BRENDA, the enzyme information system in 2011.

ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res (2011) 14.51

Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res (2011) 2.87

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res (2012) 2.33

Ascaris suum draft genome. Nature (2011) 2.16

Nutritional metabolomics: progress in addressing complexity in diet and health. Annu Rev Nutr (2012) 1.89

Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol (2012) 1.71

MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res (2011) 1.67

IUPHAR-DB: updated database content and new features. Nucleic Acids Res (2012) 1.66

SABIO-RK--database for biochemical reaction kinetics. Nucleic Acids Res (2011) 1.63

Cyanobacterial conversion of carbon dioxide to 2,3-butanediol. Proc Natl Acad Sci U S A (2013) 1.52

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. Nat Biotechnol (2013) 1.36

Engineering a cyanobacterial cell factory for production of lactic acid. Appl Environ Microbiol (2012) 1.32

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) (2013) 1.31

Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet (2015) 1.30

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics (2012) 1.26

Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res (2011) 1.21

BKM-react, an integrated biochemical reaction database. BMC Biochem (2011) 1.19

Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol Evol (2014) 1.18

Inference of functional properties from large-scale analysis of enzyme superfamilies. J Biol Chem (2011) 1.17

Systematic construction of kinetic models from genome-scale metabolic networks. PLoS One (2013) 1.16

TDR Targets: a chemogenomics resource for neglected diseases. Nucleic Acids Res (2011) 1.15

Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform (2012) 1.14

A survey of metabolic databases emphasizing the MetaCyc family. Arch Toxicol (2011) 1.14

Development of a classification scheme for disease-related enzyme information. BMC Bioinformatics (2011) 1.14

Exploring metabolic engineering design principles for the photosynthetic production of lactic acid by Synechocystis sp. PCC6803. Biotechnol Biofuels (2014) 1.13

EcoliWiki: a wiki-based community resource for Escherichia coli. Nucleic Acids Res (2011) 1.12

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science (2013) 1.11

FastAnnotator--an efficient transcript annotation web tool. BMC Genomics (2012) 1.09

Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. Proc Natl Acad Sci U S A (2013) 1.06

Network-level architecture and the evolutionary potential of underground metabolism. Proc Natl Acad Sci U S A (2014) 1.03

Topology of molecular interaction networks. BMC Syst Biol (2013) 1.03

Systematic approaches towards the development of host-directed antiviral therapeutics. Int J Mol Sci (2011) 1.01

Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. Gut Pathog (2012) 1.00

Emergent biosynthetic capacity in simple microbial communities. PLoS Comput Biol (2014) 0.99

Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. Philos Trans R Soc Lond B Biol Sci (2013) 0.99

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. Hum Mol Genet (2013) 0.99

WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Res (2012) 0.98

MetaBase--the wiki-database of biological databases. Nucleic Acids Res (2011) 0.98

Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One (2012) 0.96

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models. BMC Syst Biol (2011) 0.94

MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res (2011) 0.94

Mining GO annotations for improving annotation consistency. PLoS One (2012) 0.94

Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site. Proc Natl Acad Sci U S A (2013) 0.94

CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism. BMC Syst Biol (2012) 0.90

Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato. Plant Physiol (2012) 0.88

Synthetic gene circuits for metabolic control: design trade-offs and constraints. J R Soc Interface (2012) 0.88

SIDD: a semantically integrated database towards a global view of human disease. PLoS One (2013) 0.87

Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. BMC Syst Biol (2012) 0.86

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst Biol (2011) 0.86

Osmoprotection of Bacillus subtilis through import and proteolysis of proline-containing peptides. Appl Environ Microbiol (2012) 0.86

The EBI enzyme portal. Nucleic Acids Res (2012) 0.86

Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism. PLoS Comput Biol (2012) 0.86

Arginine-based inhibitors of nitric oxide synthase: therapeutic potential and challenges. Mediators Inflamm (2012) 0.86

A constraint-based model of Scheffersomyces stipitis for improved ethanol production. Biotechnol Biofuels (2012) 0.86

MetNet Online: a novel integrated resource for plant systems biology. BMC Bioinformatics (2012) 0.86

Spatially-resolved metabolic cooperativity within dense bacterial colonies. BMC Syst Biol (2015) 0.85

Metabolomics and in-silico analysis reveal critical energy deregulations in animal models of Parkinson's disease. PLoS One (2013) 0.84

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC Genomics (2015) 0.84

Semantic text mining support for lignocellulose research. BMC Med Inform Decis Mak (2012) 0.84

INOH: ontology-based highly structured database of signal transduction pathways. Database (Oxford) (2011) 0.83

Complete absence of the αGal xenoantigen and isoglobotrihexosylceramide in α1,3galactosyltransferase knock-out pigs. Xenotransplantation (2012) 0.83

Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. J Biol Chem (2013) 0.83

Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Res (2015) 0.83

The glycerophospholipid inventory of Pseudomonas putida is conserved between strains and enables growth condition-related alterations. Microb Biotechnol (2011) 0.83

Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. BMC Syst Biol (2013) 0.82

Enzyme activity in the crowded milieu. PLoS One (2012) 0.82

Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course. Biochem Mol Biol Educ (2015) 0.81

Systematic analysis of stability patterns in plant primary metabolism. PLoS One (2012) 0.81

Analyzing clonal variation of monoclonal antibody-producing CHO cell lines using an in silico metabolomic platform. PLoS One (2014) 0.81

Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation. Microb Inform Exp (2012) 0.81

Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa. Planta (2013) 0.81

In silico prediction of antimalarial drug target candidates. Int J Parasitol Drugs Drug Resist (2012) 0.80

Systems-level analysis of mechanisms regulating yeast metabolic flux. Science (2016) 0.80

A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Syst Biol (2012) 0.80

Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. BMC Genomics (2012) 0.80

Computational tools for rational protein engineering of aldolases. Comput Struct Biotechnol J (2012) 0.79

LigSearch: a knowledge-based web server to identify likely ligands for a protein target. Acta Crystallogr D Biol Crystallogr (2013) 0.79

Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PLoS One (2013) 0.79

Changes in SAM2 expression affect lactic acid tolerance and lactic acid production in Saccharomyces cerevisiae. Microb Cell Fact (2014) 0.79

phiBIOTICS: catalogue of therapeutic enzybiotics, relevant research studies and practical applications. BMC Microbiol (2013) 0.79

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories. Microbiol Mol Biol Rev (2015) 0.79

Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in 'Chlorochromatium aggregatum'. ISME J (2013) 0.79

Molecular tools for chemical biotechnology. Curr Opin Biotechnol (2013) 0.78

A systems chemical biology study of malate synthase and isocitrate lyase inhibition in Mycobacterium tuberculosis during active and NRP growth. Comput Biol Chem (2013) 0.78

Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae. PLoS Comput Biol (2013) 0.78

In silico mechanistic profiling to probe small molecule binding to sulfotransferases. PLoS One (2013) 0.78

Proteolysis controls endogenous substance P levels. PLoS One (2013) 0.78

RNApathwaysDB--a database of RNA maturation and decay pathways. Nucleic Acids Res (2012) 0.78

Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics (2014) 0.78

Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst Biol (2016) 0.77

Computationally Modeling Lipid Metabolism and Aging: A Mini-review. Comput Struct Biotechnol J (2014) 0.77

Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications. PLoS One (2012) 0.77

An integrative analysis of small molecule transcriptional responses in the human malaria parasite Plasmodium falciparum. BMC Genomics (2015) 0.77

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Brief Funct Genomics (2013) 0.77

Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals. Comput Struct Biotechnol J (2012) 0.77

Efficient CO2-reducing activity of NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA for formate production from CO2 gas. PLoS One (2014) 0.76

Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. Malar J (2013) 0.76

Molecular cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of a purine nucleoside phosphorylase from Bacillus subtilis strain 168. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 0.76

Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLoS One (2013) 0.76

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 32.92

KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60

The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res (2009) 19.70

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2009) 12.51

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res (2009) 7.33

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res (2008) 4.75

PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2009) 3.48

BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21

BRENDA, enzyme data and metabolic information. Nucleic Acids Res (2002) 7.92

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res (2008) 4.75

IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65

PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res (2004) 3.93

QMEAN: A comprehensive scoring function for model quality assessment. Proteins (2008) 3.90

GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett (2005) 3.29

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res (2007) 2.94

Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics (2005) 2.82

CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res (2006) 2.38

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res (2012) 2.33

MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal Chem (2009) 2.17

BRENDA: a resource for enzyme data and metabolic information. Trends Biochem Sci (2002) 1.97

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res (2010) 1.71

JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res (2006) 1.69

The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues. J Mol Biol (2006) 1.63

Top down mass spectrometry of < 60-kDa proteins from Methanosarcina acetivorans using quadrupole FRMS with automated octopole collisionally activated dissociation. Mol Cell Proteomics (2006) 1.57

Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics (2004) 1.56

SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. Nucleic Acids Res (2007) 1.55

Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J (2003) 1.35

The substrate specificity-determining amino acid code of 4-coumarate:CoA ligase. Proc Natl Acad Sci U S A (2003) 1.35

Biochemical characterization and identification of the catalytic residues of a family 43 beta-D-xylosidase from Geobacillus stearothermophilus T-6. Biochemistry (2005) 1.29

The importance of uniformity in reporting protein-function data. Trends Biochem Sci (2005) 1.27

New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species. Archaea (2008) 1.27

Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks. Bioinformatics (2006) 1.26

Atomic resolution structures of R-specific alcohol dehydrogenase from Lactobacillus brevis provide the structural bases of its substrate and cosubstrate specificity. J Mol Biol (2005) 1.25

