Published in Annu Rev Pharmacol Toxicol on October 17, 2011
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. PLoS Comput Biol (2016) 1.42
What is the likelihood of an active compound to be promiscuous? Systematic assessment of compound promiscuity on the basis of PubChem confirmatory bioassay data. AAPS J (2013) 1.35
Polypharmacology: drug discovery for the future. Expert Rev Clin Pharmacol (2013) 1.18
Molecular signatures from omics data: from chaos to consensus. Biotechnol J (2012) 1.17
How promiscuous are pharmaceutically relevant compounds? A data-driven assessment. AAPS J (2012) 1.04
How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol (2014) 1.00
Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PLoS Comput Biol (2013) 1.00
Harnessing Big Data for Systems Pharmacology. Annu Rev Pharmacol Toxicol (2016) 0.99
Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS One (2012) 0.97
Predicting drug-target interactions using restricted Boltzmann machines. Bioinformatics (2013) 0.95
CANDO and the infinite drug discovery frontier. Drug Discov Today (2014) 0.94
Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PLoS One (2013) 0.94
Toward more realistic drug-target interaction predictions. Brief Bioinform (2014) 0.92
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence. Int J Antimicrob Agents (2012) 0.90
Systems Pharmacology Links GPCRs with Retinal Degenerative Disorders. Annu Rev Pharmacol Toxicol (2015) 0.89
Understanding resistance to combination chemotherapy. Drug Resist Updat (2012) 0.88
Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol (2014) 0.87
A semi-supervised method for drug-target interaction prediction with consistency in networks. PLoS One (2013) 0.85
Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem. Front Pharmacol (2015) 0.83
Target essentiality and centrality characterize drug side effects. PLoS Comput Biol (2013) 0.83
Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors. PLoS One (2013) 0.82
Rule-based multi-scale simulation for drug effect pathway analysis. BMC Med Inform Decis Mak (2013) 0.82
Molecular modeling, docking and ADMET studies towards development of novel Disopyramide analogs for potential inhibition of human voltage gated sodium channel proteins. Bioinformation (2012) 0.81
Curation and analysis of multitargeting agents for polypharmacological modeling. J Chem Inf Model (2014) 0.81
Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. J Med Chem (2016) 0.81
From drug response profiling to target addiction scoring in cancer cell models. Dis Model Mech (2015) 0.80
Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. Sci Rep (2016) 0.79
Drug-target interaction prediction by integrating chemical, genomic, functional and pharmacological data. Pac Symp Biocomput (2014) 0.79
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. Bioinformatics (2012) 0.78
Drug target inference through pathway analysis of genomics data. Adv Drug Deliv Rev (2013) 0.78
Many approved drugs have bioactive analogs with different target annotations. AAPS J (2014) 0.78
Providing data science support for systems pharmacology and its implications to drug discovery. Expert Opin Drug Discov (2016) 0.78
Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis. Bioinformatics (2014) 0.78
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics (2016) 0.78
Multi-target pharmacology: possibilities and limitations of the "skeleton key approach" from a medicinal chemist perspective. Front Pharmacol (2015) 0.77
Historeceptomic Fingerprints for Drug-Like Compounds. Front Physiol (2015) 0.77
Leveraging systems biology approaches in clinical pharmacology. Biopharm Drug Dispos (2013) 0.77
Novel phytochemical-antibiotic conjugates as multitarget inhibitors of Pseudomononas aeruginosa GyrB/ParE and DHFR. Drug Des Devel Ther (2013) 0.77
Drug-target and disease networks: polypharmacology in the post-genomic era. In Silico Pharmacol (2013) 0.77
Insights from systems pharmacology into cardiovascular drug discovery and therapy. BMC Syst Biol (2014) 0.76
Computer-aided drug discovery. F1000Res (2015) 0.76
Computational identification of potential multi-drug combinations for reduction of microglial inflammation in Alzheimer disease. Front Pharmacol (2015) 0.75
Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study. J Mol Graph Model (2016) 0.75
A Bacterial Component to Alzheimer's-Type Dementia Seen via a Systems Biology Approach that Links Iron Dysregulation and Inflammagen Shedding to Disease. J Alzheimers Dis (2016) 0.75
A miRNA-driven inference model to construct potential drug-disease associations for drug repositioning. Biomed Res Int (2015) 0.75
Inducing G2/M Cell Cycle Arrest and Apoptosis through Generation Reactive Oxygen Species (ROS)-Mediated Mitochondria Pathway in HT-29 Cells by Dentatin (DEN) and Dentatin Incorporated in Hydroxypropyl-β-Cyclodextrin (DEN-HPβCD). Int J Mol Sci (2016) 0.75
