R39W42 last accessed: 2022-11-04

brenda
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

Other names: BRaunschweig ENzyme DAtabase, the comprehensive enzyme information system, brenda

BRENDA is the main collection of enzyme functional data available to the scientific community.

Webpage:

http://www.brenda-enzymes.org

Licence:

Name: BRENDA License
URL: http://www.brenda-enzymes.org/copy.php

Publications: (17)

Publications
More detailed information about this field from each metasource.

BRENDA, the enzyme database: updates and major new developments
PMID: 14681450
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

BRENDA, the enzyme information system in 2011
PMID: 21062828
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA
PMID: 23203881
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

BRENDA, enzyme data and metabolic information
PMID: 11752250
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009
PMID: 18984617
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

BRENDA in 2015: exciting developments in its 25th year of existence
PMID: 25378310
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007
PMID: 17202167
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

BRENDA: a resource for enzyme data and metabolic information
PMID: 11796225
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

The BRENDA enzyme information system-From a database to an expert system
PMID: 28438579
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Review of the BRENDA Database
PMID: 12850129
metasource: Fairsharing.org
version: FAIRsharing.org: BRENDA; BRENDA; DOI: https://doi.org/10.25504/FAIRsharing.etp533; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/gkaa1025
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/nar/gku1068
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

http://dx.doi.org/10.1093/nar/gkn820
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

http://dx.doi.org/10.1093/nar/gkq1089
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

http://dx.doi.org/10.1186/1471-2105-12-329
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

http://dx.doi.org/10.1093/nar/gks1049
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

http://dx.doi.org/10.1093/nar/gkq968
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

BRENDA, the enzyme database: updates and major new developments PubMed citations: 224.

224 articles citing: BRENDA, the enzyme database: updates and major new developments

