Published in PLoS Comput Biol on May 15, 2009
Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med (2011) 5.77
PubChem as a public resource for drug discovery. Drug Discov Today (2010) 3.40
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics (2010) 2.94
Data-driven prediction of drug effects and interactions. Sci Transl Med (2012) 2.93
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Network analyses in systems pharmacology. Bioinformatics (2009) 2.55
A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J Am Med Inform Assoc (2011) 2.53
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
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
MicroRNA-210: a unique and pleiotropic hypoxamir. Cell Cycle (2010) 2.18
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07
Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet (2012) 2.02
Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol (2010) 1.97
PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res (2010) 1.69
Network-based relating pharmacological and genomic spaces for drug target identification. PLoS One (2010) 1.68
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res (2010) 1.50
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
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J Am Med Inform Assoc (2012) 1.43
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
Visualization of macromolecular structures. Nat Methods (2010) 1.34
Predicting drug side-effect profiles: a chemical fragment-based approach. BMC Bioinformatics (2011) 1.34
Systematic identification of proteins that elicit drug side effects. Mol Syst Biol (2013) 1.28
Predicting drug side-effects by chemical systems biology. Genome Biol (2009) 1.26
Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol (2011) 1.25
A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol (2010) 1.19
Automatic construction of a large-scale and accurate drug-side-effect association knowledge base from biomedical literature. J Biomed Inform (2014) 1.18
Network neighbors of drug targets contribute to drug side-effect similarity. PLoS One (2011) 1.17
Role of systems pharmacology in understanding drug adverse events. Wiley Interdiscip Rev Syst Biol Med (2010) 1.16
Assessing drug target association using semantic linked data. PLoS Comput Biol (2012) 1.14
The emerging paradigm of network medicine in the study of human disease. Circ Res (2012) 1.12
Relating drug-protein interaction network with drug side effects. Bioinformatics (2012) 1.10
A structure-based approach for mapping adverse drug reactions to the perturbation of underlying biological pathways. PLoS One (2010) 1.10
FunSimMat update: new features for exploring functional similarity. Nucleic Acids Res (2009) 1.04
Methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase as a target for bis-indole alkaloids with antibacterial activities. J Biol Chem (2011) 1.03
New Perspectives on How to Discover Drugs from Herbal Medicines: CAM's Outstanding Contribution to Modern Therapeutics. Evid Based Complement Alternat Med (2013) 1.00
Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding. PLoS Comput Biol (2011) 1.00
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res (2010) 1.00
Harnessing Big Data for Systems Pharmacology. Annu Rev Pharmacol Toxicol (2016) 0.99
Personalized cardiovascular medicine and drug development: time for a new paradigm. Circulation (2012) 0.98
PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem. Bioinformatics (2011) 0.94
Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PLoS One (2013) 0.94
Cloud computing for protein-ligand binding site comparison. Biomed Res Int (2013) 0.90
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. J Chem Inf Model (2012) 0.90
Improving integrative searching of systems chemical biology data using semantic annotation. J Cheminform (2012) 0.89
DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. Nucleic Acids Res (2014) 0.89
Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol (2014) 0.87
Combining machine learning systems and multiple docking simulation packages to improve docking prediction reliability for network pharmacology. PLoS One (2013) 0.86
Pocket-based drug design: exploring pocket space. AAPS J (2012) 0.86
Mechanistic systems modeling to guide drug discovery and development. Drug Discov Today (2012) 0.86
Familial hypercholesterolemia: present and future management. Curr Cardiol Rep (2011) 0.86
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol (2013) 0.86
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PLoS One (2013) 0.85
Modeling metabolic adjustment in Mycobacterium tuberculosis upon treatment with isoniazid. Syst Synth Biol (2011) 0.84
Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines. PLoS One (2014) 0.82
Rule-based multi-scale simulation for drug effect pathway analysis. BMC Med Inform Decis Mak (2013) 0.82
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics (2010) 0.81
Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. J Med Chem (2016) 0.81
Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins. PLoS One (2009) 0.80
Exploring the relationship between drug side-effects and therapeutic indications. AMIA Annu Symp Proc (2013) 0.80
Human structural proteome-wide characterization of Cyclosporine A targets. Bioinformatics (2014) 0.79
Predicting drug target interactions using meta-path-based semantic network analysis. BMC Bioinformatics (2016) 0.79
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics (2016) 0.78
Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms. Wiley Interdiscip Rev Syst Biol Med (2015) 0.78
Providing data science support for systems pharmacology and its implications to drug discovery. Expert Opin Drug Discov (2016) 0.78
Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning. J Am Med Inform Assoc (2013) 0.78
Predicting drugs side effects based on chemical-chemical interactions and protein-chemical interactions. Biomed Res Int (2013) 0.78
Identification of distant drug off-targets by direct superposition of binding pocket surfaces. PLoS One (2013) 0.78
An integrated network platform for contextual prioritization of drugs and pathways. Mol Biosyst (2015) 0.77
Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. Bioorg Med Chem Lett (2015) 0.76
IsoMIF Finder: online detection of binding site molecular interaction field similarities. Bioinformatics (2015) 0.76
An Ensemble Approach for Drug Side Effect Prediction. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2013) 0.75
Systematic Analysis of the Associations between Adverse Drug Reactions and Pathways. Biomed Res Int (2015) 0.75
Identifying problematic drugs based on the characteristics of their targets. Front Pharmacol (2015) 0.75
Correlation between protein function and ligand binding profiles. J Proteome Res (2011) 0.75
Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem. Sci Rep (2016) 0.75
Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success. Ann Biomed Eng (2016) 0.75
Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. BMC Pharmacol Toxicol (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
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09
Mammalian MAP kinase signalling cascades. Nature (2001) 18.89
Effects of torcetrapib in patients at high risk for coronary events. N Engl J Med (2007) 18.78
ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model (2005) 16.75
Macrophage-specific PPARgamma controls alternative activation and improves insulin resistance. Nature (2007) 11.59
Drug target identification using side-effect similarity. Science (2008) 9.24
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res (2006) 9.19
Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov (2004) 7.57
A SUMOylation-dependent pathway mediates transrepression of inflammatory response genes by PPAR-gamma. Nature (2005) 6.83
Relating protein pharmacology by ligand chemistry. Nat Biotechnol (2007) 6.61
Oxidative metabolism and PGC-1beta attenuate macrophage-mediated inflammation. Cell Metab (2006) 6.44
Reciprocal regulation of inflammation and lipid metabolism by liver X receptors. Nat Med (2003) 6.21
A critical assessment of docking programs and scoring functions. J Med Chem (2006) 5.78
Fatty acid-binding proteins: role in metabolic diseases and potential as drug targets. Nat Rev Drug Discov (2008) 5.78
Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics (2003) 5.46
Global mapping of pharmacological space. Nat Biotechnol (2006) 4.99
Effects of infection and inflammation on lipid and lipoprotein metabolism: mechanisms and consequences to the host. J Lipid Res (2004) 4.67
Predicting protein function from sequence and structural data. Curr Opin Struct Biol (2005) 4.31
Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today (2006) 4.24
Neural regulation of innate immunity: a coordinated nonspecific host response to pathogens. Nat Rev Immunol (2006) 4.05
Transcriptional repression of atherogenic inflammation: modulation by PPARdelta. Science (2003) 3.97
Integration of metabolism and inflammation by lipid-activated nuclear receptors. Nature (2008) 3.94
Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol (2005) 3.85
The glucocorticoid receptor inhibits NFkappaB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev (2000) 3.71
Systems biology and combination therapy in the quest for clinical efficacy. Nat Chem Biol (2006) 3.63
Peroxisome proliferator-activated receptor alpha negatively regulates the vascular inflammatory gene response by negative cross-talk with transcription factors NF-kappaB and AP-1. J Biol Chem (1999) 3.57
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci (2003) 2.98
Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem (2003) 2.87
Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des (2007) 2.79
A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol (2002) 2.79
iHOP web services. Nucleic Acids Res (2007) 2.65
Selective cooperation between fatty acid binding proteins and peroxisome proliferator-activated receptors in regulating transcription. Mol Cell Biol (2002) 2.58
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44
