Published in Nucleic Acids Res on January 01, 2005
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res (2006) 13.44
The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res (2006) 10.39
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res (2006) 7.57
Next generation tools for the annotation of human SNPs. Brief Bioinform (2009) 6.61
The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Res (2005) 4.90
MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res (2012) 4.43
The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res (2006) 4.27
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res (2014) 3.57
MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res (2008) 2.84
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol (2007) 2.81
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res (2007) 2.69
Therapeutic strategies for targeting ras proteins. Genes Cancer (2011) 2.45
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44
euHCVdb: the European hepatitis C virus database. Nucleic Acids Res (2006) 2.41
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
dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res (2006) 2.28
Integrating protein annotation resources through the Distributed Annotation System. Nucleic Acids Res (2005) 2.21
The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res (2007) 2.19
CEP: a conformational epitope prediction server. Nucleic Acids Res (2005) 2.14
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04
MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2008) 2.02
MODOMICS: a database of RNA modification pathways. Nucleic Acids Res (2006) 1.95
The PMDB Protein Model Database. Nucleic Acids Res (2006) 1.94
Frequency and isostericity of RNA base pairs. Nucleic Acids Res (2009) 1.88
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
MutDB services: interactive structural analysis of mutation data. Nucleic Acids Res (2005) 1.62
(PS)2: protein structure prediction server. Nucleic Acids Res (2006) 1.59
The UCSC Genome Browser. Curr Protoc Bioinformatics (2009) 1.59
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. BMC Bioinformatics (2005) 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
Characterization of the archaeal thermophile Sulfolobus turreted icosahedral virus validates an evolutionary link among double-stranded DNA viruses from all domains of life. J Virol (2006) 1.44
Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res (2009) 1.43
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol (2007) 1.40
Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res (2006) 1.37
SIMAP--structuring the network of protein similarities. Nucleic Acids Res (2007) 1.37
Protein structure database search and evolutionary classification. Nucleic Acids Res (2006) 1.36
High-energy water sites determine peptide binding affinity and specificity of PDZ domains. Protein Sci (2009) 1.35
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol (2007) 1.30
3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Res (2007) 1.27
Cysteine pKa depression by a protonated glutamic acid in human DJ-1. Biochemistry (2008) 1.26
Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics (2005) 1.25
Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol (2011) 1.25
pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res (2005) 1.17
SuperToxic: a comprehensive database of toxic compounds. Nucleic Acids Res (2008) 1.17
(PS)2-v2: template-based protein structure prediction server. BMC Bioinformatics (2009) 1.15
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol (2006) 1.12
SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res (2014) 1.11
Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Res (2011) 1.11
Combinations of protein-chemical complex structures reveal new targets for established drugs. PLoS Comput Biol (2011) 1.07
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res (2010) 1.03
MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res (2007) 1.03
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. Genomics (2012) 1.02
Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum. BMC Genomics (2010) 1.02
Structural implication of splicing stochastics. Nucleic Acids Res (2009) 1.01
POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Res (2005) 1.00
Harnessing Big Data for Systems Pharmacology. Annu Rev Pharmacol Toxicol (2016) 0.99
DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res (2010) 0.98
Multiple sites in the N-terminal half of simian immunodeficiency virus capsid protein contribute to evasion from rhesus monkey TRIM5α-mediated restriction. Retrovirology (2010) 0.97
Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics (2012) 0.97
ProtChemSI: a network of protein-chemical structural interactions. Nucleic Acids Res (2011) 0.96
A fast SCOP fold classification system using content-based E-Predict algorithm. BMC Bioinformatics (2006) 0.93
Structural characterization of naturally occurring RNA single mismatches. Nucleic Acids Res (2010) 0.92
Characterization of protein secondary structure from NMR chemical shifts. Prog Nucl Magn Reson Spectrosc (2009) 0.92
A comprehensive resource for integrating and displaying protein post-translational modifications. BMC Res Notes (2009) 0.91
