Dietmar Schomburg - Academia.edu (original) (raw)

Papers by Dietmar Schomburg

Research paper thumbnail of Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful

Perspectives in Science, 2014

Research paper thumbnail of A large-scale protein-function database

Nature Chemical Biology, 2010

Research paper thumbnail of Oxidative Stickland reactions in an obligate aerobic organism - amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus

The FEBS journal, 2017

The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adapt... more The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adaptation to extreme environments and renowned for its ability to degrade a broad variety of substrates. It has been well characterised concerning the utilisation of numerous carbohydrates as carbon source. However, its amino acid metabolism, especially the degradation of single amino acids, is not as well understood. In this work, we performed metabolic modelling as well as metabolome, transcriptome and proteome analysis on cells grown on caseinhydrolysate as carbon source in order to draw a comprehensive picture of amino acid metabolism in S. solfataricus P2. We found that 10 out of 16 detectable amino acids are imported from the growth medium. Overall, uptake of glutamate, methionine, leucine, phenylalanine and isoleucine was the highest of all observed amino acids. Our simulations predict an incomplete degradation of leucine and tyrosine to organic acids, and in accordance with this, we ...

Research paper thumbnail of BRENDA in 2017: new perspectives and new tools in BRENDA

Nucleic acids research, Jan 4, 2017

The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme... more The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence. The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. Approximately 3 million data from 83 000 enzymes and 137 000 literature references constitute the manually annotated core. Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data. Prediction algorithms contribute locations and genome annotations. External data and links complete the data with sequences and 3D structures. A total of 206 000 enzyme ligands provide functional and structural data. BRENDA offers a complex query tool engine allowing the users an efficient access to the data via different search methods and explorers. The new design of the BRENDA entry page and the enzyme summary pages improves the user a...

Research paper thumbnail of A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeonSulfolobus solfataricusin response to the carbon source L-fucose versus D-glucose

Molecular Microbiology, 2016

Research paper thumbnail of BRENDA in 2015: exciting developments in its 25th year of existence

Nucleic Acids Research, 2014

Research paper thumbnail of Optimised amino acid specific weighting factors for unbound protein docking

Research paper thumbnail of Class 2–3.2 Transferases, Hydrolases

ABSTRACT EC number 2.4.2.41 Systematic name UDP-d-xylose:xylogalacturonan β-1,3-xylosyltransferas... more ABSTRACT EC number 2.4.2.41 Systematic name UDP-d-xylose:xylogalacturonan β-1,3-xylosyltransferase Recommended name xylogalacturonan β-1,3-xylosyltransferase Synonyms Xgd1 [1]

Research paper thumbnail of Enzyme databases

Methods in Molecular Biology, 2010

Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a ke... more Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a key role in the regulation of metabolic steps within the cells, as drug targets, and in a wide range of biotechnological applications. With respect to reaction type, they are grouped into six classes, namely oxidoreductases, transferases, hydrolases, lyases, and ligases. EC-Numbers are assigned by the IUBMB. Enzyme functional databases cover a wide range of properties and functions, such as occurrence, kinetics of enzyme-catalyzed reactions, structure, or metabolic function. BRENDA stores a large variety of different data for all classified enzymes whereas KEGG, MEROPS, MetaCyc, REBASE, CAzy, ESTHER, PeroxiBase, and KinBase specialize in either certain aspects of enzyme function or specific enzyme classes, organisms, or metabolic pathways. Databases covering enzyme nomenclature are ExplorEnz, SIB-ENZYME, and IntEnz.

Research paper thumbnail of BRENDA, enzyme data and metabolic information

Nucleic Acids Research, 2002

Research paper thumbnail of The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

Nucleic Acids Research, 2011

Research paper thumbnail of BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

Nucleic Acids Research, 2013

Research paper thumbnail of Automatic assignment of reaction operators to enzymatic reactions

Research paper thumbnail of BRENDA, the enzyme information system in 2011

Nucleic Acids …, 2011

The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information syste... more The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community. The majority of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. The number of manually annotated references increased by 30% to more than 100 000, the number of ligand structures by 45% to almost 100 000. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models.

Research paper thumbnail of BRENDA, the enzyme database: updates and major new developments

Research paper thumbnail of Experimental Enzyme Data as Presented in Brenda-A Database for Metabolic Research, Enzyme Technology and Systems Biology

BRENDA represents the most comprehensive information system on enzyme and metabolic information, ... more BRENDA represents the most comprehensive information system on enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation, and

Research paper thumbnail of BRENDA: a resource for enzyme data and metabolic information

Research paper thumbnail of BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

Nucleic Acids Research, 2009

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest ... more The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system contain- ing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calcu- lating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants

Research paper thumbnail of Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine

The number of fully sequenced genomes available is rapidly increasing, and experiments are underw... more The number of fully sequenced genomes available is rapidly increasing, and experiments are underway to get quantitative information of the transcription and expression of the different gene products. As this is progressing and projects on structural genomics are starting, the lack ...

Research paper thumbnail of STRENDA DB: enabling the validation and sharing of enzyme kinetics data

The FEBS journal, Jan 2, 2018

Standards for reporting enzymology data (STRENDA) DB is a validation and storage system for enzym... more Standards for reporting enzymology data (STRENDA) DB is a validation and storage system for enzyme function data that incorporates the STRENDA Guidelines. It provides authors who are preparing a manuscript with a user-friendly, web-based service that checks automatically enzymology data sets entered in the submission form that they are complete and valid before they are submitted as part of a publication to a journal.