Identification of gefitinib off-targets using a structure-based systems biology approach; their validation with reverse docking and retrospective data mining. Sci Rep (2016) 0.75
Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach. J Cheminform (2016) 0.75
Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem. Sci Rep (2016) 0.75
On the importance of composite protein multiple ligand interactions in protein pockets. J Comput Chem (2016) 0.75
Modeling enzyme-ligand binding in drug discovery. J Cheminform (2015) 0.75
Procaine Induces Epigenetic Changes in HCT116 Colon Cancer Cells. Genet Res Int (2016) 0.75
Systems Pharmacology in Small Molecular Drug Discovery. Int J Mol Sci (2016) 0.75
A structure- and chemical genomics-based approach for repositioning of drugs against VCP/p97 ATPase. Sci Rep (2017) 0.75
Editorial: Computational and Experimental Approaches in Multi-target Pharmacology. Front Pharmacol (2017) 0.75
Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association. NPJ Syst Biol Appl (2016) 0.75
The Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2002) 14.44
The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (2005) 7.81
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
Ten simple rules for getting published. PLoS Comput Biol (2005) 7.22
The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res (2012) 5.73
BioLit: integrating biological literature with databases. Nucleic Acids Res (2008) 4.85
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
Mechanism for alternating access in neurotransmitter transporters. Proc Natl Acad Sci U S A (2008) 3.24
Ten simple rules for getting grants. PLoS Comput Biol (2006) 3.13
Ten simple rules for a successful collaboration. PLoS Comput Biol (2007) 3.12
BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (2012) 2.94
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
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics (2005) 2.60
Ten simple rules for making good oral presentations. PLoS Comput Biol (2007) 2.57
Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol (2005) 2.48
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44
Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A (2005) 2.37
Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput Biol (2009) 2.35
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput Biol (2011) 2.31
Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics (2010) 2.28
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26
Open access: taking full advantage of the content. PLoS Comput Biol (2008) 2.14
Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol (2007) 2.14
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci U S A (2006) 2.10
Immune epitope database analysis resource. Nucleic Acids Res (2012) 2.09
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04
An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics (2002) 1.97
Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol (2010) 1.97
Biodiversity data should be published, cited, and peer reviewed. Trends Ecol Evol (2013) 1.97
Safety and efficacy of teriparatide in elderly women with established osteoporosis: bone anabolic therapy from a geriatric perspective. J Am Geriatr Soc (2006) 1.96
Ten simple rules for reviewers. PLoS Comput Biol (2006) 1.84
Ten simple rules for selecting a postdoctoral position. PLoS Comput Biol (2006) 1.77
History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci U S A (2010) 1.71
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics (2007) 1.70
PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res (2010) 1.69
Influenza H7N9 and H9N2 viruses: coexistence in poultry linked to human H7N9 infection and genome characteristics. J Virol (2014) 1.67
Environmental connections of novel avian-origin H7N9 influenza virus infection and virus adaptation to the human. Sci China Life Sci (2013) 1.66
Findings from 2010 Global Adult Tobacco Survey: implementation of MPOWER policy in China. Biomed Environ Sci (2010) 1.65
Computational biology resources lack persistence and usability. PLoS Comput Biol (2008) 1.65
CE-MC: a multiple protein structure alignment server. Nucleic Acids Res (2004) 1.64
Topic pages: PLoS Computational Biology meets Wikipedia. PLoS Comput Biol (2012) 1.60
Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLoS One (2013) 1.56
Ten simple rules for a good poster presentation. PLoS Comput Biol (2007) 1.55
MicroRNA-21 regulates breast cancer invasion partly by targeting tissue inhibitor of metalloproteinase 3 expression. J Exp Clin Cancer Res (2010) 1.51
Partitioning protein structures into domains: why is it so difficult? J Mol Biol (2006) 1.51
Relationship between domestic and wild birds in live poultry market and a novel human H7N9 virus in China. J Infect Dis (2013) 1.50
S-1-based therapy versus S-1 monotherapy in advanced gastric cancer: a meta-analysis. Tumour Biol (2014) 1.48