Does adding the drug-drug similarity to drug-target interaction prediction methods make a noticeable improvement in their efficiency? PMID:35836119
Structural Thermokinetic Modelling. PMID:35629936
RoFDT: Identification of Drug-Target Interactions from Protein Sequence and Drug Molecular Structure Using Rotation Forest. PMID:35625469
MSPEDTI: Prediction of Drug-Target Interactions via Molecular Structure with Protein Evolutionary Information. PMID:35625468
A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility. PMID:35448501
Machine learning modeling of family wide enzyme-substrate specificity screens. PMID:35143485
Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley. PMID:35095268
The Discovery of New Drug-Target Interactions for Breast Cancer Treatment. PMID:34946556
Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India. PMID:34913714
NeuRank: learning to rank with neural networks for drug-target interaction prediction. PMID:34836495
Model Balancing: A Search for In-Vivo Kinetic Constants and Consistent Metabolic States. PMID:34822407
A unified drug-target interaction prediction framework based on knowledge graph and recommendation system. PMID:34811351
Whole genome sequence data of Chromobacterium violaceum WCH4, a human pathogenic strain from Sabah, Malaysia. PMID:34805463
Drug-target interaction prediction using unifying of graph regularized nuclear norm with bilinear factorization. PMID:34789169
DeepStack-DTIs: Predicting Drug-Target Interactions Using LightGBM Feature Selection and Deep-Stacked Ensemble Classifier. PMID:34731411
Graph representation learning for structural proteomics. PMID:34665257
Hierarchical Pooling in Graph Neural Networks to Enhance Classification Performance in Large Datasets. PMID:34577277
DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning. PMID:34551818
Prediction of Drug-Target Interactions by Combining Dual-Tree Complex Wavelet Transform with Ensemble Learning Method. PMID:34500792
Multimorbidity prediction using link prediction. PMID:34385524
Predicting Drug-Target Interactions Based on the Ensemble Models of Multiple Feature Pairs. PMID:34202954
Secretome Analysis of Arabidopsis-Trichoderma atroviride Interaction Unveils New Roles for the Plant Glutamate:Glyoxylate Aminotransferase GGAT1 in Plant Growth Induced by the Fungus and Resistance against Botrytis cinerea. PMID:34202732
An Ensemble Learning-Based Method for Inferring Drug-Target Interactions Combining Protein Sequences and Drug Fingerprints. PMID:33987446
HCGA: Highly comparative graph analysis for network phenotyping. PMID:33982022
Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. PMID:33947801
Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead. PMID:33917427
Drug-Target Interaction Prediction via Dual Laplacian Graph Regularized Logistic Matrix Factorization. PMID:33855072
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
PreDTIs: prediction of drug-target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques. PMID:33709119
Molecular basis for protein-protein interactions. PMID:33488826
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors. PMID:33476554
An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features. PMID:33472664
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Ensemble Learning Prediction of Drug-Target Interactions Using GIST Descriptor Extracted from PSSM-Based Evolutionary Information. PMID:32908888
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers. PMID:32873645
Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. PMID:32804944
Drug-target interactions prediction using marginalized denoising model on heterogeneous networks. PMID:32703151
Impact of Facultative Bacteria on the Metabolic Function of an Obligate Insect-Bacterial Symbiosis. PMID:32665268
Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper (Piper nigrum L.) Varieties. PMID:32399475
Gene-Wise Burden of Coding Variants Correlates to Noncoding Pharmacogenetic Risk Variants. PMID:32349395
Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth. PMID:32234775
In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis - A Kinetic Modeling Approach. PMID:32211028
FRnet-DTI: Deep convolutional neural network for drug-target interaction prediction. PMID:32154410
A Multi-Task Representation Learning Architecture for Enhanced Graph Classification. PMID:31998065
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Drug-target interaction prediction using Multi Graph Regularized Nuclear Norm Minimization. PMID:31945078
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors. PMID:31919110
Comparative analysis of differential proteome-wide protein-protein interaction network of Methanobrevibacter ruminantium M1. PMID:31763465
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
Dual pathway for metabolic engineering of Escherichia coli to produce the highly valuable hydroxytyrosol. PMID:31682615
Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii. PMID:31578249
Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar. PMID:31467100
Drug-Target Interaction Prediction Based on Drug Fingerprint Information and Protein Sequence. PMID:31430892
Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. PMID:31221760
NRLMFβ: Beta-distribution-rescored neighborhood regularized logistic matrix factorization for improving the performance of drug-target interaction prediction. PMID:30793050
Drug-Target Interaction Prediction via Dual Laplacian Graph Regularized Matrix Completion. PMID:30627536
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains. PMID:30626384
BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242
A new chemoinformatics approach with improved strategies for effective predictions of potential drugs. PMID:30311095
FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways. PMID:30283416
Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses. PMID:30209043
A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering. PMID:30108559
Characterization of esterase activity from an Acetomicrobium hydrogeniformans enzyme with high structural stability in extreme conditions. PMID:30014242
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. PMID:29914475
A physical model of cell metabolism. PMID:29844352
Selenium-Dependent Antioxidant Enzymes: Actions and Properties of Selenoproteins. PMID:29758013
An Integrated Approach of Proteomics and Computational Genetic Modification Effectiveness Analysis to Uncover the Mechanisms of Flood Tolerance in Soybeans. PMID:29701710
Structural and functional characterization of the Vindoline biosynthesis pathway enzymes of Catharanthus roseus. PMID:29442186
Open-source chemogenomic data-driven algorithms for predicting drug-target interactions. PMID:29420684
Structure-guided design of Serratia marcescens short-chain dehydrogenase/reductase for stereoselective synthesis of (R)-phenylephrine. PMID:29396495
iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting. PMID:29255285
Reconstruction of Oryza sativa indica Genome Scale Metabolic Model and Its Responses to Varying RuBisCO Activity, Light Intensity, and Enzymatic Cost Conditions. PMID:29250098
Drug-Target Interaction Prediction through Label Propagation with Linear Neighborhood Information. PMID:29186828
DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. PMID:29186331
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria. PMID:29147021
Metabolomic Modularity Analysis (MMA) to Quantify Human Liver Perfusion Dynamics. PMID:29137180
In silico prediction of drug-target interaction networks based on drug chemical structure and protein sequences. PMID:28894115
Aspergillus niger Secretes Citrate to Increase Iron Bioavailability. PMID:28824560
Genome-Scale Modeling of NADPH-Driven β-Lapachone Sensitization in Head and Neck Squamous Cell Carcinoma. PMID:28762750
Prediction of Drug-Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures. PMID:28678206
Detecting similar binding pockets to enable systems polypharmacology. PMID:28662117
Drug repositioning for enzyme modulator based on human metabolite-likeness. PMID:28617219
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities. PMID:28531184
Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory. PMID:28453640
Cooperative Metabolism in a Three-Partner Insect-Bacterial Symbiosis Revealed by Metabolic Modeling. PMID:28348026
SELF-BLM: Prediction of drug-target interactions via self-training SVM. PMID:28192537
Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points. PMID:28169831
Predicting drug-target interactions by dual-network integrated logistic matrix factorization. PMID:28079135
Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. PMID:27991516
Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology. PMID:27989793
EstDZ3: A New Esterolytic Enzyme Exhibiting Remarkable Thermostability. PMID:27899916
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization. PMID:27812109
Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli. PMID:27775018
In Vivo Analysis of NH4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth. PMID:27637876
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. PMID:27613112
The Need for Integrated Approaches in Metabolic Engineering. PMID:27527588
Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PMID:27272929
Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. PMID:27029646
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. PMID:26987649
DASPfind: new efficient method to predict drug-target interactions. PMID:26985240
Systems biology of the structural proteome. PMID:26969117
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. PMID:26951675
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction. PMID:26872142
Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique. PMID:26851083
