) 4.31
Mechanisms of disease: is osteoporosis the obesity of bone? Nat Clin Pract Rheumatol (2006) 4.18
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol (2006) 3.54
Melanomas require HEDGEHOG-GLI signaling regulated by interactions between GLI1 and the RAS-MEK/AKT pathways. Proc Natl Acad Sci U S A (2007) 3.20
The L1 major capsid protein of human papillomavirus type 11 recombinant virus-like particles interacts with heparin and cell-surface glycosaminoglycans on human keratinocytes. J Biol Chem (1999) 3.16
Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol (2009) 2.84
Automated docking screens: a feasibility study. J Med Chem (2009) 2.14
Elucidating mechanisms of drug-induced toxicity. Nat Rev Drug Discov (2005) 2.06
Variants in DNA double-strand break repair genes and breast cancer susceptibility. Hum Mol Genet (2002) 2.04
Mapping adverse drug reactions in chemical space. J Med Chem (2009) 1.77
Prospective evaluation of prostate cancer risk in candidates for inguinal hernia repair. J Am Coll Surg (2009) 1.59
Keynote review: in vitro safety pharmacology profiling: an essential tool for successful drug development. Drug Discov Today (2005) 1.55
eHiTS: a new fast, exhaustive flexible ligand docking system. J Mol Graph Model (2006) 1.44
Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42
Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis. J Chem Inf Model (2009) 1.40
Glycosaminoglycan hydrogel films as bio-interactive dressings for wound healing. Biomaterials (2002) 1.38
Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet (2008) 1.37
The hedgehog pathway transcription factor GLI1 promotes malignant behavior of cancer cells by up-regulating osteopontin. J Biol Chem (2009) 1.36
Analysis of drug-induced effect patterns to link structure and side effects of medicines. Nat Chem Biol (2005) 1.33
Analysis of system structure-function relationships. ChemMedChem (2007) 1.24
Breast cancer risk associated with genotypic polymorphism of the nonhomologous end-joining genes: a multigenic study on cancer susceptibility. Cancer Res (2003) 1.21
A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol (2010) 1.19
Glycosaminoglycan-binding microbial proteins in tissue adhesion and invasion: key events in microbial pathogenicity. J Med Microbiol (1999) 1.19
Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome. PLoS Comput Biol (2009) 1.18
Link between diabetes and osteoporosis. Diabetes Care (2000) 1.15
Extracellular mycobacterial DNA-binding protein 1 participates in mycobacterium-lung epithelial cell interaction through hyaluronic acid. J Biol Chem (2004) 1.10
Bone metabolism in type 2 diabetes mellitus. Acta Diabetol (1999) 1.08
Metabolic profiling of Parkinson's disease: evidence of biomarker from gene expression analysis and rapid neural network detection. J Biomed Sci (2009) 1.03
Enhanced bacterial virulence through exploitation of host glycosaminoglycans. Mol Microbiol (2002) 1.03
Osteonecrosis in the foot. J Am Acad Orthop Surg (2007) 0.98
The role of BRCA1 in non-homologous end-joining. Cancer Lett (2005) 0.93
Simple prophylactic procedure of inguinal hernia after radical retropubic prostatectomy: isolation of the spermatic cord. Int J Urol (2009) 0.91
Corticosteroid osteoporosis. Best Pract Res Clin Rheumatol (2001) 0.90
Postentry events are responsible for restriction of productive varicella-zoster virus infection in Chinese hamster ovary cells. J Virol (2006) 0.86
The glycosaminoglycans of Dupuytren's disease. Connect Tissue Res (1982) 0.84
Aggravation of acute pancreatitis by heparan sulfate in mice. Scand J Gastroenterol (2009) 0.84
Review: the controversy over the pathophysiology of ascites formation in cirrhosis. J Gastroenterol Hepatol (1997) 0.79
Procollagen gene expression is down-regulated by taurine and niacin at the transcriptional level in the bleomycin hamster model of lung fibrosis. J Pharmacol Exp Ther (1996) 0.77
Heparan sulphate proteoglycan in scleromyxedema promotes FGF-2 activity. Pathol Res Pract (2002) 0.76
Nicotinic acid and nicotinamide metabolism in ascites cells in vitro. J Biol Chem (1962) 0.76
DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (2008) 3.51
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (2007) 3.15
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res (2007) 2.67
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics (2008) 2.38
PRISM: a data management system for high-throughput proteomics. Proteomics (2006) 1.80
Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PLoS One (2009) 1.58
Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. J Proteome Res (2007) 1.52
Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry. Genome Res (2007) 1.46
Allosteric inhibition of the protein-protein interaction between the leukemia-associated proteins Runx1 and CBFbeta. Chem Biol (2007) 1.44
Accurate mass measurements in proteomics. Chem Rev (2007) 1.36
Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer. Mol Cell Proteomics (2009) 1.35
The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. Bioinformatics (2009) 1.24
Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample. J Proteome Res (2009) 1.24
Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration. Anal Chem (2006) 1.18
Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content. Anal Chem (2007) 1.06
Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling. Anal Chem (2007) 1.04
Application of the accurate mass and time tag approach in studies of the human blood lipidome. J Chromatogr B Analyt Technol Biomed Life Sci (2008) 0.98
The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage. J Proteome Res (2008) 0.95
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. BMC Bioinformatics (2013) 0.95
A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. J Comput Biol (2004) 0.92
Virtual decoy sets for molecular docking benchmarks. J Chem Inf Model (2011) 0.88
Proteomic approaches to bacterial differentiation. J Microbiol Methods (2006) 0.88
Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition. J Proteome Res (2007) 0.88
Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments. Anal Chem (2008) 0.87
Unusual aggregates from the oxidation of alkene self-assembled monolayers: a previously unrecognized mechanism for SAM ozonolysis? Phys Chem Chem Phys (2005) 0.82
Novel Ser/Thr protein phosphatase 5 (PP5) regulated targets during DNA damage identified by proteomics analysis. J Proteome Res (2010) 0.82
Applying medicinal chemistry transformations and multiparameter optimization to guide the search for high-quality leads and candidates. J Chem Inf Model (2011) 0.79
Normalizing molecular docking rankings using virtually generated decoys. J Chem Inf Model (2011) 0.76
Predicting multiple ligand binding modes using self-consistent pharmacophore hypotheses. J Chem Inf Model (2009) 0.75