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Enzyme databases | Protein sequence analysis

Enzymes make the wonderful diversity of life possible, from thermophiles that exist under incredibly harsh conditions to the complexity of higher organisms, such as humans. However, despite their importance and our continued fascination with these…
MEROPS
Dataset

MEROPS

An integrated source of information about peptidases, their substrates and…

An integrated source of information about peptidases, their substrates and inhibitors, which are of great relevance to biology, medicine and biotechnology. The hierarchical classification of the…

BRENDA
Dataset

BRENDA BRaunschweig ENzyme DAtabase

Contains manually annotated literature-based data on a wide range of aspects of…

Contains manually annotated literature-based data on a wide range of aspects of enzyme function, their metabolic role, involvement in disease processes, genomic and protein sequences, and enzyme…

BTO
Dataset

BTO BRENDA Tissue Ontology

Gathers annotated literature-based data on enzyme and enzyme-ligand. BTO…

Gathers annotated literature-based data on enzyme and enzyme-ligand. BTO contains information about manually curated of more than 82 00 enzymes and about 7.2 million enzyme sequences from UniProt.…

CSA
Dataset

CSA Catalytic Site Atlas

A database documenting enzyme active sites and catalytic residues in enzymes of…

A database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be…

CAZy
Dataset

CAZy Carbohydrate-Active Enzymes database

Describes the families of structurally-related catalytic and…

Describes the families of structurally-related catalytic and carbohydrate-binding modules of enzymes that degrade, modify or create glycosidic bonds. CAZY is a knowledge-based resource that aims to…

ENZYME
Dataset

ENZYME Enzyme nomenclature database

Contains information related to the nomenclature of enzymes. ENZYME is…

Contains information related to the nomenclature of enzymes. ENZYME is structured so, it is usable by human readers as well as by computer programs. It describes each type of characterized enzyme for…

dbCAN
Dataset

dbCAN

A web server and DataBase for automated Carbohydrate-active enzyme ANnotation,…

A web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE.

IntEnz
Dataset
FunTree
Dataset

FunTree

A resource that brings together protein sequence, structure and functional…

A resource that brings together protein sequence, structure and functional information, including overall chemical reaction and mechanistic data, for structurally defined domain superfamilies.…

Degradome…
Dataset

Degradome database

Contains the results of the manual annotation of every protease gene in the…

Contains the results of the manual annotation of every protease gene in the genomes of human, chimpanzee, mouse, and rat, along with relationships between protease alterations and hereditary…

ExplorEnz
Dataset

ExplorEnz

Developed at Trinity College Dublin in 2005 as a new way to access the data of…

Developed at Trinity College Dublin in 2005 as a new way to access the data of the IUBMB Enzyme Nomenclature List.

MACiE
Dataset
KinMap
Web

KinMap

Facilitates the interactive navigation through kinase knowledge by linking…

Facilitates the interactive navigation through kinase knowledge by linking biochemical, structural, and disease association data to the human kinome tree. KinMap represents a new generation of kinome…

GPS-CCD
Desktop
Web

GPS-CCD Calpain Cleavage Detector

Predicts calpain cleavage sites. GPS-CCD is a computational program that was…

Predicts calpain cleavage sites. GPS-CCD is a computational program that was used to annotate potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites…

BYKdb
Dataset

BYKdb The Bacterial protein tYrosine-Kinase database

Provides information about Bacterial tyrosine kinase (BYK) sequences with…

Provides information about Bacterial tyrosine kinase (BYK) sequences with standardized annotations, updated on a monthly basis. BYKdb is divided in two parts: the static part includes general…

Rhea
Dataset

Rhea

A comprehensive and non-redundant resource of expert-curated biochemical…

A comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea…

TECRDB
Dataset

TECRDB Thermodynamics of Enzyme-Catalyzed Reactions DataBase

A comprehensive collection of thermodynamic data on enzyme-catalyzed reactions.…

A comprehensive collection of thermodynamic data on enzyme-catalyzed reactions. The data, which consist of apparent equilibrium constants and calorimetrically determined molar enthalpies of reaction,…

CAT
Dataset

CAT CAZymes Analysis Toolkit

A repository of tools for analysis and annotation of CAZYmes (Carbohydrate…

A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes).