A multiple kernel learning algorithm for drug-target interaction prediction. PMID:26801218
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica. PMID:26443104
The Augmenting Effects of Desolvation and Conformational Energy Terms on the Predictions of Docking Programs against mPGES-1. PMID:26305898
Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula. PMID:26285202
PINGU: PredIction of eNzyme catalytic residues usinG seqUence information. PMID:26261982
Deciding when to stop: efficient experimentation to learn to predict drug-target interactions. PMID:26153434
Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. PMID:26091851
HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. PMID:25937701
Determining similarity of scientific entities in annotation datasets. PMID:25725057
Genome-scale modeling for metabolic engineering. PMID:25578304
Predictive sulfur metabolism - a field in flux. PMID:25477892
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. PMID:25300491
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PMID:25029527
Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model. PMID:24565082
Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. PMID:24244318
Manipulating the sleeping beauty mutase operon for the production of 1-propanol in engineered Escherichia coli. PMID:24074355
Protonation and pK changes in protein-ligand binding. PMID:23889892
Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile. PMID:23840562
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. PMID:23088596
Erythrocytic stage-dependent regulation of oligomerization of Plasmodium ribosomal protein P2. PMID:23060439
Shrinking the metabolic solution space using experimental datasets. PMID:22956899
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. PMID:22730453
Analyzing large biological datasets with association networks. PMID:22638576
Prediction of drug-target interactions and drug repositioning via network-based inference. PMID:22589709
High similarity of phylogenetic profiles of rate-limiting enzymes with inhibitory relation in Human, Mouse, Rat, budding Yeast and E. coli. PMID:22369203
In silico insights into the symbiotic nitrogen fixation in Sinorhizobium meliloti via metabolic reconstruction. PMID:22319621
Bioinformatic Analysis of Leishmania donovani Long-Chain Fatty Acid-CoA Ligase as a Novel Drug Target. PMID:22091399
Bioinformatics and systems biology of the lipidome. PMID:21939287
Integrative analysis of transgenic alfalfa (Medicago sativa L.) suggests new metabolic control mechanisms for monolignol biosynthesis. PMID:21625579
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. PMID:21609491
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. PMID:21605342
Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. PMID:21572178
Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PMID:21423717
Bacterial protein structures reveal phylum dependent divergence. PMID:21315656
Searching the protein structure database for ligand-binding site similarities using CPASS v.2. PMID:21269480
Parameter balancing in kinetic models of cell metabolism. PMID:21038890
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. PMID:20961407
Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development. PMID:20860850
Computational systems chemical biology. PMID:20838980
KID--an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes. PMID:20626859
Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis. PMID:20543878
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. PMID:20529913
Metabolic pathway relationships revealed by an integrative analysis of the transcriptional and metabolic temperature stress-response dynamics in yeast. PMID:20455750
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. PMID:20406431
The smallest chemical reaction system with bistability. PMID:19737387
Development and validation of a species-independent functional gene microarray that targets lactic acid bacteria. PMID:19684161
Supervised prediction of drug-target interactions using bipartite local models. PMID:19605421
A mathematical model to derive N-glycan structures and cellular enzyme activities from mass spectrometric data. PMID:19506293
Stochasticity in protein levels drives colinearity of gene order in metabolic operons of Escherichia coli. PMID:19492041
An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. PMID:19486676
MirZ: an integrated microRNA expression atlas and target prediction resource. PMID:19468042
A theoretical model for template-free synthesis of long DNA sequence. PMID:19343541
Recent developments in parameter estimation and structure identification of biochemical and genomic systems. PMID:19327372
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. PMID:19144170
Questioning the ubiquity of neofunctionalization. PMID:19119408
Reconstruction of biochemical networks in microorganisms. PMID:19116616
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. PMID:18984617
ExplorEnz: the primary source of the IUBMB enzyme list. PMID:18776214
Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. PMID:18767192
Histoplasma capsulatum secreted gamma-glutamyltransferase reduces iron by generating an efficient ferric reductant. PMID:18761625
Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. PMID:18757736
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PMID:18670595
Metabolic network fluxes in heterotrophic Arabidopsis cells: stability of the flux distribution under different oxygenation conditions. PMID:18667721
Metal ions in biological catalysis: from enzyme databases to general principles. PMID:18604568
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. PMID:18586719
Phototroph genomics ten years on. PMID:18568416
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. PMID:18559112
Blast2GO: A comprehensive suite for functional analysis in plant genomics. PMID:18483572
SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. PMID:18447902
Metabolic pathways of the wheat (Triticum aestivum) endosperm amyloplast revealed by proteomics. PMID:18419817
Extremely thermostable esterases from the thermoacidophilic euryarchaeon Picrophilus torridus. PMID:18330499
Replacement of the arginine biosynthesis operon in Xanthomonadales by lateral gene transfer. PMID:18305979
Prediction of enzymes and non-enzymes from protein sequences based on sequence derived features and PSSM matrix using artificial neural network. PMID:18288334
Thiamine biosynthesis in algae is regulated by riboswitches. PMID:18093957
Quantitative systems-level determinants of human genes targeted by successful drugs. PMID:18083776
PRIDE: new developments and new datasets. PMID:18033805
A fault model for ontology mapping, alignment, and linking systems. PMID:17990495
Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE. PMID:17956990
Visualizing regulatory interactions in metabolic networks. PMID:17939866
qPIPSA: relating enzymatic kinetic parameters and interaction fields. PMID:17919319
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. PMID:17916232
ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature. PMID:17662133
Applying negative rule mining to improve genome annotation. PMID:17659089
Systems chemical biology. PMID:17637771
Integrative content-driven concepts for bioinformatics "beyond the cell". PMID:17426389
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks. PMID:17408512
Regulation of metabolic networks by small molecule metabolites. PMID:17352833
A network perspective on the evolution of metabolism by gene duplication. PMID:17326820
Global reconstruction of the human metabolic network based on genomic and bibliomic data. PMID:17267599
SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. PMID:17202169
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. PMID:17202167
Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. PMID:17173670
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. PMID:17173669
PduL is an evolutionarily distinct phosphotransacylase involved in B12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2. PMID:17158662
Correcting ligands, metabolites, and pathways. PMID:17132165
Parameter estimate of signal transduction pathways. PMID:17118160
Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. PMID:17094225
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. PMID:17082206
Meta-All: a system for managing metabolic pathway information. PMID:17059592
ORENZA: a web resource for studying ORphan ENZyme activities. PMID:17026747
ProSAT2--Protein Structure Annotation Server. PMID:16845114
Accelerating the reconstruction of genome-scale metabolic networks. PMID:16772023
Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. PMID:16672622
Predicting genes for orphan metabolic activities using phylogenetic profiles. PMID:16507154
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. PMID:16397293
EndoNet: an information resource about endocrine networks. PMID:16381928
MODOMICS: a database of RNA modification pathways. PMID:16381833
EHPred: an SVM-based method for epoxide hydrolases recognition and classification. PMID:16365918
Structural characterization of glucooligosaccharide oxidase from Acremonium strictum. PMID:16332885
In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. PMID:16269766
MACiE: a database of enzyme reaction mechanisms. PMID:16188925
metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. PMID:15745999
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. PMID:15608254
IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. PMID:15312235
Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase. PMID:15287962
Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate. PMID:15175111
BRENDA, the enzyme information system in 2011 PubMed citations: 169.

