Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Metalloprotein Site Database Resource Report Resource Website 1+ mentions |
Metalloprotein Site Database (RRID:SCR_007780) | MDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. Database and Browser containing quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?, and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms). This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins. | software, web service |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NIGMS P01-GM48495 | PMID:11752342 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03116 | SCR_007780 | Metalloprotein Database and Browser | 2026-08-10 09:33:16 | 1 | |||||
|
MfunGD - MIPS Mouse Functional Genome Database Resource Report Resource Website 50+ mentions |
MfunGD - MIPS Mouse Functional Genome Database (RRID:SCR_007783) | MfunGD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.Database for annotated mouse proteins and their occurrence in protein networks. It contains cDNA and protein sequences, annotation, gene models and mapping, FunCat, UCSC Genome Viewer, SIMAP, pseudogenes (Genome Viewer Track), InterPro, and splice variants. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system. To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database. The gene models are based on the RefSeq mouse cDNAs. The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database and the Comprehensive Resource of Mammalian Protein Complexes are linked to the MfunGD dataset. Links to external resources are also provided. MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture. | bio.tools |
is listed by: Debian is listed by: bio.tools |
GSF National Research Center for Environment and Health ; German Federal Ministry of Research and Education |
PMID:16381934 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03121, biotools:mfungd | https://bio.tools/mfungd | SCR_007783 | Mouse Functional Genome Database | 2026-08-10 09:33:16 | 90 | ||||
|
NucleaRDB Resource Report Resource Website 10+ mentions |
NucleaRDB (RRID:SCR_007782) | data or information resource, database | A database of information on nuclear receptors. Included in the database are sequence information, structural information, and mutation data. Users can BLAST sequences, view 2D structural data, see the chromosomal location of nuclear receptors genes, and utilize other tools found on the website. | has parent organization: Radboud University; Nijmegen; The Netherlands | nif-0000-03206 | SCR_007782 | NucleaRDB | 2026-08-10 09:33:17 | 10 | ||||||||||
|
NetworKIN Resource Report Resource Website 100+ mentions |
NetworKIN (RRID:SCR_007818) | data or information resource, database | A method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins. This website allows a user to browse/search and investigate predictions made using the NetworKIN algorithm. The site is powered by the latest phosphoproteome in Phospho.ELM. Alternatively users can submit their own protein sequences and phosphorylation sites and obtain new NetworKIN predictions. | FASEB list | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | nif-0000-03190 | SCR_007818 | NetworKIN | 2026-08-10 09:33:19 | 112 | |||||||||
|
PIDD Resource Report Resource Website 10+ mentions |
PIDD (RRID:SCR_007854) | PIDD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database for the study of protein inter-atomic distance distribution. Currently, the distances are extracted from the protein structures determined through X-ray Crystallography, but they could also be obtained from NMR structural models. The known structures with the resolution higher than 2A and less than 70% sequence similarities are selected. Each type of distances is specified in terms of the types of the atoms it involves, the types of the residues containing the atoms, and the types of the residues in between the two end residues in sequence. An automated system is built to generate and process the data dynamically. The system consists of two levels of databases. The first one stores the sequence and structure information for a large set of high-resolution protein structures, with a similar data structure as the structural data represented in the PDB Data Bank. The second one stores the information for the distance distributions, with each record corresponding to a distribution function. The second database is built dynamically from the first one. The database can provide structural information in terms of distance distributions to structural biologists. Such information can be valuable for the study of many fundamental biological problems including protein structure prediction and determination, protein dynamics simulation, molecular design, protein structural analysis and classification, etc. | has parent organization: Iowa State University; Iowa; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03287 | http://pidd.math.iastate.edu | SCR_007854 | Protein Inter-Atomic Distance Distribution Database | 2026-08-10 09:33:17 | 25 | |||||||
|
PINT Resource Report Resource Website 100+ mentions |
