Tag: metabolic and signaling pathways

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

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.

IntAct provides a database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. IntAct (with MINT) is a Core Data Resource of ELIXIR. IntAct contains data from all ...

MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT ...

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 PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...

MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological ro ...

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.

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

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely av ...

The Metabolomics Workbench serves as a national and international repository for metabolomics data and metadata and provides analysis tools and access to metabolite standards, protocols, tutorials, training, and more.

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

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 ...

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, ...

VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.

Thermodynamics calculator for biochemical reactions. eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provi ...

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, su ...

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 ...

BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.

TriTrypDB is one of the databases that can be accessed through the VEuPathDB portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these ...

The SIGnaling Network Open Resource. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are comp ...

VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions. vir ...

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. Meta ...

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

Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated ...

iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate, filter, browse, search, analyze, visualize ...

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 ...

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 ...

Database of interaction Hotspots across the proteome. Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Ho ...

HIPPIE integrates human protein-protein interactions from several manually curated source databases. It provides a web tool to query the interaction data, generate highly reliable, context-specific interaction networks and to make sense out of them.

KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase ...

Arabidopsis Protein Phosphorylation Site Database

PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins.

FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes compara ...

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

FunCoup is a framework to infer genome-wide functional couplings in 11 model organisms. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of d ...

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...

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

The SugarBind Database (SugarBindDB) was created in 2002 as part of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture technology based on the binding of viral, bacterial and biotoxin lectins to specific glycans ( ...

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 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 ...

SigMol is a specialized repository of quorom sensing signaling molecules (QSSMs) in prokaryotes. SigMol harbors information on QSSMs pertaining to different quorum sensing signaling systems namely acylated homoserine lactones (AHLs), diketopiperazine ...

DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. The database includes published and unpublished low and high throughput data sets, ...

The Library of Apicomplexan Metabolic Pathways (LAMP, http://www.llamp.net) is a web database that provides near complete mapping from genes to the central metabolic functions for some of the prominent intracellular parasites of the phylum Apicomplex ...

Protein interaction predictions by several different methods

Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.

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 ...

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 ...

Known and predicted protein domain interactions observed in PDB entries,

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.

Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. ...

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 ...

Allostery is the most direct and efficient way for regulation of biological macromolecule function induced by the binding of a ligand at an allosteric site topographically distinct from the orthosteric site. Due to the inherent high receptor selectiv ...

Evolution of protein-protein Interfaces InterEvol is a resource for researchers to investigate the structural interaction of protein molecules and sequences using a variety of tools and resources.

UniPathway (http://www.unipathway.org) is a fully manually curated resource for the representation and annotation of metabolic pathways. UniPathway provides explicit representations of enzyme-catalyzed and spontaneous chemical reactions, as well as a ...

Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites

Data Repository for Yeast Genetic Interaction Networks

Protein Common Interface Database

A database of non-interacting proteins

Quality assessed protein-protein interactions in 9 species

A non-redundant database of protein-peptide complexes

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 ...

Regulatory Network in Protein Phosphorylation

Predicted Arabidopsis Interactome Resource

Prokaryotic 2-Component Systems database

DNA repair pathways of human, yeast and E.coli

Kazusa Plant Pathway Viewer

Domain interaction map: experimental and predicted protein domain interactions

IsoRank PPI Network Alignment Based Ortholog Database

Mouse Multiple Tissue Metabolomics Database

Integration, navigation, visualization, and analysis of gene interaction networks. This record has been marked as "Uncertain" because its homepage no longer exists. If you have any information on the current status of this resource, please contact us ...

Arabidopsis thaliana Protein Interactome Database

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

Genome-WIde Docking Database: 3D structures of protein complexes

The Dynamic Proteomics database is a compendium of endogenously YFP-tagged human proteins and their time-lapse microscopy movies. These movies show the protein dynamics in space and in time in individual living human cancer cells in response to an an ...

Protein-protein interactions for mammalian TRP channels

Database for integration of human functional interactions

Crosstalk among signaling pathways

Interacting and non-interacting protein pairs

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator cu ...

Presaging Critical Residues in Protein interface DataBase

FCP is a publicly accessible web tool dedicated to analysing the current state and trends on the population of available structures along the classification schemes of enzymes and nuclear receptors, offering both graphical and quantitative data on th ...

Binary SubComplexes in Proteins Database

A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

The signal molecules and pathways are classified and illustrated by graphs in this database.

NCI-Nature Pathway Interaction Database

Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling

Domain peptide interactions

A database of quorum-sensing peptides

The compartmentalized protein-protein interaction database (ComPPI), provides qualitative information on the interactions, proteins and their localizations integrated from multiple databases for protein-protein interaction network analysis.