169 articles citing: BRENDA, the enzyme information system in 2011

A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications. PMID:35604933
Stable Isotopes for Tracing Cardiac Metabolism in Diseases. PMID:34859064
Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm. PMID:34757076
Systems Biology Approaches to Enzyme Kinetics. PMID:34272703
Combination of network and molecule structure accurately predicts competitive inhibitory interactions. PMID:34136091
Identification of immucillin analogue natural compounds to inhibit Helicobacter pylori MTAN through high throughput virtual screening and molecular dynamics simulation. PMID:33786292
Crosstalk and ultrasensitivity in protein degradation pathways. PMID:33370258
Exploiting the biological response of two Serratia fonticola strains to the critical metals, gallium and indium. PMID:33230153
A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity. PMID:32977700
Proteolytic profile of larval developmental stages of Penaeus vannamei: An activity and mRNA expression approach. PMID:32946520
Whole-Genome Sequencing and Bioinformatics Analysis of Apiotrichum mycotoxinivorans: Predicting Putative Zearalenone-Degradation Enzymes. PMID:32849454
Fabrication of Zero Mode Waveguides for High Concentration Single Molecule Microscopy. PMID:32478723
Personalized whole-body models integrate metabolism, physiology, and the gut microbiome. PMID:32463598
A Systems Chemoproteomic Analysis of Acyl-CoA/Protein Interaction Networks. PMID:31836350
The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling. PMID:31294216
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. PMID:31293525
Essential metabolism for a minimal cell. PMID:30657448
BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242
Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. PMID:30218605
In Silico Prediction of Large-Scale Microbial Production Performance: Constraints for Getting Proper Data-Driven Models. PMID:30105090
An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PMID:30040834
Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics. PMID:29702650
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
Predicting novel substrates for enzymes with minimal experimental effort with active learning. PMID:29030274
Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA. PMID:28609293
Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens. PMID:28553270
Observing Single-Molecule Dynamics at Millimolar Concentrations. PMID:28116856
The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum. PMID:28103880
The Kinetics of Enzyme Mixtures. PMID:27843974
Systems-level analysis of mechanisms regulating yeast metabolic flux. PMID:27789812
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. PMID:27602057
Inhibition of Escherichia coli CTP Synthetase by NADH and Other Nicotinamides and Their Mutual Interactions with CTP and GTP. PMID:27571563
Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. PMID:27372244
Multidimensional monitoring of anaerobic/aerobic azo dye based wastewater treatments by hyphenated UPLC-ICP-MS/ESI-Q-TOF-MS techniques. PMID:27328673
Evaluation of rate law approximations in bottom-up kinetic models of metabolism. PMID:27266508
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. PMID:27252693
Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PMID:26992093
Whole Cell Modeling: From Single Cells to Colonies. PMID:26989262
Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach. PMID:26913242
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. PMID:26692227
Chirality Matters: Synthesis and Consumption of the d-Enantiomer of Lactic Acid by Synechocystis sp. Strain PCC6803. PMID:26682849
An integrative analysis of small molecule transcriptional responses in the human malaria parasite Plasmodium falciparum. PMID:26637195
In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories. PMID:26609052
Engineering Triterpene and Methylated Triterpene Production in Plants Provides Biochemical and Physiological Insights into Terpene Metabolism. PMID:26603654
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease. PMID:26504511
Protein Analysis of Sapienic Acid-Treated Porphyromonas gingivalis Suggests Differential Regulation of Multiple Metabolic Pathways. PMID:26483519
Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism. PMID:26469081
A novel intracellular mutualistic bacterium in the invasive ant Cardiocondyla obscurior. PMID:26172209
Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course. PMID:26148241
Mathematical modelling of metabolic regulation in aging. PMID:25923415
Spatially-resolved metabolic cooperativity within dense bacterial colonies. PMID:25890263
PathwayBooster: a tool to support the curation of metabolic pathways. PMID:25887214
Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework. PMID:25874228
Reconstructing genome-scale metabolic models with merlin. PMID:25845595
Computationally Modeling Lipid Metabolism and Aging: A Mini-review. PMID:25750699
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses. PMID:25545100
Self-organization of signal transduction. PMID:25506419
Engineering microorganisms based on molecular evolutionary analysis: a succinate production case study. PMID:25469170
Efficient searching and annotation of metabolic networks using chemical similarity. PMID:25417203
Changes in SAM2 expression affect lactic acid tolerance and lactic acid production in Saccharomyces cerevisiae. PMID:25359316
Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains. PMID:25347188
A novel glucose 6-phosphate isomerase from Listeria monocytogenes. PMID:25194846
Network-level architecture and the evolutionary potential of underground metabolism. PMID:25071190
Efficient CO2-reducing activity of NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA for formate production from CO2 gas. PMID:25061666
Emergent biosynthetic capacity in simple microbial communities. PMID:24992662
Exploring metabolic engineering design principles for the photosynthetic production of lactic acid by Synechocystis sp. PCC6803. PMID:24991233
Determining enzyme kinetics for systems biology with nuclear magnetic resonance spectroscopy. PMID:24957764
Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals. PMID:24688665
Computational tools for rational protein engineering of aldolases. PMID:24688657
Analyzing clonal variation of monoclonal antibody-producing CHO cell lines using an in silico metabolomic platform. PMID:24632968
Weighting schemes in metabolic graphs for identifying biochemical routes. PMID:24592291
In silico prediction of antimalarial drug target candidates. PMID:24533280
Constraint-based models predict metabolic and associated cellular functions. PMID:24430943
Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering". PMID:24416282
Genome degeneration and adaptation in a nascent stage of symbiosis. PMID:24407854
Systematic construction of kinetic models from genome-scale metabolic networks. PMID:24324546
LigSearch: a knowledge-based web server to identify likely ligands for a protein target. PMID:24311580
Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in 'Chlorochromatium aggregatum'. PMID:24285361
Enzyme reaction annotation using cloud techniques. PMID:24222895
SIDD: a semantically integrated database towards a global view of human disease. PMID:24146757
Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. PMID:24129579
A systems chemical biology study of malate synthase and isocitrate lyase inhibition in Mycobacterium tuberculosis during active and NRP growth. PMID:24121675
OptZyme: computational enzyme redesign using transition state analogues. PMID:24116038
Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae. PMID:24098096
Topology of molecular interaction networks. PMID:24041013
In silico mechanistic profiling to probe small molecule binding to sulfotransferases. PMID:24039991
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. PMID:24034347
SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria. PMID:23975204
Metabolomics and in-silico analysis reveal critical energy deregulations in animal models of Parkinson's disease. PMID:23935941
Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. PMID:23908403
Proteolysis controls endogenous substance P levels. PMID:23894327
Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PMID:23825549
Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site. PMID:23798413
Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. PMID:23793264
Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa. PMID:23765265
Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. PMID:23744946
Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PMID:23704901
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:23537208
Molecular tools for chemical biotechnology. PMID:23528237
phiBIOTICS: catalogue of therapeutic enzybiotics, relevant research studies and practical applications. PMID:23497033
Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. PMID:23492669
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. PMID:23482073
Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. PMID:23479751
Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. PMID:23455438
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
An adhesive bone marrow scaffold and bone morphogenetic-2 protein carrier for cartilage tissue engineering. PMID:23320412
Cyanobacterial conversion of carbon dioxide to 2,3-butanediol. PMID:23297225
FastAnnotator--an efficient transcript annotation web tool. PMID:23281853
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. PMID:23203881
Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. PMID:23194438
WholeCellKB: model organism databases for comprehensive whole-cell models. PMID:23175606
The EBI enzyme portal. PMID:23175605
Reconciliation of metabolites and biochemical reactions for metabolic networks. PMID:23172809
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
Osmoprotection of Bacillus subtilis through import and proteolysis of proline-containing peptides. PMID:23144141
Enzyme informatics. PMID:23116471
IUPHAR-DB: updated database content and new features. PMID:23087376
Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications. PMID:23082187
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Synthetic gene circuits for metabolic control: design trade-offs and constraints. PMID:23054953
A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. PMID:23046614
Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. PMID:23025710
A constraint-based model of Scheffersomyces stipitis for improved ethanol production. PMID:22998943
Arginine-based inhibitors of nitric oxide synthase: therapeutic potential and challenges. PMID:22988346
Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PMID:22952675
Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. PMID:22937810
CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism. PMID:22929619
Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato. PMID:22872775
Engineering a cyanobacterial cell factory for production of lactic acid. PMID:22865063
Mining GO annotations for improving annotation consistency. PMID:22848383
The cloning, expression, purification, characterization and modeled structure of Caulobacter crescentus β-Xylosidase I. PMID:22806729
Enzyme activity in the crowded milieu. PMID:22761790
Complete absence of the αGal xenoantigen and isoglobotrihexosylceramide in α1,3galactosyltransferase knock-out pigs. PMID:22702471
Semantic text mining support for lignocellulose research. PMID:22595090
Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation. PMID:22587916
Computer analysis of metagenomic data--prediction of quantitative value of specific activity of proteins. PMID:22562630
Nutritional metabolomics: progress in addressing complexity in diet and health. PMID:22540256
Systematic analysis of stability patterns in plant primary metabolism. PMID:22514655
Targeting imidazoline site on monoamine oxidase B through molecular docking simulations. PMID:22426510
Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism. PMID:22379410
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. PMID:22233419
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. PMID:22156394
MetaBase--the wiki-database of biological databases. PMID:22139927
Rhea--a manually curated resource of biochemical reactions. PMID:22135291
Semantic annotation of biological concepts interplaying microbial cellular responses. PMID:22122862
INOH: ontology-based highly structured database of signal transduction pathways. PMID:22120663
TDR Targets: a chemogenomics resource for neglected diseases. PMID:22116064
SABIO-RK--database for biochemical reaction kinetics. PMID:22102587
Databases and bioinformatics tools for the study of DNA repair. PMID:22091405
MetaCrop 2.0: managing and exploring information about crop plant metabolism. PMID:22086948
Pocketome: an encyclopedia of small-molecule binding sites in 4D. PMID:22080553
Inference of functional properties from large-scale analysis of enzyme superfamilies. PMID:22069325
EcoliWiki: a wiki-based community resource for Escherichia coli. PMID:22064863
MACiE: exploring the diversity of biochemical reactions. PMID:22058127
Ascaris suum draft genome. PMID:22031327
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. PMID:21995956
ChEMBL: a large-scale bioactivity database for drug discovery. PMID:21948594
The glycerophospholipid inventory of Pseudomonas putida is conserved between strains and enables growth condition-related alterations. PMID:21895997
Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models. PMID:21867520
Development of a classification scheme for disease-related enzyme information. PMID:21827651
BKM-react, an integrated biochemical reaction database. PMID:21824409
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Molecular cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of a purine nucleoside phosphorylase from Bacillus subtilis strain 168. PMID:21543875
A survey of metabolic databases emphasizing the MetaCyc family. PMID:21523460
Protein databases on the internet. PMID:18265344
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA PubMed citations: 146.