The crucial role of trehalose and structurally related oligosaccharides in the biosynthesis and transfer of mycolic acids in Corynebacterineae. J Biol Chem (2005) 1.24

BKM-react, an integrated biochemical reaction database. BMC Biochem (2011) 1.19

Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea. Arch Microbiol (2008) 1.18

Genome copy numbers and gene conversion in methanogenic archaea. J Bacteriol (2010) 1.18

Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. BMC Genomics (2011) 1.17

Structural and functional investigation of a putative archaeal selenocysteine synthase. Biochemistry (2005) 1.15

Development of a classification scheme for disease-related enzyme information. BMC Bioinformatics (2011) 1.14

EnzymeDetector: an integrated enzyme function prediction tool and database. BMC Bioinformatics (2011) 1.12

The crystal structure of R-specific alcohol dehydrogenase from Lactobacillus brevis suggests the structural basis of its metal dependency. J Mol Biol (2003) 1.08

Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans. J Bacteriol (2004) 1.05

Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry. Biol Chem (2004) 1.03

The structure of a bacterial L-amino acid oxidase from Rhodococcus opacus gives new evidence for the hydride mechanism for dehydrogenation. J Mol Biol (2006) 1.02

Molecular analysis of laminin N-terminal domains mediating self-interactions. J Biol Chem (2004) 1.02

Differential regulation of the three methanol methyltransferase isozymes in Methanosarcina acetivorans C2A. J Bacteriol (2006) 1.01

Crp induces switching of the CsrB and CsrC RNAs in Yersinia pseudotuberculosis and links nutritional status to virulence. Front Cell Infect Microbiol (2012) 0.99

Automatic assignment of EC numbers. PLoS Comput Biol (2010) 0.99

X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 A resolution. J Mol Biol (2002) 0.98

KID--an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes. BMC Bioinformatics (2010) 0.98

Concept-based annotation of enzyme classes. Bioinformatics (2005) 0.98

Intraclonal diversity of the Pseudomonas aeruginosa cystic fibrosis airway isolates TBCF10839 and TBCF121838: distinct signatures of transcriptome, proteome, metabolome, adherence and pathogenicity despite an almost identical genome sequence. Environ Microbiol (2012) 0.97

Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One (2012) 0.96

Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environ Microbiol (2013) 0.96

Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics (2009) 0.95

Human embryonic stem cells and embryonal carcinoma cells have overlapping and distinct metabolic signatures. PLoS One (2012) 0.95

Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity. Biochemistry (2002) 0.95

Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility. Proteins (2007) 0.95

How Pseudomonas aeruginosa adapts to various environments: a metabolomic approach. Environ Microbiol (2010) 0.94

SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochem Soc Trans (2009) 0.93

Automatic assignment of reaction operators to enzymatic reactions. Bioinformatics (2009) 0.93

Crystal structure of full length topoisomerase I from Thermotoga maritima. J Mol Biol (2006) 0.93

A high-throughput method for microbial metabolome analysis using gas chromatography/mass spectrometry. Anal Biochem (2007) 0.92

Adaptation of Phaeobacter inhibens DSM 17395 to growth with complex nutrients. Proteomics (2013) 0.92

In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans. Mol Microbiol (2009) 0.92

Glycosynthase activity of Geobacillus stearothermophilus GH52 beta-xylosidase: efficient synthesis of xylooligosaccharides from alpha-D-xylopyranosyl fluoride through a conjugated reaction. Chembiochem (2007) 0.92

"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus. Extremophiles (2009) 0.91

Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential. Protein Sci (2005) 0.90

Function and regulation of isoforms of carbon monoxide dehydrogenase/acetyl coenzyme A synthase in Methanosarcina acetivorans. J Bacteriol (2012) 0.90

Selenoproteins in Archaea and Gram-positive bacteria. Biochim Biophys Acta (2009) 0.90

A method for enzyme quenching in microbial metabolome analysis successfully applied to gram-positive and gram-negative bacteria and yeast. Anal Biochem (2009) 0.89

The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach. Microb Cell Fact (2012) 0.89

Fine specificity of autoantibodies to soluble liver antigen and liver/pancreas. Hepatology (2002) 0.89

Codon optimized Thermobifida fusca hydrolase secreted by Bacillus megaterium. Biotechnol Bioeng (2007) 0.89

The relevance of compartmentation for cysteine synthesis in phototrophic organisms. Protoplasma (2012) 0.89

Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins. Proteins (2004) 0.89

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. BMC Bioinformatics (2013) 0.88

JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins. Bioinformatics (2006) 0.88

A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR. J Biotechnol (2008) 0.88

Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax. Proteins (2008) 0.87

Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions. PLoS One (2013) 0.87

A large-scale protein-function database. Nat Chem Biol (2010) 0.86

Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines. Proteins (2008) 0.86

Influence of carbon monoxide on metabolite formation in Methanosarcina acetivorans. FEMS Microbiol Lett (2009) 0.85

Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences. Extremophiles (2011) 0.85