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. Nucleic Acids Res (2007) 0.91
Evaluation of influenza virus A/H3N2 and B vaccines on the basis of cross-reactivity of postvaccination human serum antibodies against influenza viruses A/H3N2 and B isolated in MDCK cells and embryonated hen eggs. Clin Vaccine Immunol (2012) 0.89
An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery. Protein Sci (2010) 0.88
Applying an empirical hydropathic forcefield in refinement may improve low-resolution protein X-ray crystal structures. PLoS One (2011) 0.87
TAP score: torsion angle propensity normalization applied to local protein structure evaluation. BMC Bioinformatics (2007) 0.87
kinDOCK: a tool for comparative docking of protein kinase ligands. Nucleic Acids Res (2006) 0.86
3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. BMC Genomics (2010) 0.86
ProSAT2--Protein Structure Annotation Server. Nucleic Acids Res (2006) 0.86
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. BMC Bioinformatics (2006) 0.86
A new method to improve network topological similarity search: applied to fold recognition. Bioinformatics (2015) 0.86
Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philos Trans R Soc Lond B Biol Sci (2006) 0.85
CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins. Protein Sci (2009) 0.84
Variation in structural location and amino acid conservation of functional sites in protein domain families. BMC Bioinformatics (2005) 0.84
A structural constraint for functional interaction between N-terminal and C-terminal domains in simian immunodeficiency virus capsid proteins. Retrovirology (2010) 0.84
A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins. BMC Bioinformatics (2008) 0.83
Lysine biotinylation and methionine oxidation in the heat shock protein HSP60 synergize in the elimination of reactive oxygen species in human cell cultures. J Nutr Biochem (2014) 0.83
Plant genome resources at the national center for biotechnology information. Plant Physiol (2005) 0.82
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation. Nucleic Acids Res (2007) 0.82
Sigma S-dependent antioxidant defense protects stationary-phase Escherichia coli against the bactericidal antibiotic gentamicin. Antimicrob Agents Chemother (2014) 0.82
Large-scale reverse docking profiles and their applications. BMC Bioinformatics (2012) 0.81
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Res (2007) 0.80
PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Res (2010) 0.79
Applying Undertaker to quality assessment. Proteins (2009) 0.79
Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots. BMC Bioinformatics (2010) 0.79
Finding motif pairs in the interactions between heterogeneous proteins via bootstrapping and boosting. BMC Bioinformatics (2009) 0.78
COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures. Nucleic Acids Res (2014) 0.77
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database (Oxford) (2011) 0.77
Dynamic domains and geometrical properties of HIV-1 gp120 during conformational changes induced by CD4 binding. J Mol Model (2006) 0.77
Citing a Data Repository: A Case Study of the Protein Data Bank. PLoS One (2015) 0.77
Curation of viral genomes: challenges, applications and the way forward. BMC Bioinformatics (2006) 0.76
SAHG, a comprehensive database of predicted structures of all human proteins. Nucleic Acids Res (2010) 0.76
Detection of a secreted metalloprotease within the nuclei of liver cells. Mol Biosyst (2011) 0.76
Basic local alignment search tool. J Mol Biol (1990) 659.07
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res (2000) 67.44
A database for post-genome analysis. Trends Genet (1997) 32.07
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37
Macromolecular Crystallographic Information File. Methods Enzymol (1997) 11.94
Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res (2004) 9.85
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
TargetDB: a target registration database for structural genomics projects. Bioinformatics (2004) 4.17
The PDB data uniformity project. Nucleic Acids Res (2001) 3.65
PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics (2004) 3.64
WebMol--a Java-based PDB viewer. Trends Biochem Sci (1997) 3.12
Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution. J Mol Biol (1997) 2.49
An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics (2002) 1.97
Genome-wide atlas of gene expression in the adult mouse brain. Nature (2006) 28.02
Prevalence of diabetes among men and women in China. N Engl J Med (2010) 19.98
Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet (2008) 16.17
Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature (2012) 15.91
The Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2002) 14.44
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet (2011) 13.25
The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37
Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study. Lancet (2012) 12.10
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
The Protein Data Bank and structural genomics. Nucleic Acids Res (2003) 8.34
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res (2006) 7.57
Ten simple rules for getting published. PLoS Comput Biol (2005) 7.22
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat Med (2009) 6.61