146 articles citing: BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

Highly sensitive, scalable, and rapid SARS-CoV-2 biosensor based on In2O3 nanoribbon transistors and phosphatase. PMID:35371413
Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis. PMID:34583645
Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli. PMID:34389727
Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations. PMID:34297714
The LASER database: Formalizing design rules for metabolic engineering. PMID:34150506
The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli. PMID:33743594
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880
Multiplex enzyme activity imaging by MALDI-IMS of substrate library conversions. PMID:32968143
Engineering of Nanoscale Coordination Polymers with Biomolecules for Advanced Applications. PMID:32863398
ENaC regulation by phospholipids and DGK explained through mathematical modeling. PMID:32811866
DNA-Scaffolded Proximity Assembly and Confinement of Multienzyme Reactions. PMID:32248317
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies. PMID:32140178
Complex I is bypassed during high intensity exercise. PMID:31699973
Engineering a Seven Enzyme Biotransformation using Mathematical Modelling and Characterized Enzyme Parts. PMID:31598184
A Pilot STEM Curriculum Designed to Teach High School Students Concepts in Biochemical Engineering and Pharmacology. PMID:31517314
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties. PMID:31430276
Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics. PMID:31235822
Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture. PMID:31183623
Nanoparticle Activation Methods in Cancer Treatment. PMID:31137744
Tunable enzyme responses in amphiphilic nanoassemblies through alterations in the unimer-aggregate equilibrium. PMID:30996882
Stochastic modelling reveals mechanisms of metabolic heterogeneity. PMID:30911683
Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance. PMID:30638812
In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production. PMID:30588397
Theranostics based on AIEgens. PMID:30429878
BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242
Promising New Antifungal Treatment Targeting Chorismate Synthase from Paracoccidioides brasiliensis. PMID:30348661
Plasmon-Enhanced Single-Molecule Enzymology. PMID:30148184
Membrane-associated human tyrosinase is an enzymatically active monomeric glycoprotein. PMID:29870551
A chitinase with two catalytic domains is required for organization of the cuticular extracellular matrix of a beetle. PMID:29590098
Label-free protein detection using terahertz time-domain spectroscopy. PMID:29541499
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
A Mathematical Model of the Phosphoinositide Pathway. PMID:29500467
Pathway design using de novo steps through uncharted biochemical spaces. PMID:29330441
Redox status of patients before cardiac surgery. PMID:29257712
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
Isolation of highly thermostable β-xylosidases from a hot spring soil microbial community using a metagenomic approach. PMID:29106502
Predicting novel substrates for enzymes with minimal experimental effort with active learning. PMID:29030274
VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization. PMID:28978313
Construction and Experimental Validation of a Quantitative Kinetic Model of Nitric Oxide Stress in Enterohemorrhagic Escherichia coli O157:H7. PMID:28952571
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition. PMID:28821741
An Ameliorated Prediction of Drug-Target Interactions Based on Multi-Scale Discrete Wavelet Transform and Network Features. PMID:28813000
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. PMID:28779005
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. PMID:28732462
Detection of Enzyme Activity and Inhibition during Studies in Solution, In Vitro and In Vivo with CatalyCEST MRI. PMID:28726131
Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth. PMID:28720699
The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. PMID:28691704
A practical strategy to design and develop an isoform-specific fluorescent probe for a target enzyme: CYP1A1 as a case study. PMID:28553516
Unfair competition governs the interaction of pCPI-17 with myosin phosphatase (PP1-MYPT1). PMID:28387646
Cancer-Associated, Stimuli-Driven, Turn on Theranostics for Multimodality Imaging and Therapy. PMID:28370546
Genomics of apicomplexan parasites. PMID:28276701
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism. PMID:28125959
Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. PMID:28106881
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains. PMID:27996047
BRENDA in 2017: new perspectives and new tools in BRENDA. PMID:27924025
Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development. PMID:27570648
Constrained Allocation Flux Balance Analysis. PMID:27355325
Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy. PMID:27336167
The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase. PMID:27274708
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. PMID:27159581
Evolutionary evidence on suitability of SecD as a target for development of antibacterial agents against Staphylococcus aureus. PMID:27087922
Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase. PMID:26928598
Characterising Complex Enzyme Reaction Data. PMID:26840640
Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms. PMID:26834640
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. PMID:26776497
Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota. PMID:26745984
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks. PMID:26597226
An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. PMID:26538500
Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). PMID:26442024
A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data. PMID:26381164
The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus. PMID:26373863
Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy. PMID:26370248
Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective. PMID:26367006
Human metabolic atlas: an online resource for human metabolism. PMID:26209309
Comprehensive comparison of large-scale tissue expression datasets. PMID:26157623
Many InChIs and quite some feat. PMID:26081259
Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics. PMID:26071768
Direct Ionic Regulation of the Activity of Myo-Inositol Biosynthesis Enzymes in Mozambique Tilapia. PMID:26066044
Metabolic energy-based modelling explains product yielding in anaerobic mixed culture fermentations. PMID:25992959
Est10: A Novel Alkaline Esterase Isolated from Bovine Rumen Belonging to the New Family XV of Lipolytic Enzymes. PMID:25973851
A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines. PMID:25960936
Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase. PMID:25960001
Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae. PMID:25911487
Annotation-based feature extraction from sets of SBML models. PMID:25904997
Predicting internal cell fluxes at sub-optimal growth. PMID:25890056
A method for multiplex gene synthesis employing error correction based on expression. PMID:25790188
Computational modeling of drug response with applications to neuroscience. PMID:25733952
Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. PMID:25566296
Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. PMID:25555398
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
Synthetic Biology: A Bridge between Artificial and Natural Cells. PMID:25532531
A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont. PMID:25527092
The glutaredoxin mono- and di-thiol mechanisms for deglutathionylation are functionally equivalent: implications for redox systems biology. PMID:25514238
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Development of bio-based fine chemical production through synthetic bioengineering. PMID:25494636
Computational strategies for a system-level understanding of metabolism. PMID:25427076
Text mining in cancer gene and pathway prioritization. PMID:25392685
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. PMID:25378328
BRENDA in 2015: exciting developments in its 25th year of existence. PMID:25378310
Emulating structural stability of Pseudomonas mendocina lipase: in silico mutagenesis and molecular dynamics studies. PMID:25367042
Intracellular metabolite levels shape sulfur isotope fractionation during microbial sulfate respiration. PMID:25362045
Computational approaches for microalgal biofuel optimization: a review. PMID:25309916
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. PMID:25300491
Enzyme clustering accelerates processing of intermediates through metabolic channeling. PMID:25262299
Targeting the C-type lectins-mediated host-pathogen interactions with dextran. PMID:25224349
Interactions of macromolecular crowding agents and cosolutes with small-molecule substrates: effect on horseradish peroxidase activity with two different substrates. PMID:25157999
Small but powerful, the primary endosymbiont of moss bugs, Candidatus Evansia muelleri, holds a reduced genome with large biosynthetic capabilities. PMID:25115011
Simulating metabolism with statistical thermodynamics. PMID:25089525
Data integration in the era of omics: current and future challenges. PMID:25032990
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PMID:25029527
Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. PMID:24998033
Expression and characterization of a β-fructofuranosidase from the parasitic protist Trichomonas vaginalis. PMID:24972630
Profiling the orphan enzymes. PMID:24906382
Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii. PMID:24894045
High-throughput single-molecule studies of protein-DNA interactions. PMID:24859086
Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade. PMID:24858085
Finding sequences for over 270 orphan enzymes. PMID:24826896
An atlas of genetic influences on human blood metabolites. PMID:24816252
Optimizing genome-scale network reconstructions. PMID:24811519
Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. PMID:24808102
XTMS: pathway design in an eXTended metabolic space. PMID:24792156
Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). PMID:24778629
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Towards a computational model of a methane producing archaeum. PMID:24729742
Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example. PMID:24723922
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. PMID:24642845
Greatwall-phosphorylated Endosulfine is both an inhibitor and a substrate of PP2A-B55 heterotrimers. PMID:24618897
Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism. PMID:24603481
The future of whole-cell modeling. PMID:24556244
Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets. PMID:24444313
Two promising alkaline β-glucosidases isolated by functional metagenomics from agricultural soil, including one showing high tolerance towards harsh detergents, oxidants and glucose. PMID:24414432
Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity. PMID:24392141
The Structure-Function Linkage Database. PMID:24271399
UniCarbKB: building a knowledge platform for glycoproteomics. PMID:24234447
BacDive--the Bacterial Diversity Metadatabase. PMID:24214959
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. PMID:24059635
Association of elevated urinary concentration of renin-angiotensin system components and severe AKI. PMID:24009222
Robustly passivated, gold nanoaperture arrays for single-molecule fluorescence microscopy. PMID:23987563
Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration. PMID:23938102
Evolutionary diversification of the multimeric states of proteins. PMID:23836639
Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB. PMID:23680785
Computational model for pathway reconstruction to unravel the evolutionary significance of melanin synthesis. PMID:23390353
BRENDA, enzyme data and metabolic information PubMed citations: 134.

