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http://www.ebi.ac.uk/intact

Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.

Proper citation: IntAct (RRID:SCR_006944) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/cardiovasculargeneontology/

Full Gene Ontology annotation to genes associated with cardiovascular processes. Every GO annotation made, is attributed to an identified source, such as a publication identifier (PMID), and an indication of the type of evidence which supports the association between the gene product and the GO term. Over 4,000 cardiovascular associated genes have been identified. A variety of tools have been provided to enable cardiovascular scientists to review the annotation of their ''''favorite'''' gene and suggest information that may be missing, inaccurate or incomplete in these annotations. Annotation suggestions can be sent through the feedback form or by email. The Gene Ontology (GO) vocabulary is the established standard for the functional annotation of gene products. By using GO to curate scientific literature and by integrating results from high-quality high-throughput experiments they will create an information-rich resource for the cardiovascular-research community, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research.

Proper citation: Cardiovascular Gene Ontology Annotation Initiative (RRID:SCR_004795) Copy   

•   Source: SciCrunch Registry

http://www.mechanobio.info/

Portal that deals with the process of mechanotransduction, providing in-depth, regularly updated reviews on the mechanics of cellular and molecular function. Each review is written by scientists and subsequently peer reviewed by experts in the field to ensure the content is accurate, reliable and up to date. Each review emphasizes the functional and mechanical aspects of a process, rather than the genetic aspects, with the aim of making this resource accessible to a wider audience. MBInfo is an ideal resource for scientists working in alternative fields, individuals working in industries where products are based on biological principles or students seeking a reliable introduction to a given cellular process. Each topic is written in a pyramid structure. The top of the pyramid is represented by an overview page, providing a basic description of a given function or process. These pages target a broad spectrum of readers and assume only a basic understanding of biology. Further down the pyramid, the reader will encounter the steps involved in the process described and functional modules that address specific mechanical aspects. These pages outline the protein complexes involved and the mechanisms by which they achieve the given process or function. These pages assume the readers have a more in-depth knowledge of scientific terms and principles. For every topic, a series of graphics and/or animations are available. These supplement the reviews, clarify information and guide the reader through complex processes pictorially. This makes MBInfo an ideal teaching resource, whether in the classroom or for clients trying to understand your product. All images and text are copyright protected and are for personal use only. Current Topics include: * Cellular Structures in Mechanosensing and Cell Motility * Methods in the Study of Mechanobiology * Nuclear Mechanotransduction Almost 100 stand alone Glossary Terms are now available. These include short definitions or summaries of proteins and processes that relate to broader topics discussed within the site. Browse an extensive range of figures, tables and videos in our resources section. New quizzes and other interactive content can also be found.

Proper citation: MBInfo (RRID:SCR_006768) Copy   

•   Source: SciCrunch Registry

http://gemdock.life.nctu.edu.tw/3D-Interologs

Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.

Proper citation: 3D-Interologs (RRID:SCR_003101) Copy   

•   Source: SciCrunch Registry

http://www.sib.swiss/

An academic, non-profit foundation recognized of public utility that coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services to the national and international research community. * The first and primary SIB mission consists of providing services, i.e. the bioinformatics research infrastructure for life science research. It is carried through in a top-down approach, with objectives set by the SIB Board of Directors and an implementation plan agreed with the concerned groups. Federal funds are almost exclusively used to fulfill this mission. * Within the second mission the SIB plays a federating role, linking the Swiss bioinformatics community and promoting and coordinating research and education. This activity is mainly performed in a bottom-up way with funding from the universities and other partners and from research grants.

Proper citation: SIB Swiss Institute of Bioinformatics (RRID:SCR_012816) Copy   

•   Source: SciCrunch Registry

http://dknet.org/

The NIDDK Information Network (dkNET) is a community-based network to serve needs of basic and clinical investigators that includes large pools of data and research resources relevant to mission of National Institute of Diabetes and Digestive and Kidney Disease.

Proper citation: NIDDK Information Network (dkNET) (RRID:SCR_001606) Copy   

•   Source: SciCrunch Registry

https://3dvcell.ncbi.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content.

Proper citation: 3DVC (RRID:SCR_001377) Copy   

•   Source: SciCrunch Registry

http://matrixdb.univ-lyon1.fr/

Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.

Proper citation: MatrixDB (RRID:SCR_001727) Copy   

•   Source: SciCrunch Registry

http://biodev.extra.cea.fr/interoporc/

Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

Proper citation: InteroPorc (RRID:SCR_002067) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resolver/SCR_002250

THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

Proper citation: OMICtools (RRID:SCR_002250) Copy   

•   Source: SciCrunch Registry

http://www.jcvi.org/mpidb

Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.

Proper citation: MPIDB (RRID:SCR_001898) Copy   

•   Source: SciCrunch Registry

http://netbio.bgu.ac.il/tissuenet/

Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues.

Proper citation: TissueNet - The Database of Human Tissue Protein-Protein Interactions (RRID:SCR_002052) Copy   

•   Source: SciCrunch Registry

http://irefindex.org

An index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. iRefIndex project has three long term objectives: # to facilitate exchange of interaction data between interaction databases. # to consolidate interaction data from multiple sources. # to provide feedback to source interaction databases. iRefIndex is made available in a number of formats: MITAB tab-delimited text files, iRefWeb interface, iRefScape plugin for Cytoscape, PSICQUIC Web services, and an interface for the R programming language environment.

Proper citation: Interaction Reference Index (RRID:SCR_002085) Copy   

•   Source: SciCrunch Registry

http://integrativebiology.org/

Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database.

Proper citation: Integrated Molecular Interaction Database (RRID:SCR_003546) Copy   

•   Source: SciCrunch Registry

http://pbildb1.univ-lyon1.fr/virhostnet/

Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy.

Proper citation: VirHostNet: Virus-Host Network (RRID:SCR_005978) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy   

•   Source: SciCrunch Registry

https://www.niddk.nih.gov/

Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country.

Proper citation: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) Copy   

•   Source: SciCrunch Registry

http://www.re3data.org/

Global registry of research data repositories from all academic disciplines that allows the easy identification of appropriate research data repositories, both for data producers and users. Information icons display principal attributes of a repository that can be used for multi-faceted searches. Repository operators can suggest their infrastructures to be listed via a simple application form. A repository is indexed when the minimum requirements are met, i.e. mode of access to the data and repository, as well as the terms of use.

Proper citation: re3data.org (RRID:SCR_006782) Copy   

•   Source: SciCrunch Registry

http://www.innatedb.com

Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.

Proper citation: InnateDB (RRID:SCR_006714) Copy   

•   Source: SciCrunch Registry

http://apid.dep.usal.es

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 data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

Proper citation: Agile Protein Interactomes DataServer (RRID:SCR_008871) Copy   

•   Source: SciCrunch Registry