Assessing scoring functions for protein-ligand interactions. J Med Chem (2004) 2.41
Fatty acids and hypolipidemic drugs regulate peroxisome proliferator-activated receptors alpha - and gamma-mediated gene expression via liver fatty acid binding protein: a signaling path to the nucleus. Proc Natl Acad Sci U S A (2001) 2.37
Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32
The protonmotive Q cycle: a general formulation. FEBS Lett (1975) 2.32
The protonmotive Q cycle. Energy transduction by coupling of proton translocation to electron transfer by the cytochrome bc1 complex. J Biol Chem (1990) 2.18
Torcetrapib-induced blood pressure elevation is independent of CETP inhibition and is accompanied by increased circulating levels of aldosterone. Br J Pharmacol (2008) 2.13
Protein function prediction using local 3D templates. J Mol Biol (2005) 2.13
Peroxisome proliferator-activated receptor gamma-dependent repression of the inducible nitric oxide synthase gene. Mol Cell Biol (2000) 2.12
Can we rationally design promiscuous drugs? Curr Opin Struct Biol (2006) 2.06
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04
Hemoglobin is expressed by mesangial cells and reduces oxidant stress. J Am Soc Nephrol (2008) 1.99
Inferring functional relationships of proteins from local sequence and spatial surface patterns. J Mol Biol (2003) 1.96
Finding new tricks for old drugs: an efficient route for public-sector drug discovery. Nat Rev Drug Discov (2005) 1.93
Quantifying the relationships among drug classes. J Chem Inf Model (2008) 1.92
Cytochrome c in the apoptotic and antioxidant cascades. FEBS Lett (1998) 1.80
Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics (2002) 1.79
FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res (2007) 1.75
Chemogenomic approaches to rational drug design. Br J Pharmacol (2007) 1.74
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
The transcription factor nuclear factor-kappa B and cancer. Clin Oncol (R Coll Radiol) (2007) 1.64
A new bioinformatic approach to detect common 3D sites in protein structures. Proteins (2003) 1.62
SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res (2006) 1.61
Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition. J Med Chem (2004) 1.57
Large-scale prediction of drug-target relationships. FEBS Lett (2008) 1.56
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
eHiTS: a new fast, exhaustive flexible ligand docking system. J Mol Graph Model (2006) 1.44
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res (2004) 1.41
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol (2007) 1.40
The diverse biological functions of phosphatidylinositol transfer proteins in eukaryotes. Crit Rev Biochem Mol Biol (2006) 1.40
Nuclear factor-kappaB affects tumor progression in a mouse model of malignant pleural effusion. Am J Respir Cell Mol Biol (2005) 1.39
Peroxisome proliferator-activated receptor gamma activators affect the maturation of human monocyte-derived dendritic cells. Eur J Immunol (2001) 1.36
Peroxisomal proliferator-activated receptor-alpha-dependent inhibition of endothelial cell proliferation and tumorigenesis. J Biol Chem (2007) 1.30
The role of calcium-binding proteins in the control of transcription: structure to function. Bioessays (2002) 1.28
Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol (2009) 1.26
AP-1--glucocorticoid receptor crosstalk taken to a higher level. J Endocrinol (2001) 1.22
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. Nucleic Acids Res (2004) 1.20
Dependence of peroxisome proliferator-activated receptor ligand-induced mitogen-activated protein kinase signaling on epidermal growth factor receptor transactivation. J Biol Chem (2003) 1.17
Cross-talk between IGF-I and TGF-beta signaling pathways. Cytokine Growth Factor Rev (2005) 1.11
Functional analysis of peroxisome-proliferator-responsive element motifs in genes of fatty acid-binding proteins. Biochem J (2004) 1.09
Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint. Comb Chem High Throughput Screen (2007) 1.09
Biological functions of phosphatidylinositol transfer proteins. Biochem Cell Biol (2004) 1.03
CD1 proteins: targets of T cell recognition in innate and adaptive immunity. Rev Immunogenet (2000) 1.03
From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. J Mol Biol (2006) 1.01
Endothelial S100A1 modulates vascular function via nitric oxide. Circ Res (2008) 1.01
Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening. Nat Rev Drug Discov (2008) 1.00
Comment on "Chromosomal instability and tumors promoted by DNA hypomethylation" and "Induction of tumors in nice by genomic hypomethylation". Science (2003) 0.99
Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Proteins (2006) 0.98
Membrane lipids and cell death: an overview. Chem Phys Lipids (2004) 0.96
The failure of torcetrapib: what have we learned? Br J Pharmacol (2008) 0.96
Exploring the chemogenomic knowledge space with annotated chemical libraries. Curr Opin Chem Biol (2004) 0.96