PhosphoPOINT
Dataset

PhosphoPOINT

Provides a human kinase interactome resource. PhosphoPOINT is a comprehensive…

Provides a human kinase interactome resource. PhosphoPOINT is a comprehensive human kinase interactome and phospho-protein database. This database integrates phospho-proteins, serine/…

DEPOD
Dataset

DEPOD DEPhOsphorylation Database

An online resource with information about active human phosphatases, their…

An online resource with information about active human phosphatases, their substrates, and the pathways in which they function. The database includes links to kinases and chemical modulators of…

CyanoLyase
Dataset

CyanoLyase

A manually curated sequence and amino acid motif database gathering all the…

A manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases. CyanoLyase provides an extensive…

EzCatDB
Dataset

EzCatDB

It has emphasized manual classification of enzyme reactions from the viewpoints…

It has emphasized manual classification of enzyme reactions from the viewpoints of enzyme active-site structures and their catalytic mechanisms based on literature information, amino acid sequences…

CleavPredict
Web

CleavPredict

A web application for substrate cleavage prediction for matrix…

A web application for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic…

ECDomainMiner
Dataset

ECDomainMiner

Automatically infers associations between enzyme commission (EC) numbers and…

Automatically infers associations between enzyme commission (EC) numbers and Pfam domains. ECDomainMiner finds a total of 20,728 non-redundant EC-Pfam associations with a F-measure of 0.95 with…

CaMPDB
Web
ProKinO
Dataset

ProKinO

An ontological framework for integrating and conceptualizing diverse forms of…

An ontological framework for integrating and conceptualizing diverse forms of information related to kinase activation and regulatory mechanisms in a machine readable, human understandable form. You…

EKPD
Dataset

EKPD Eukaryotic protein Kinase and protein Phosphatase Database

A hierarchical database of eukaryotic protein kinases (PKs) and protein…

A hierarchical database of eukaryotic protein kinases (PKs) and protein phosphatases (PPs), the key molecules responsible for the reversible phosphorylation of proteins that are involved in almost…

Kinome Render
Web
Desktop

Kinome Render

It enables the annotation of the human kinome tree while reducing the amount of…

It enables the annotation of the human kinome tree while reducing the amount of work involved and the risk of errors. Kinome Render works by overlaying annotations of specific kinases on a template…

dEMBF
Dataset

dEMBF Database of Enzymes of Microalgal Biofuel Feedstock

The first curated and integrated web-based relational database on the entire…

The first curated and integrated web-based relational database on the entire repertoire of enzymes responsible for lipid synthesis in microalgae. dEMBF catalogues the complete list of identified…

GASS-WEB
Web

GASS-WEB Genetic Active Site Search-WEB

Can use catalytic and binding sites templates to search similar sites in a…

Can use catalytic and binding sites templates to search similar sites in a protein. GASS-WEB is a free and a user-friendly web server created for searching similar active sites based on data from the…

GASS
Desktop

GASS Genetic Active Site Search

A heuristic method which searches for given active site 3D templates in unknown…

A heuristic method which searches for given active site 3D templates in unknown proteins. The method can perform non-exact amino acid matches (conservative mutations). GASS is able to find amino…

GALT protein…
Dataset

GALT protein database

A Web-accessible data repository for the storage and interrogation of…

A Web-accessible data repository for the storage and interrogation of structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), the impairment of which leads to…

ArchaeaFun
Web

ArchaeaFun

Detects and classifies enzymes from sequence alone. ArchaeaFun finds…

Detects and classifies enzymes from sequence alone. ArchaeaFun finds information on various post-translational and localizational aspects of the protein by querying feature prediction. This…

FUNGALOXPHOS
Dataset

FUNGALOXPHOS FUNGALOXPHOS

An integrated database for oxidative phosphorylation in fungi. FUNGALOXPHOS…

An integrated database for oxidative phosphorylation in fungi. FUNGALOXPHOS stores OXPHOS proteins encoded in fungal nuclear genomes and that incorporates tools for the extraction, classification and…

KinG
Dataset

KinG Kinases encoded in Genomes

This site provides a detailed classification based on sequence similarity of…

This site provides a detailed classification based on sequence similarity of eukaryotic protein kinases (Hanks and Hunter classification). The assignment of functional domains to the gene products…

ESTHER
Dataset

ESTHER ESTerases and alpha/beta-Hydrolase Enzymes and Relatives

It is dedicated to the analysis of proteins or protein domains belonging to the…

It is dedicated to the analysis of proteins or protein domains belonging to the superfamily of alpha/beta-hydrolases, exemplified by the cholinesterases.