134 articles citing: BRENDA, enzyme data and metabolic information

Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria. PMID:35888693
Experimental and computational studies of cellulases as bioethanol enzymes. PMID:35730402
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Emerging Roles of β-Glucanases in Plant Development and Adaptative Responses. PMID:35567119
A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. PMID:35205348
Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche. PMID:35190575
Biocatalysed synthesis planning using data-driven learning. PMID:35181654
Capturing Biomarkers and Molecular Targets in Cellular Landscapes From Dynamic Reaction Network Models and Machine Learning. PMID:35127516
Altered muscle mitochondrial, inflammatory and trophic markers, and reduced exercise training adaptations in type 1 diabetes. PMID:34995365
Stable Isotopes for Tracing Cardiac Metabolism in Diseases. PMID:34859064
Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates. PMID:34759911
Cell-Free Multi-Enzyme Synthesis and Purification of Uridine Diphosphate Galactose. PMID:34637168
Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment. PMID:34572839
Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. PMID:34222327
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Low-power infrared laser modulates telomere length in heart tissue from an experimental model of acute lung injury. PMID:34009632
A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression. PMID:33970902
Bagasse minority pathway expression: Real time study of GH2 β-mannosidases from bacteroidetes. PMID:33730062
Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. PMID:33251208
KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. PMID:33247931
Role of Glutathione in Cancer: From Mechanisms to Therapies. PMID:33050144
Assessment of Techno-Functional and Nutraceutical Potential of Tomato (Solanum lycopersicum) Seed Meal. PMID:32942707
Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction. PMID:32932905
Transcriptomic Analysis of Rhodococcus opacus R7 Grown on o-Xylene by RNA-Seq. PMID:32903390
iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model. PMID:32277147
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies. PMID:32140178
Comprehensive Flux Modeling of Chlamydia trachomatis Proteome and qRT-PCR Data Indicate Biphasic Metabolic Differences Between Elementary Bodies and Reticulate Bodies During Infection. PMID:31681215
Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook. PMID:31656120
The effects of naringin on different cyclophosphamide-induced organ toxicities in rats: investigation of changes in some metabolic enzyme activities. PMID:31292874
New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. PMID:30873404
Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. PMID:30532008
Xylose metabolism in the pig. PMID:30359396
Membrane-associated human tyrosinase is an enzymatically active monomeric glycoprotein. PMID:29870551
Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532. PMID:29797222
Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. PMID:29468116
Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model. PMID:29316921
The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations. PMID:29220445
Standardization of a Continuous Assay for Glycosidases and Its Use for Screening Insect Gut Samples at Individual and Populational Levels. PMID:28553236
Modeling fructose-load-induced hepatic de-novo lipogenesis by model simplification. PMID:28469410
Proteolysis of mature HIV-1 p6 Gag protein by the insulin-degrading enzyme (IDE) regulates virus replication in an Env-dependent manner. PMID:28388673
Characterization of the first naturally thermostable terpene synthases and development of strategies to improve thermostability in this family of enzymes. PMID:28371548
Structural modeling and functional analysis of the essential ribosomal processing protease Prp from Staphylococcus aureus. PMID:28187498
Structural Analysis of the Catalytic Mechanism and Substrate Specificity of Anabaena Alkaline Invertase InvA Reveals a Novel Glucosidase. PMID:27777307
Genome Sequence Variability Predicts Drug Precautions and Withdrawals from the Market. PMID:27690231
SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. PMID:27525735
Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes. PMID:27516767
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. PMID:27379044
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. PMID:26692227
In Silico Prediction of Human Sulfotransferase 1E1 Activity Guided by Pharmacophores from Molecular Dynamics Simulations. PMID:26542807
Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli. PMID:26501058
Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis. PMID:26453433
Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology. PMID:26236316
kpath: integration of metabolic pathway linked data. PMID:26055101
Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases. PMID:25814993
Computational protein design enables a novel one-carbon assimilation pathway. PMID:25775555
Identification and characterization of a novel phosphodiesterase from the metagenome of an Indian coalbed. PMID:25658120
A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. PMID:25379147
Near-isogenic lines of Triticum aestivum with distinct modes of resistance exhibit dissimilar transcriptional regulation during Diuraphis noxia feeding. PMID:25361582
Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. PMID:25253284
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
Systematic applications of metabolomics in metabolic engineering. PMID:24957776
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. PMID:24766808
Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity. PMID:24392141
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. PMID:24034347
Identification of a new class of adenosine deaminase from Helicobacter pylori with homologs among diverse taxa. PMID:23852874
ExtremeDB: a unified web repository of extremophilic archaea and bacteria. PMID:23696792
Metabolic states following accumulation of intracellular aggregates: implications for neurodegenerative diseases. PMID:23667676
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PMID:23555215
Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholerae targeted by Piper betel derived compounds. PMID:23382822
Glutamyl phosphate is an activated intermediate in actin crosslinking by actin crosslinking domain (ACD) toxin. PMID:23029200
Understanding regulation of metabolism through feasibility analysis. PMID:22808034
Investigating metabolite-protein interactions: an overview of available techniques. PMID:22750303
Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics. PMID:22570597
The use of EST expression matrixes for the quality control of gene expression data. PMID:22412959
Exploring the gap between dynamic and constraint-based models of metabolism. PMID:22306209
Advanced stoichiometric analysis of metabolic networks of mammalian systems. PMID:22196224
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. PMID:22151823
Computational Approaches for Automated Classification of Enzyme Sequences. PMID:22114367
Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation. PMID:22073143
Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PMID:21980418
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. PMID:21962087
Synergistic use of plant-prokaryote comparative genomics for functional annotations. PMID:21810204
Systems-biology approaches for predicting genomic evolution. PMID:21808261
Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism. PMID:21731702
Metalloproteins and the pyrite-based origin of life: a critical assessment. PMID:21431891
Purification and characterization of dimethylsulfide monooxygenase from Hyphomicrobium sulfonivorans. PMID:21216999
ModBase, a database of annotated comparative protein structure models, and associated resources. PMID:21097780
Analysis of protein pathway networks using hybrid properties. PMID:21076385
Dynamics and control of the central carbon metabolism in hepatoma cells. PMID:20426867
Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt. PMID:20409457
Towards a genome-scale kinetic model of cellular metabolism. PMID:20109182
Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines. PMID:20066123
MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. PMID:19958484
A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. PMID:19754970
Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli. PMID:19372223
A theoretical model for template-free synthesis of long DNA sequence. PMID:19343541
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. PMID:19144170
Efficient reconstruction of metabolic pathways by bidirectional chemical search. PMID:19101770
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PMID:18974823
Update of KDBI: Kinetic Data of Bio-molecular Interaction database. PMID:18971255
Impact of limited solvent capacity on metabolic rate, enzyme activities, and metabolite concentrations of S. cerevisiae glycolysis. PMID:18846199
Web-based applications for building, managing and analysing kinetic models of biological systems. PMID:18805901
Validating annotations for uncharacterized proteins in Shewanella oneidensis. PMID:18687039
Enzymatic, immunological and phylogenetic characterization of Brucella suis urease. PMID:18638408
Developing a protein-interactions ontology. PMID:18629092
Interoperability of CABRI Services and Biochemical Pathways Databases. PMID:18629057
Extraction of elementary rate constants from global network analysis of E. coli central metabolism. PMID:18462493
Biosynthetic potentials of metabolites and their hierarchical organization. PMID:18392147
Towards ontology-driven navigation of the lipid bibliosphere. PMID:18315858
Impact of the solvent capacity constraint on E. coli metabolism. PMID:18215292
Nonequilibrium thermodynamics of thiol/disulfide redox systems: a perspective on redox systems biology. PMID:18155672
The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. PMID:17908294
Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene. PMID:17586769
Distinguishing enzymes using metabolome data for the hybrid dynamic/static method. PMID:17511884
MetaPath Online: a web server implementation of the network expansion algorithm. PMID:17483511
Formal TCA cycle description based on elementary actions. PMID:17426387
Purification and characterization of mycobacterial phospholipase A: an activity associated with mycobacterial cutinase. PMID:17416658
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. PMID:17202167
A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics. PMID:17184531
Correcting ligands, metabolites, and pathways. PMID:17132165
Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets. PMID:16887020
Expanding metabolic networks: scopes of compounds, robustness, and evolution. PMID:16155745
EzCatDB: the Enzyme Catalytic-mechanism Database. PMID:15608227
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. PMID:15608178
Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. coli. PMID:15599512
Network analysis of metabolic enzyme evolution in Escherichia coli. PMID:15113413
Text mining neuroscience journal articles to populate neuroscience databases. PMID:15046245
LEON: multiple aLignment Evaluation Of Neighbours. PMID:14982955
IntEnz, the integrated relational enzyme database. PMID:14681451
BRENDA, the enzyme database: updates and major new developments. PMID:14681450
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. PMID:14681376
Enzyme-specific profiles for genome annotation: PRIAM. PMID:14602924
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. PMID:12824396
TRANSFAC: transcriptional regulation, from patterns to profiles. PMID:12520026
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 PubMed citations: 132.