Spotlight on HDL-raising therapies: insights from the torcetrapib trials. Nat Clin Pract Cardiovasc Med (2008) 0.95
Chemogenomics and biotechnology. Trends Biotechnol (2008) 0.95
Expression of HbC and HbS, but not HbA, results in activation of K-Cl cotransport activity in transgenic mouse red cells. Blood (2003) 0.94
Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr Opin Drug Discov Devel (2004) 0.94
Lipids and the immune response: from molecular mechanisms to clinical applications. Curr Opin Clin Nutr Metab Care (2003) 0.93
Mechanisms of exocytosis. Acta Physiol (Oxf) (2007) 0.91
A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening. J Comput Aided Mol Des (2006) 0.89
Efficient similarity search in protein structure databases by k-clique hashing. Bioinformatics (2004) 0.89
A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. J Chem Inf Model (2006) 0.86
Chemogenomics: drug discovery's panacea? Mol Biosyst (2006) 0.86
Strategies for multiple signalling inhibition. J Chemother (2004) 0.83
JTT-705 blocks cell proliferation and angiogenesis through p38 kinase/p27(kip1) and Ras/p21(waf1) pathways. Atherosclerosis (2005) 0.80
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
Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol (2002) 4.67
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
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
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins (2003) 3.04
BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (2012) 2.94
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
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
Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol (2011) 1.76
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
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
Partitioning protein structures into domains: why is it so difficult? J Mol Biol (2006) 1.51
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
Toward consistent assignment of structural domains in proteins. J Mol Biol (2004) 1.42
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol (2007) 1.40
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput (2008) 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
Inhibition of insulin-like growth factor-I receptor (IGF-IR) signaling and tumor cell growth by a fully human neutralizing anti-IGF-IR antibody. Mol Cancer Ther (2005) 1.36
On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol (2003) 1.34
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
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
Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol (2011) 1.25
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
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
Regulation of Nur77 expression by β-catenin and its mitogenic effect in colon cancer cells. FASEB J (2010) 1.14
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
The evolutionary history of protein domains viewed by species phylogeny. PLoS One (2009) 1.09
Epidemiological and etiological characteristics of hand, foot, and mouth disease in Ningbo, China, 2008-2011. J Clin Virol (2012) 1.09
Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol (2009) 1.07
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics (2006) 1.05
Ten simple rules for graduate students. PLoS Comput Biol (2007) 1.04
Wiggle-predicting functionally flexible regions from primary sequence. PLoS Comput Biol (2006) 1.03
A machine learning-based method to improve docking scoring functions and its application to drug repurposing. J Chem Inf Model (2011) 1.03
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct (2009) 1.01
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res (2010) 1.00
Statistically rigorous automated protein annotation. Bioinformatics (2004) 0.97
Proviral insertion in murine lymphomas 2 (PIM2) oncogene phosphorylates pyruvate kinase M2 (PKM2) and promotes glycolysis in cancer cells. J Biol Chem (2013) 0.95
Oncogenic potential of retinoic acid receptor-gamma in hepatocellular carcinoma. Cancer Res (2010) 0.95
Institutional Profile: University of California San Diego Pharmacogenomics Education Program (PharmGenEd™): bridging the gap between science and practice. Pharmacogenomics (2011) 0.94
TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK. Pac Symp Biocomput (2008) 0.94
Metagenomic insights into metabolic capacities of the gut microbiota in a fungus-cultivating termite (Odontotermes yunnanensis). PLoS One (2013) 0.94
What Big Data means to me. J Am Med Inform Assoc (2014) 0.94
Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins (2005) 0.93
IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res (2010) 0.93
Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One (2010) 0.92
A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biol (2003) 0.92
PLoS Computational Biology conference postcards from PSB 2010. PLoS Comput Biol (2010) 0.92
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics (2010) 0.91
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence. Int J Antimicrob Agents (2012) 0.90