Kinomer
Dataset

Kinomer

A continually updated resource where direct comparison of kinase sequences…

A continually updated resource where direct comparison of kinase sequences across kinase groups and across species can give insights into kinase function and evolution.

PlantsP
Dataset

PlantsP

Focuses on plant protein kinases and protein phosphatases.

Focuses on plant protein kinases and protein phosphatases.

Kinome NetworkX
Dataset

Kinome NetworkX

A systems biology-based framework to catalogue the human kinome, including 538…

A systems biology-based framework to catalogue the human kinome, including 538 kinase genes, in the broader context of the human interactome. This comprehensive human kinome interactome map sheds…

CaspDB
Dataset

CaspDB

Provides information about potential cleavage sites in a verified set of all…

Provides information about potential cleavage sites in a verified set of all human proteins collected in Uniprot and their orthologs, allowing for tracing of cleavage motif conservation. CaspDB also…

ENZYMAP
Dataset

ENZYMAP ENZYMatic Annotation Predictor

A technique to characterize and predict EC number changes based on annotations…

A technique to characterize and predict EC number changes based on annotations from UniProt/Swiss-Prot using a supervised learning approach. ENZYMAP has shown to be more accurate than DETECT, getting…

iCataly-PseAAC
Web

iCataly-PseAAC

Identifies enzymes catalytic sites using sequence evolution information. In the…

Identifies enzymes catalytic sites using sequence evolution information. In the prediction system, the peptide sample was formulated with sequence evolution information via grey system model GM(2,1).…

novPTMenzy
Dataset

novPTMenzy

Catalogs information on the sequence, structure, active site and genomic…

Catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation,…

A A A
The L.…
Dataset

The L. monocytogenes 10403S BioCyc database

A resource for researchers studying Listeria and related organisms. The L.…

A resource for researchers studying Listeria and related organisms. The L. monocytogenes 10403S BioCyc database allows users to (i) have a comprehensive view of all reactions and pathways predicted…

mycoCLAP
Dataset

mycoCLAP

A searchable database of fungal and bacterial genes encoding…

A searchable database of fungal and bacterial genes encoding lignocellulose-active proteins that have been biochemically characterized. All the biochemical properties and functional annotations…

CRpred
Desktop

CRpred

An accurate sequence-based method for the prediction of catalytic residues.…

An accurate sequence-based method for the prediction of catalytic residues. CRpred uses SVM classifier that takes five types of interpretable features, including (1) residue type, (2) PSSM values,…

KEA
Desktop
Web

KEA Kinase Enrichment Analysis

A web-based tool with an underlying database providing users with the ability…

A web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them. The system draws from several…

Kinannote
Desktop

Kinannote

Identifies and classifies protein kinases in a user-provided fasta file using…

Identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and…

PhosphoChain
Desktop

PhosphoChain Phosphorylation-driven Regulatory Chains

Predict kinases, phosphatases and chains of phosphorylation events in signaling…

Predict kinases, phosphatases and chains of phosphorylation events in signaling networks by combining mRNA expression levels of regulators and targets with a motif detection algorithm and optional…

HuPho
Dataset

HuPho Human Phosphatase portal

A website designed to facilitate the retrieval of information about human…

A website designed to facilitate the retrieval of information about human protein phosphatases. HuPho is designed to retrieve information about 245 proteins either containing a phosphatase domain or…

PROSPER
Web

PROSPER PROtease Specificity Prediction servER

An integrated feature-based server for in silico identification of protease…

An integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity…

HEMD
Dataset

HEMD Human Epigenetic Enzyme and Modulator Database

Provides a central resource for the display, search, and analysis of the…

Provides a central resource for the display, search, and analysis of the structure, function, and related annotation for human epigenetic enzymes and chemical modulators focused on epigenetic…

PlantCAZyme
Dataset

PlantCAZyme

A database built upon dbCAN (database for automated carbohydrate active enzyme…

A database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to…

EnzymeDetector
Dataset

EnzymeDetector

Provides a fast and comprehensive overview of the available enzyme function…

Provides a fast and comprehensive overview of the available enzyme function annotations for a genome of interest. The web interface allows the user to work with customisable weighting schemes and…

BKM-react
Dataset

BKM-react

Stores known enzyme-catalyzed and spontaneous reactions. BKM-react is an…

Stores known enzyme-catalyzed and spontaneous reactions. BKM-react is an integrated and non-redundant reaction database implementing a combined approach of structure and name based comparison.…

