Tag: enzyme

Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the re ...

STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synth ...

The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.

The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps ...

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

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-ca ...

A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequen ...

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that ...

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughou ...

BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. Our current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model ...

The Protein Circular Dichroism Data Bank (PCDDB) is an open-access online repository for protein circular dichroism spectral- and meta-data. Users may freely extract and deposit validated data and the validation process is conveniently integrated int ...

ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each t ...

STRENDA stands for “Standards for Reporting Enzymology Data”. For researchers it is essential to be able to compare, evaluate, interpret and reproduce experimental research results published in the literature and databases. Thus, for enzyme research, ...

SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification ...

Structure Function Linkage Database (SFLD) is a database of enzymes classified by linking sequences to chemical function. A hierachical systems is used to classify enzymes by family or superfamily other category levels include functional domain, subg ...

SignaLink is an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. it allows browsing of signaling pathways, cross-talks and multi-pathway proteins; selection of transcriptional, post- ...

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of hundreds of organisms with completely sequenced genomes. Each database contains the genome, predicted metabolic pathways, p ...

DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...

This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, using UniRef50 clusters.

HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.

Manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.

CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology pr ...

The Protein Structural Change DataBase (PSCDB) presents the structural changes found in proteins, represented by pairs of ligand-free and ligand-bound structures of identical proteins, and links these changes to ligand-binding.

The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of informa ...

The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textboo ...

ChannelsDB is a comprehensive and regularly updated resource of channels, pores and tunnels found in biomacromolecules deposited in the Protein Data Bank.

In English, PRIAM stands for enzyme-specific profiles for metabolic pathway prediction. PRIAM is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.

Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.

SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.

The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. ...

M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA: 'Detailed mechanism' entries are mor ...

KiMoSys is a user-friendly platform that includes a public data repository of relevant published measurements, including metabolite concentrations (time-series and steady-state), flux data, and enzyme measurements in order to build ODE-based kinetic ...

The Enzyme Portal is for those interested in the biology of enzymes and proteins with enzymatic activity. It integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds. It contai ...

KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. This resources provides plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme ...

The Enzyme Database was developed as a new way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards.

CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, pro ...

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the EAWAG-BBD is to provide information on microbial enzyme-catalyzed reactions that are impo ...

Enzymes are nature's catalysts, essential for the chemistry of life. Industrially relevant applications range from food science to laundry. We have now released MACiE, an electronic database of well-characterised enzymatic reactions. MACiE is the res ...

The "Enzyme Mechanism Ontology " describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.

Thioester-active enzymes

mycoCLAP is a searchable resource for the knowledge and annotation of Characterized Lignocellulose-Active Proteins of fungal origin.

Metagenomic BioMining Engine: homologs of commercially useful enzymes in metagenomic datasets

Experimentally Characterized Protein annotations

The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional an ...

In silico drug docking against SARS-CoV2 targets

Comprehensive database of fragments linking metabolites, toxic molecules and drugs

STRENDA DB is a storage and search platform supported by the Beilstein-Institut that incorporates the STRENDA Guidelines in a user-friendly, web-based system. If you are an author who is preparing a manuscript containing functional enzymology data, S ...

The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcript ...

DNAzymes i.e. DNA molecules with catalytic activity

A genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. An on-line source for Mycobacterium abscessus modeled structural proteome. MabeLLINI ...

BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are tre ...

Conserved Unique Peptide Patterns (CUPP) is a approach for sequence analysis employing conserved peptide patterns for determination of similarities between proteins. CUPP performs unsupervised clustering of proteins for formation of protein groups an ...

AcetoBase is a dedicated repository and curated database for the analysis of acetogenic bacteria based on the key functional gene formyltetrahydrofolate synthetase (FTHFS/fhs) of Wood-Ljungdahl Pathway for Acetogenesis.

Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online re ...

OGT Protein Interaction Network (OGT-PIN) is a curated and comprehensive database of experimentally identified interaction proteins of OGT and its orthologues in multiple species studied in the past several decades.

an integrated resource for glycosyltransferase sequences and annotations. Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natu ...

a manually curated database of lysosomal enzymes associated with rare diseases. RareLSD: Database for Human Lysosomal Enzymes. RareLSD: A Database for Human Lysosomal Enzymes. RareLSD is a manually curated database of 63 lysosomal enzymes present i ...

a database of promiscuous proteins. Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing c ...

D3DistalMutation is a database to explore the effect of distal mutations on enzyme activity. In general, D3DistalMutation describes the effect of distal mutation (mutations more than 10 Å away from the active site) on enzyme activity and classified e ...

A comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species.

FermFooDb is a database of peptides derived from fermented foods contains 2325 entries of unique peptides from the fermented foods.

A database for improving the rational design of glucose-tolerant β-glucosidases. A database of mutant β-glucosidases. Glutantbase is a database, webtool and method to evaluate mutations for β-glucosidases proteins used in industrial applications. G ...

A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules.

an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific per ...

new binding kinetics database and its integration in an open-source binding analysis software. Kinetics OF Featured Interactions. KOFFI-DB (???) is an article based database for kinetic constants of biomolecular interactions. We focused on interact ...

In its report in 1961, the first Enzyme Commission devised a system for enzyme classification that also serves as a basis for assigning code numbers. These code numbers, prefixed by EC, contain four elements separated by points / full stops and are n ...

IND-enzymes is a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage.

YeastCyc is a Pathway/Genome Database of the model eukaryote Saccharomyces cerevisiae S288c. In addition to genomic information, the database contains metabolic pathway, reaction, enzyme, and compound information, which has been manually curated from ...

A web application gathering information about food enzyme preparations available on the European market.

A curated RNA-seq database of palmitoylating and de-palmitoylating enzyme expression in the mouse brain.

!!! >>> the repository is offline >>> !!! GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on represent ...

The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in p ...

The Alberta Food Composition Database (AFCDB) is the first comprehensive resource on food constituents, chemistry and biology dedicated to major Alberta-grown produce. It provides information on both macronutrients and micronutrients, including many ...

Formerly known as mycoCLAP, CLAE is a curated database of Characterized Lignocellulose-Active Enzymes

A webtool to identify and analyze bacterial microcompartment types in sequence data.

A database of microorganisms and proteins linked to plastic biodegradation.

DiZyme open access resource for quantitative prediction of nanozyme catalytic activity

Sift-PUL database is a public repository providing predicted PULs with specific functional annotations. The key difference between sift-PUL and other PUL databases (e.g. PULDB, CGCs and dbCAN-PUL) is the functional annotation for each predicted PUL.

Plant cytochrome P450 database and web-based tools for structural construction and ligand docking. It is a reliable template-based structure prediction method (PCPCM), and predicted the structures of 180 plant P450s with known functions. In addition, ...

The Bacterial Microcompartment Database. MCPdb – The Bacterial Microcompartment Databse. MCPDB A bacterial microcompartment database and structure viewer include Carboxysome Pdu Eut BMC BMV MCP organelle encapsulin protein capsid. MCPdb is an onli ...

EMBF is a database of enzymes of microalgal biofuel feedstock.

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products. decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER). Alexander M. Kloosterman, Peter Cimermancic, Somayah S. Elsayed, Chao ...

A database of monosaccharide biosynthesis pathways. Monosaccharide Biosynthesis Pathways Database. Pathways for monosaccharide biosynthesis. Welcome to MonoPathDB, a database of biosynthesis pathways and enzymes for monosaccharides.