Tag: molecular interaction

Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.

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 ...

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

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 ...

Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...

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 ...

InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactio ...

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.

BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interacti ...

ProteomicsDB is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of ...

PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.

The PSI-MI interchange format and accompanying controlled vocabularies was originally designed by a consortium of molecular interaction data providers from both academia and industry, including BIND, DIP, IntAct, MINT, MIPS, GlaxoSmithKline, CellZome ...

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.

NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytosc ...

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 ...

MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and m ...

MIMIx is a community guideline advising the user on how to fully describe a molecular interaction experiment and which information it is important to capture. The document is designed as a compromise between the necessary depth of information to desc ...

The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles ( ...

The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

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 ...

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondin ...

AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transc ...

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins.

The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.

The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is fr ...

The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing sta ...

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 ...

The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces ...

Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS) is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and c ...

The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research ...

The MITAB27 format is an extension of the PSI-MI 2.5 (1) and 2.6 standard. It has been derived from the tabular format provided by BioGrid. MITAB27 only describes binary interactions, with one pair of interactors per row.

MIABE is intended to be used as a guideline which should be consulted prior to the publication of data describing small molecules and their interactions with one or more target molecules. It was developed by representatives of pharmaceutical companie ...

HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad ...

Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.

TargetMine integrates many types of data for human, rat and mouse. Flexible queries, export of results and data analysis are available.

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome ...

ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.

The Human Transcriptional Regulation Interactions database (HTRIdb) is a repository of experimentally verified interactions among human transcription factors (TFs) and their respective target genes. It has been constructed to be an open-access and us ...

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 ...

The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest.

The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also ...

IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature) is a collection of experimentally-verified intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. IDEAL ...

TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiati ...

Collaborative resource for the Bacillus community.

Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.

BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-cura ...

Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...

iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, M ...

The Leaf Senescence Database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. LSD includes data types such as leaf senescence-associated transcriptomics, phenotype and interaction data.

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 purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic techno ...

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

PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. Both a command-line tool and a web-server are available.

The Interaction Network Ontology (INO) aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It models general interactions (e.g., molecular interactions) and interact ...

The scopes of molecular interactions and protein affinity reagents are largely overlapping but are also partially unique. This fact is reflected in the PSI-PAR CV, which contains the majority of the terms from the PSI-MI CV and an additional ∼200 new ...

The dbDEPC is a database of differentially expressed proteins in human cancers.

ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.

Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.

Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molec ...

A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative. The Molecular Interactions Working group page can be found at http://www.psidev.i ...

Human Integrated Pathway Database (hiPathDB) provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. The entity-level integration creates a super ...

The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.

SNAPPI-DB is an object-oriented database of domain-domain interactions observed in structural data. The structural data is obtained from the MSD data warehouse as the MSD provides consistent data with links to many types of data about proteins and nu ...

A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.

The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.

RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data.

wiki-pain.org is a wiki containing molecular interactions that are relevant to pain. Each molecular interaction is shown in relation to pain, disease, mutations, anatomy and a summary of its mentions throughout the literature is provided.

MONOCLdb is an integrative and interactive database designed to retrieve and visualize annotations and expression profiles of long-non coding RNAs (lncRNAs) expressed in Collaborative Cross (http://compgen.unc.edu/) founder mice in response to respir ...

The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has incorporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed following the OBO Foundry principle ...

MolMeDB is an open chemistry database concerning the interaction of molecules with membranes.

The pharmacovigilance ontology connects known facts on drugs, disease, ADEs, and their molecular mechanisms.

SupraBank is a resource for intermolecular interactions, in particular host:guest but also ligand:protein and polymer interactions as well as surface adsorption processes. The reporting of conditions during the analysis of intermolecular interactions ...

Database of MacroMolecular INteractions

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) guidelines describe the minimum and necessary information to depict causal interactions in molecular biology, as well as contextual details. The aim is to homogenize the ...

The aim of the Unified Data Model (UDM) project is to create and publish an open and freely available data format for storage and exchange of experimental information about compound synthesis and biological testing. Originally maintained by Elsevier, ...