CAZy Tools
Desktop

CAZy Tools

These tools are to assist especially CAZyme researchers around the world with…

These tools are to assist especially CAZyme researchers around the world with an easy "one-click-get-all"-system, to get better access to the immense amount of data that is available in the…

KEGG ENZYME
Dataset

KEGG ENZYME

Offers Enzyme Nomenclature (EC number). KEGG ENZYME is a database with Enzyme…

Offers Enzyme Nomenclature (EC number). KEGG ENZYME is a database with Enzyme Commission (EC) number list given by the IUBMB Nomenclature Committee (formerly, Enzyme Commission) based on published…

Kinase SARfari
Dataset

Kinase SARfari

Provides a central resource for Protein Kinase knowledge. Kinase SARfari offers…

Provides a central resource for Protein Kinase knowledge. Kinase SARfari offers a chemogenomics research and discovery workbench for protein kinases. This database contains protein, compound and…

TREEspot
Mobile

TREEspot

Allows to fully visualize compound interactions across industries leading…

Allows to fully visualize compound interactions across industries leading kinase & bromodomain protein panels. TREEspot is a secure access, web-based, compound profile visualization tool for…

restover
Desktop

restover

Finds restriction enzymes producing a specific overhang. restover identifies…

Finds restriction enzymes producing a specific overhang. restover identifies restriction enzymes from the REBASE database that create the specified overhang sequence when they cut the input…

findkm
Desktop

findkm

Calculates and plots enzyme reaction data. findkm reads a file of enzymatic…

Calculates and plots enzyme reaction data. findkm reads a file of enzymatic reaction data (substrate concentration [S] versus reaction velocity [V]) and draws Michaelis Menten and Hanes Woolf plots…

pepdigest
Desktop

pepdigest

Reports on protein proteolytic enzyme or reagent cleavage sites. pepdigest is…

Reports on protein proteolytic enzyme or reagent cleavage sites. pepdigest is an Emboss tool that allows to input one or more protein sequences and to specify one proteolytic agent from a list, which…

redata
Desktop

redata

Retrieves information from REBASE restriction enzyme database. redata searches…

Retrieves information from REBASE restriction enzyme database. redata searches the REBASE database for information on a specified restriction enzyme. It writes an output file with information on the…

Enzyme Portal
Dataset

Enzyme Portal

Integrates publicly available information about enzymes and displays them in a…

Integrates publicly available information about enzymes and displays them in a unified user-friendly view. The Enzyme Portal searches major public resources including the UniProt Knowledgebase…

Kinase.com
Dataset

Kinase.com

Explores the functions, evolution and diversity of protein kinases, the key…

Explores the functions, evolution and diversity of protein kinases, the key controllers of cell behavior. We focus on the kinome, the full complement of protein kinases in any sequenced genome.

PlantPIs
Dataset

PlantPIs

An interactive web resource on Plant Protease Inhibitors. Contains information…

An interactive web resource on Plant Protease Inhibitors. Contains information extracted principally from MEROPS database, filtered, annotated and compared with data stored in other protein and gene…

REBASE
Dataset

REBASE

A comprehensive and fully curated database of information about the components…

A comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. REBASE contains fully referenced information about recognition and cleavage…

PRECISE
Dataset

PRECISE Predicted and Consensus Interaction Sites in Enzymes

A database of interactions between the amino acid residues of an enzyme and its…

A database of interactions between the amino acid residues of an enzyme and its ligands (substrate and transition state analogs, cofactors, inhibitors and products). All information on interactions…

PTP-central
Dataset

PTP-central

A comprehensive resource on eukaryotic protein tyrosine phosphatases (PTPs). It…

A comprehensive resource on eukaryotic protein tyrosine phosphatases (PTPs). It relies on the development of a novel computational method, called Y-Phosphatomer, for the genome-wide prediction of…

DegraBase
Dataset

DegraBase

Compiles 8090 unique N termini from 3206 proteins directly identified in…

Compiles 8090 unique N termini from 3206 proteins directly identified in subtiligase-based positive enrichment mass spectrometry experiments in healthy and apoptotic human cell lines. We include both…

PKR
Dataset

PKR Protein kinase resource

Provides an integrated view of the protein kinase superfamily by linking data…

Provides an integrated view of the protein kinase superfamily by linking data with their visual representation. Thus, human kinases can be mapped onto the human kinome tree via an interactive display.

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