The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36
A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat Genet (2009) 6.31
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (2008) 5.94
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res (2012) 5.73
RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
Selective small-molecule inhibitor reveals critical mitotic functions of human CDK1. Proc Natl Acad Sci U S A (2006) 5.16
The TEAD/TEF family of transcription factor Scalloped mediates Hippo signaling in organ size control. Dev Cell (2008) 4.90
Remediation of the protein data bank archive. Nucleic Acids Res (2007) 4.89
Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc Natl Acad Sci U S A (2002) 4.85
BioLit: integrating biological literature with databases. Nucleic Acids Res (2008) 4.85
An outbreak of hand, foot, and mouth disease associated with subgenotype C4 of human enterovirus 71 in Shandong, China. J Clin Virol (2009) 4.62
Dicer is required for embryonic angiogenesis during mouse development. J Biol Chem (2004) 4.40
Outcome of the first electron microscopy validation task force meeting. Structure (2012) 4.35
Biventricular pacing in patients with bradycardia and normal ejection fraction. N Engl J Med (2009) 4.17
TargetDB: a target registration database for structural genomics projects. Bioinformatics (2004) 4.17
The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc Natl Acad Sci U S A (2005) 4.16
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res (2003) 4.12
Genetic variants influencing circulating lipid levels and risk of coronary artery disease. Arterioscler Thromb Vasc Biol (2010) 4.08
DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature (2011) 3.90
Lung cancer signatures in plasma based on proteome profiling of mouse tumor models. Cancer Cell (2011) 3.88
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
Obesity: a challenge to esophagogastric junction integrity. Gastroenterology (2006) 3.72
PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics (2004) 3.64
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Single-layer MoS2 phototransistors. ACS Nano (2011) 3.43
Quantifying esophageal peristalsis with high-resolution manometry: a study of 75 asymptomatic volunteers. Am J Physiol Gastrointest Liver Physiol (2006) 3.41
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
Benign prostatic hyperplasia: prostatic arterial embolization versus transurethral resection of the prostate--a prospective, randomized, and controlled clinical trial. Radiology (2013) 3.32
EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res (2010) 3.32
ST2 as a marker for risk of therapy-resistant graft-versus-host disease and death. N Engl J Med (2013) 3.27
Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature (2011) 3.19
Design of the Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Study: A Genome-wide association meta-analysis involving more than 22 000 cases and 60 000 controls. Circ Cardiovasc Genet (2010) 3.15
Ten simple rules for getting grants. PLoS Comput Biol (2006) 3.13
Quantifying EGJ morphology and relaxation with high-resolution manometry: a study of 75 asymptomatic volunteers. Am J Physiol Gastrointest Liver Physiol (2006) 3.12
Tissue Doppler imaging is superior to strain rate imaging and postsystolic shortening on the prediction of reverse remodeling in both ischemic and nonischemic heart failure after cardiac resynchronization therapy. Circulation (2004) 3.12
Ten simple rules for a successful collaboration. PLoS Comput Biol (2007) 3.12
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2004) 3.11
Gene dosage of the common variant 9p21 predicts severity of coronary artery disease. J Am Coll Cardiol (2010) 3.07
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04
Human chromosome 7: DNA sequence and biology. Science (2003) 3.02
BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (2012) 2.94
VHL loss actuates a HIF-independent senescence programme mediated by Rb and p400. Nat Cell Biol (2008) 2.93
Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol (2004) 2.91
Histopathologic variability and endoscopic correlates in adults with eosinophilic esophagitis. Gastrointest Endosc (2006) 2.89
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
Hermansky-Pudlak syndrome type 7 (HPS-7) results from mutant dysbindin, a member of the biogenesis of lysosome-related organelles complex 1 (BLOC-1). Nat Genet (2003) 2.78
Potential clinical and economic consequences of noncardiac incidental findings on cardiac computed tomography. J Am Coll Cardiol (2009) 2.76
Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science (2002) 2.67
A randomized controlled trial of Licartin for preventing hepatoma recurrence after liver transplantation. Hepatology (2007) 2.66
Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. Cancer Discov (2014) 2.64
Ambient air pollution, birth weight and preterm birth: a systematic review and meta-analysis. Environ Res (2012) 2.63
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics (2005) 2.60
Darbepoetin alpha for the treatment of anemia in patients with active cancer not receiving chemotherapy or radiotherapy: results of a phase III, multicenter, randomized, double-blind, placebo-controlled study. J Clin Oncol (2008) 2.60