Online maps of metabolic and signaling pathways

A database of RNA processing pathways

Proteolysis Map

Escherichia coli Metabolome Database

Integrated access to various metabolic databases

Microbial PKS/NRPS Biosynthesis

Circadian Gene database

Pathways of age-related processes

Protein domain interactions and interfaces

Carbon flux data of central metabolism in various organisms

Curated information about biodegradation-related genes and proteins

Pathway data integration and analysis portal

Moonlighting Proteins DataBase

Disease Chemical Biology Database

A database on the structural synaptome

Thermodynamics of enzyme-catalyzed reactions

Network approach to human protein kinases and their substrate proteins

Chromatin Regulators and histone modifications in human and mouse

Predicted human protein-protein interactions

Macromolecular complexes from key model organisms

Enzyme Catalytic Mechanism Database

Binding Mother of All Databases: a database of protein-ligand crystal structures

Protein-protein interactions involving PDZ domains

Putative protein domain interactions

Predicted and experimentally determined protein-protein interactions for yeast and human

Protein cognate ligands for the domains in enzyme structures

Protein-protein interfaces in co-crystallized protein structures

Joint Evolutionary Trees: Protein-protein interaction patches in known structures

Hot spots (functionally and structurally important residues) in protein interfaces

Human protein interactions mediated by phosphoprotein-binding domains

Genes and proteins involved in human and yeast cell cycle

Database of protein interactions in Helicobacter pylori

Host-pathogen protein-protein interactions

Protein-protein interactions in various evolutionary lineages

SYSTOMONAS (SYSTems biology of pseudOMONAS, http://www.systomonas.de) is a database on pseudomonads providing data and tools on metabolic network reconstruction, gene-regulatory networks, visualization of genomic structures or metabolic pathways, com ...

Human protein interaction database

Enzyme active sites and catalytic residues in enzymes of known 3D structure

Interacting residues in protein-protein interfaces in PDB

Pathguide: the Pathway Resource List (http://pathguide.org) is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic pathways, signaling pathways, tran ...

Protein-protein interactions mediated by interchain beta-sheet formation

SCOPPI is a database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain associations and are annotated with various in ...

The Protein Kinase Resource (PKR) is a curated information source which provides an integrated view of sequence and structure data combined with biochemical and genetic function data focused on a single family of proteins, the protein kinases. In add ...

TRANSPATH® is a database on signal transduction pathways that are modeled as bipartite graphs with molecules and reactions as node classes [1,2,3,4,5]. The molecule entries include polypeptides, modified forms, multicomponent complexes, high-order ab ...

The Affinity Database 'AffinDB' contains affinity data for protein-ligand complexes of the PDB. Its purpose is to provide direct and free access to the experimental affinity of a given complex structure. As of Monday, November 28th, 2005, AffinDB con ...

The most commonly employed analytical tools used in high-throughput metabolic profiling, known as metabolomics or metabonomics, are nuclear magnetic resonance (NMR) and mass spectrometry (MS). However, bioinformatics resources for identifying common ...

Wnt proteins form a family of highly conserved secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Wnt genes and Wnt signaling are also implicated in cancer. Insights into the mechanisms of Wnt action have emerg ...

More than one third of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) are found to be not associated with any amino acid sequence in public database ...

PathoPlant® has been developed as a relational database to display relevant components and reactions involved in signal transduction related to plant-pathogen interactions. Signal transduction pathways are modeled as consecutive sequences of known m ...

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways, and kinetic characteristics of elementary processes. In the past two years, the GeneNet structure was considerably im ...

EndoNet is a new database that provides information about the components of endocrine networks and their relations. It focuses on the endocrine cell-to-cell communication and enables the analysis of intercellular regulatory pathways in humans. In the ...

WholeCellKB is a collection of open-access model organism databases specifically designed to enable whole-cell models. Currently, WholeCellKB contains a database of Mycoplasma genitalium, a Gram-positive bacterium and common human pathogen. The M. ge ...

SENTRA (http://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html) is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and meth ...

Better characterization of binding sites in proteins and the ability to accurately predict their location and energetic properties are major challenges which, if addressed, would have many valuable practical applications. Unfortunately, reliable benc ...

High-throughput experiments are being performed at an ever-increasing rate to systematically elucidate protein-protein interaction (PPI) networks for model organisms, while similar experiments for human networks have lagged far behind. The Online Pre ...

CellCircuits (http://www.cellcircuits.org) is an open-access database of molecular network models, designed to bridge the gap between databases of individual pair-wise molecular interactions and databases of validated pathways. CellCircuits captures ...

The first release of Protein-protein Interactions Thermodynamic Database (PINT) contains more than 1500 data of several thermodynamic parameters along with sequence and structural information, experimental conditions and literature information. Each ...

Systematic mapping of protein-protein interactions (PPIs) has become a central task of functional genomics. To map the human interactome, several strategies have recently been pursued. The generated interaction datasets are valuable resources for sci ...

The Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) is responsible for the maintenance of the enzyme list first published in 1961 and with the last printed edition in 1992 (1). Since 1992 the list ha ...

The ModelSEED (https://modelseed.org) biochemistry database serves as the foundation of biochemical data underlying the in-silico reconstruction of metabolism in ModelSEED and KBase (https://kbase.org). The database is continually updated with improv ...

Het-PDB Navi is a database that collects small molecules found in Protein Data Bank (PDB). An atomic reality of protein function is based on interactions between a protein and another molecule. One of the approaches to assume protein functions from t ...

The Noncoding RNAs and Protein related biomacromolecules Interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents experimentally determined functional interactions between nonc ...

G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GLIDA is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information ...

Structural motifs are central to the integrity of the fold and require careful analysis for their identification. IMOTdb is a repertoire of spatially interacting motifs in single protein structures as well as those among distantly related protein str ...

Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals ...

In past number of databases (e.g. MHCPEP, MHCBN, AntijenDB, IEDB, BCIPEP, IMGT) have been developed to assists the researchers working in the field of adaptive immunity. Best of author’s knowledge no method have been developed in the field of ...

The reversible phosphorylation of proteins is one of the most important post-translational modifications, which is involved in varieties of cellular processes and plays a critical role in activation, inactivation and regulation of proteins. Two types ...