Research paper thumbnail of Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful

Perspectives in Science, 2014

Research paper thumbnail of A large-scale protein-function database

Nature Chemical Biology, 2010

Research paper thumbnail of Oxidative Stickland reactions in an obligate aerobic organism - amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus

The FEBS journal, 2017

The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adapt... more The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adaptation to extreme environments and renowned for its ability to degrade a broad variety of substrates. It has been well characterised concerning the utilisation of numerous carbohydrates as carbon source. However, its amino acid metabolism, especially the degradation of single amino acids, is not as well understood. In this work, we performed metabolic modelling as well as metabolome, transcriptome and proteome analysis on cells grown on caseinhydrolysate as carbon source in order to draw a comprehensive picture of amino acid metabolism in S. solfataricus P2. We found that 10 out of 16 detectable amino acids are imported from the growth medium. Overall, uptake of glutamate, methionine, leucine, phenylalanine and isoleucine was the highest of all observed amino acids. Our simulations predict an incomplete degradation of leucine and tyrosine to organic acids, and in accordance with this, we ...

Research paper thumbnail of BRENDA in 2017: new perspectives and new tools in BRENDA

Nucleic acids research, Jan 4, 2017

The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme... more The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence. The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. Approximately 3 million data from 83 000 enzymes and 137 000 literature references constitute the manually annotated core. Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data. Prediction algorithms contribute locations and genome annotations. External data and links complete the data with sequences and 3D structures. A total of 206 000 enzyme ligands provide functional and structural data. BRENDA offers a complex query tool engine allowing the users an efficient access to the data via different search methods and explorers. The new design of the BRENDA entry page and the enzyme summary pages improves the user a...

Research paper thumbnail of A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeonSulfolobus solfataricusin response to the carbon source L-fucose versus D-glucose

Molecular Microbiology, 2016

Research paper thumbnail of BRENDA in 2015: exciting developments in its 25th year of existence

Nucleic Acids Research, 2014

Research paper thumbnail of Optimised amino acid specific weighting factors for unbound protein docking

Research paper thumbnail of Class 2–3.2 Transferases, Hydrolases

ABSTRACT EC number 2.4.2.41 Systematic name UDP-d-xylose:xylogalacturonan β-1,3-xylosyltransferas... more ABSTRACT EC number 2.4.2.41 Systematic name UDP-d-xylose:xylogalacturonan β-1,3-xylosyltransferase Recommended name xylogalacturonan β-1,3-xylosyltransferase Synonyms Xgd1 [1]

Research paper thumbnail of Enzyme databases

Methods in Molecular Biology, 2010

Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a ke... more Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a key role in the regulation of metabolic steps within the cells, as drug targets, and in a wide range of biotechnological applications. With respect to reaction type, they are grouped into six classes, namely oxidoreductases, transferases, hydrolases, lyases, and ligases. EC-Numbers are assigned by the IUBMB. Enzyme functional databases cover a wide range of properties and functions, such as occurrence, kinetics of enzyme-catalyzed reactions, structure, or metabolic function. BRENDA stores a large variety of different data for all classified enzymes whereas KEGG, MEROPS, MetaCyc, REBASE, CAzy, ESTHER, PeroxiBase, and KinBase specialize in either certain aspects of enzyme function or specific enzyme classes, organisms, or metabolic pathways. Databases covering enzyme nomenclature are ExplorEnz, SIB-ENZYME, and IntEnz.

Research paper thumbnail of BRENDA, enzyme data and metabolic information

Nucleic Acids Research, 2002

Research paper thumbnail of The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

Nucleic Acids Research, 2011

Research paper thumbnail of BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

Nucleic Acids Research, 2013

Research paper thumbnail of Automatic assignment of reaction operators to enzymatic reactions

Research paper thumbnail of BRENDA, the enzyme information system in 2011

Nucleic Acids …, 2011

The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information syste... more The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community. The majority of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. The number of manually annotated references increased by 30% to more than 100 000, the number of ligand structures by 45% to almost 100 000. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models.

Research paper thumbnail of BRENDA, the enzyme database: updates and major new developments

Research paper thumbnail of Experimental Enzyme Data as Presented in Brenda-A Database for Metabolic Research, Enzyme Technology and Systems Biology

BRENDA represents the most comprehensive information system on enzyme and metabolic information, ... more BRENDA represents the most comprehensive information system on enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation, and

Research paper thumbnail of BRENDA: a resource for enzyme data and metabolic information

Research paper thumbnail of BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

Nucleic Acids Research, 2009

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest ... more The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system contain- ing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calcu- lating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants

Research paper thumbnail of Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine

The number of fully sequenced genomes available is rapidly increasing, and experiments are underw... more The number of fully sequenced genomes available is rapidly increasing, and experiments are underway to get quantitative information of the transcription and expression of the different gene products. As this is progressing and projects on structural genomics are starting, the lack ...

Research paper thumbnail of STRENDA DB: enabling the validation and sharing of enzyme kinetics data

The FEBS journal, Jan 2, 2018

Standards for reporting enzymology data (STRENDA) DB is a validation and storage system for enzym... more Standards for reporting enzymology data (STRENDA) DB is a validation and storage system for enzyme function data that incorporates the STRENDA Guidelines. It provides authors who are preparing a manuscript with a user-friendly, web-based service that checks automatically enzymology data sets entered in the submission form that they are complete and valid before they are submitted as part of a publication to a journal.