Biocurators: contributors to the world of science. PLoS Comput Biol (2006) 1.46
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics (2009) 1.46
Performance and microbial community analysis of the anaerobic reactor with coke oven gas biomethanation and in situ biogas upgrading. Bioresour Technol (2013) 1.45
Toward consistent assignment of structural domains in proteins. J Mol Biol (2004) 1.42
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput (2008) 1.40
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol (2007) 1.40
Ten simple rules for starting a company. PLoS Comput Biol (2012) 1.39
Curation of complex, context-dependent immunological data. BMC Bioinformatics (2006) 1.36
The growth and metastasis of human hepatocellular carcinoma xenografts are inhibited by small interfering RNA targeting to the subunit ATP6L of proton pump. Cancer Res (2005) 1.36
Effects of teriparatide in postmenopausal women with osteoporosis on prior alendronate or raloxifene: differences between stopping and continuing the antiresorptive agent. J Clin Endocrinol Metab (2009) 1.35
Teaching bioinformatics at the secondary school level. PLoS Comput Biol (2011) 1.34
Ten simple rules for doing your best research, according to Hamming. PLoS Comput Biol (2007) 1.32
Superimpose: a 3D structural superposition server. Nucleic Acids Res (2008) 1.31
Cantharidin, a potent and selective PP2A inhibitor, induces an oxidative stress-independent growth inhibition of pancreatic cancer cells through G2/M cell-cycle arrest and apoptosis. Cancer Sci (2010) 1.31
Risk factors of hepatocellular carcinoma--current status and perspectives. Asian Pac J Cancer Prev (2012) 1.30
Knockdown of astrocyte elevated gene-1 inhibits proliferation and enhancing chemo-sensitivity to cisplatin or doxorubicin in neuroblastoma cells. J Exp Clin Cancer Res (2009) 1.29
SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res (2011) 1.29
Ten simple rules for organizing a scientific meeting. PLoS Comput Biol (2008) 1.26
Munc18-1 is critical for plasma membrane localization of syntaxin1 but not of SNAP-25 in PC12 cells. Mol Biol Cell (2007) 1.26
Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol (2011) 1.25
Rescue of Munc18-1 and -2 double knockdown reveals the essential functions of interaction between Munc18 and closed syntaxin in PC12 cells. Mol Biol Cell (2009) 1.24
Munc13-1 deficiency reduces insulin secretion and causes abnormal glucose tolerance. Diabetes (2006) 1.22
Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics (2010) 1.22
A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol (2010) 1.19
Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering. Proteins (2006) 1.18
Cancer incidence among adolescents and young adults in urban Shanghai, 1973-2005. PLoS One (2012) 1.15
A biologist's guide to synchrotron facilities: the BioSync web resource. Trends Biochem Sci (2002) 1.15
An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res (2005) 1.15
Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins (2006) 1.14
Cholesterol derivatives based charged liposomes for doxorubicin delivery: preparation, in vitro and in vivo characterization. Theranostics (2012) 1.13
Association of COMT Val158Met polymorphism and breast cancer risk: an updated meta-analysis. Diagn Pathol (2012) 1.12
Effect of aspirin and other non-steroidal anti-inflammatory drugs on prostate cancer incidence and mortality: a systematic review and meta-analysis. BMC Med (2014) 1.12
The effects of teriparatide on the incidence of back pain in postmenopausal women with osteoporosis. Curr Med Res Opin (2005) 1.11
EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Res (2007) 1.10
MicroRNA-146a is down-regulated in gastric cancer and regulates cell proliferation and apoptosis. Med Oncol (2011) 1.10
Tax and overlapping rex sequences do not confer the distinct transformation tropisms of human T-cell leukemia virus types 1 and 2. J Virol (2003) 1.10
Inhibition of cholesterol biosynthesis impairs insulin secretion and voltage-gated calcium channel function in pancreatic beta-cells. Endocrinology (2008) 1.10
The evolutionary history of protein domains viewed by species phylogeny. PLoS One (2009) 1.09
A phase II randomized study of subcutaneous ixekizumab, an anti-interleukin-17 monoclonal antibody, in rheumatoid arthritis patients who were naive to biologic agents or had an inadequate response to tumor necrosis factor inhibitors. Arthritis Rheumatol (2014) 1.08
Microelectronic cell sensor assay for detection of cytotoxicity and prediction of acute toxicity. Toxicol In Vitro (2006) 1.08
Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol (2009) 1.07
Meta-analysis of randomized controlled trials on the efficacy of probiotics in Helicobacter pylori eradication therapy in children. Eur J Pediatr (2013) 1.07
Rapid and efficient reprogramming of human amnion-derived cells into pluripotency by three factors OCT4/SOX2/NANOG. Differentiation (2010) 1.07