132 articles citing: BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

The Enzymatic Core of Scorpion Venoms. PMID:35448857
Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways. PMID:35387341
Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. PMID:35351103
Curating COBRA Models of Microbial Metabolism. PMID:34719001
Integrative Modeling of Gene Expression and Metabolic Networks of Arabidopsis Embryos for Identification of Seed Oil Causal Genes. PMID:33889166
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880
FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation. PMID:31748517
An expansin-like protein expands forage cell walls and synergistically increases hydrolysis, digestibility and fermentation of livestock feeds by fibrolytic enzymes. PMID:31689330
BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. PMID:29713790
Community-driven roadmap for integrated disease maps. PMID:29688273
Engineering Thermostable Microbial Xylanases Toward its Industrial Applications. PMID:29380253
Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism. PMID:29134060
Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. PMID:28903046
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism. PMID:28511646
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PMID:28114351
A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. PMID:27883890
The Need for Integrated Approaches in Metabolic Engineering. PMID:27527588
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PMID:27467583
The Proteasix Ontology. PMID:27259807
Systems biology of the structural proteome. PMID:26969117
Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence. PMID:26853625
Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. PMID:26374290
The thioredoxin system and not the Michaelis-Menten equation should be fitted to substrate saturation datasets from the thioredoxin insulin assay. PMID:26102065
Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism. PMID:26086807
Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes. PMID:26070087
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support. PMID:25754864
Prediction of distal residue participation in enzyme catalysis. PMID:25627867
Ischaemic accumulation of succinate controls reperfusion injury through mitochondrial ROS. PMID:25383517
BRENDA in 2015: exciting developments in its 25th year of existence. PMID:25378310
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. PMID:25254202
Involvement of PG2212 zinc finger protein in the regulation of oxidative stress resistance in Porphyromonas gingivalis W83. PMID:25225267
Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942. PMID:25141288
Metabolome variations in the Porphyromonas gingivalis vimA mutant during hydrogen peroxide-induced oxidative stress. PMID:25055986
Bridging the gaps in systems biology. PMID:24728588
AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes. PMID:24130738
Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load. PMID:24086517
Network-based approaches in drug discovery and early development. PMID:24025802
Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions. PMID:23967252
Protonation and pK changes in protein-ligand binding. PMID:23889892
Protein engineering for metabolic engineering: current and next-generation tools. PMID:23589443
Role of the phenylalanine-hydroxylating system in aromatic substance degradation and lipid metabolism in the oleaginous fungus Mortierella alpina. PMID:23503309
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. PMID:23203881
Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity. PMID:23131096
A text mining approach to detect mentions of protein glycosylation in biomedical text. PMID:23055626
The use of glycoinformatics in glycochemistry. PMID:23015842
Regulatory network operations in the Pathway Tools software. PMID:22998532
Orchestrating hi-fi annotations. PMID:22987007
Global probabilistic annotation of metabolic networks enables enzyme discovery. PMID:22960854
In vitro Ca(2+)-dependent maturation of milk-clotting recombinant Epr: minor extracellular protease: from Bacillus licheniformis. PMID:22736063
Cloning, expression and characterization of a metagenome derived thermoactive/thermostable pectinase. PMID:22711301
iAK692: a genome-scale metabolic model of Spirulina platensis C1. PMID:22703714
A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction. PMID:22664637
Rethinking glycolysis: on the biochemical logic of metabolic pathways. PMID:22596202
An in silico platform for the design of heterologous pathways in nonnative metabolite production. PMID:22578364
Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance. PMID:22558125
Redox balance is key to explaining full vs. partial switching to low-yield metabolism. PMID:22443685
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. PMID:22233419
Genome characterization of the oleaginous fungus Mortierella alpina. PMID:22174787
VimA-dependent modulation of acetyl coenzyme A levels and lipid A biosynthesis can alter virulence in Porphyromonas gingivalis. PMID:22144476
Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont. PMID:22102823
Origins of specificity and promiscuity in metabolic networks. PMID:22052908
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. PMID:22041191
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. PMID:21999653
Fungal biodegradation and enzymatic modification of lignin. PMID:21968746
EnzymeDetector: an integrated enzyme function prediction tool and database. PMID:21943292
Biochemical characterization of the tetrahydrobiopterin synthesis pathway in the oleaginous fungus Mortierella alpina. PMID:21852350
Enzyme kinetics of the mitochondrial deoxyribonucleoside salvage pathway are not sufficient to support rapid mtDNA replication. PMID:21829339
A retrosynthetic biology approach to metabolic pathway design for therapeutic production. PMID:21819595
Response of Pseudomonas putida KT2440 to increased NADH and ATP demand. PMID:21803911
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. PMID:21714867
Curation of characterized glycoside hydrolases of fungal origin. PMID:21622642
Extending biochemical databases by metabolomic surveys. PMID:21566124
Recent insights into the structure and function of comparative gene identification-58. PMID:21494142
Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies. PMID:21489242
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
Systems glycobiology: biochemical reaction networks regulating glycan structure and function. PMID:21436236
Measuring enzyme activity in single cells. PMID:21316781
Complete genome sequence of Archaeoglobus profundus type strain (AV18). PMID:21304717
Aphid genome expression reveals host-symbiont cooperation in the production of amino acids. PMID:21282658
The logic of kinetic regulation in the thioredoxin system. PMID:21266044
Mining bacterial genomes for novel arylesterase activity. PMID:21255363
Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. PMID:21251315
Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention. PMID:21182926
Simulation of cellular biochemical system kinetics. PMID:21171044
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation. PMID:21122127
Constructing a fish metabolic network model. PMID:21114829
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. PMID:21083885
PROMISCUOUS: a database for network-based drug-repositioning. PMID:21071407
BRENDA, the enzyme information system in 2011. PMID:21062828
P2CS: a database of prokaryotic two-component systems. PMID:21051349
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. PMID:20961407
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. PMID:20959820
Computational systems chemical biology. PMID:20838980
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. PMID:20823849
Characterizing the metabolism of Dehalococcoides with a constraint-based model. PMID:20811585
Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. PMID:20808766
Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. PMID:20807400
A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. PMID:20682560
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. PMID:20628073
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. PMID:20594333
On the pH-optimum of activity and stability of proteins. PMID:20589630
A multilevel data integration resource for breast cancer study. PMID:20525248
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. PMID:20522724
Massively parallel sequencing and analysis of the Necator americanus transcriptome. PMID:20485481
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. PMID:20433725
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
Systems metabolic engineering: genome-scale models and beyond. PMID:20151446
Simulation of a Petri net-based model of the terpenoid biosynthesis pathway. PMID:20144236
Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. PMID:20139469
PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. PMID:20089154
Human liver rate-limiting enzymes influence metabolic flux via branch points and inhibitors. PMID:19958496
Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PMID:19911043
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PMID:19907644
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. PMID:19906710
Chemical Entities of Biological Interest: an update. PMID:19854951
Evidence for the adaptation of protein pH-dependence to subcellular pH. PMID:19849832
Regulation by glutathionylation of isocitrate lyase from Chlamydomonas reinhardtii. PMID:19847013
The University of Minnesota Biocatalysis/Biodegradation Database: improving public access. PMID:19767608
EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts. PMID:19758466
Automated inference of molecular mechanisms of disease from amino acid substitutions. PMID:19734154
On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. PMID:19703275
Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. PMID:19678920
A metabolic network described in absolute terms. PMID:19620991
Missing in action: enzyme functional annotations in biological databases. PMID:19620987
Borrelia burgdorferi bb0426 encodes a 2'-deoxyribosyltransferase that plays a central role in purine salvage. PMID:19460093
FMM: a web server for metabolic pathway reconstruction and comparative analysis. PMID:19401437
Designing and encoding models for synthetic biology. PMID:19364720