PINT (RRID:SCR_007856) | PINT | data or information resource, database | A protein-protein interactions thermodynamic database which contains data of several thermodynamic parameters along with sequence and structural information experimental conditions and literature information. Each entry contains numerical data for features of the interacting proteins such as the free energy change, dissociation constant, association constant, enthalpy change, and heat capacity change. PINT includes: the name and source of the proteins involved in binding, SWISS-PROT and Protein Data Bank (PDB) codes, secondary structure and solvent accessibility of residues at mutant positions, measuring methods, and experimental conditions such as buffers, ions and additives, and literature information. PINT is cross-linked with other related databases such as PIR, SWISS-PROT, PDB and the NCBI PUBMED literature database. | database, protein protein interaction, thermodynamic, protein structure, protein database, FASEB list |
uses: UniProtKB uses: PubMed |
nif-0000-03291 | SCR_007856 | Protein-protein Interactions Thermodynamic Database | 2026-08-10 09:33:19 | 119 | ||||||||
|
Phytome Resource Report Resource Website |
Phytome (RRID:SCR_007852) | data or information resource, database | An online comparative genomics resource that is built upon publicly available sequence and map information from a diverse set of plant species, with a focus on the angiosperms, or flowering plants. It provides an interface to the results from a variety of phylogenomic analyses. Phytome is designed to facilitate functional genomics, molecular breeding and evolutionary studies in model and non-model plant species. Currently, Phytome contains phylogenetic and functional information for predicted protein sequences ("Unipeptides"). Future development will incorporate data and tools for analysis of sequence-based comparative maps. | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | nif-0000-03284 | SCR_007852 | Phytome | 2026-08-10 09:33:20 | 0 | ||||||||||
|
Plant Protein Phosphorylation Database Resource Report Resource Website 10+ mentions |
Plant Protein Phosphorylation Database (RRID:SCR_007841) | P3DB | data or information resource, database | It was established with an overall objective to provide a resource of protein phosphorylation data from multiple plants. P3DB was constructed with a dataset from oilseed rape. The data was obtained using a combination of data-dependent neutral loss and multistage activation mass spectrometry. The dataset includes 14,670 non-redundant phosphorylation sites from 8,894 phospho-peptides in 6,382 substrate proteins. | FASEB list | has parent organization: University of Missouri; Missouri; USA | nif-0000-03235 | SCR_007841 | Plant Protein Phosphorylation Database | 2026-08-10 09:33:20 | 34 | ||||||||
|
ORENZA : a database of ORphan ENZyme Activities Resource Report Resource Website 1+ mentions |
ORENZA : a database of ORphan ENZyme Activities (RRID:SCR_007836) | data or information resource, database | ORENZA is a relational database of Orphan Enzyme Activities. ORENZA provides an accurate and up to date list of Enzyme Activities for which no sequences are available in the main sequence protein databases. Orphan enzyme activities correpond to the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), and which are not associated with any amino acid sequences in the major public databases. | nif-0000-03224 | SCR_007836 | ORENZA | 2026-08-10 09:33:18 | 3 | |||||||||||
|
IRIS - International Rice Information System Resource Report Resource Website 1+ mentions |
IRIS - International Rice Information System (RRID:SCR_007755) | data or information resource, database | IRIS is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars. This includes germplasm pedigrees, field evaluations, structural and functional genomic data (including links to external plant databases) and environmental (GIS) data. | crop, rice, rice funcitonal genomics, rice genetics, rice germplasm | nif-0000-03048 | SCR_007755 | IRIS | 2026-08-10 09:33:16 | 8 | ||||||||||
|
iProLINK Resource Report Resource Website 1+ mentions |
iProLINK (RRID:SCR_007752) | data or information resource, database | iProLINK (integrated Protein Literature, INformation and Knowledge) has been developed as a resource to facilitate text mining in the area of literature-based database curation, named entity recognition, and protein ontology development. The collection of data sources can be utilized by computational and biological researchers to explore literature information on proteins and their features or properties. The data sources for bibliography mapping and feature evidence attribution include mapped citations (PubMed ID to protein entry and feature line mapping) and annotation-tagged literature corpora. The latter includes several hundred abstracts and full-text articles tagged with experimentally validated post-translational modifications (PTMs) annotated in the PIR protein sequence database. | nif-0000-03045 | SCR_007752 | iProLINK | 2026-08-10 09:33:15 | 3 | |||||||||||
|
L1Base Resource Report Resource Website 10+ mentions |
L1Base (RRID:SCR_007750) | data or information resource, database | L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included in the database. | fl-l1, flni-l1, full length l1, full length non-intact l1, l1, line, line-1, orf2-l1 | nif-0000-03076 | SCR_007750 | L1Base | 2026-08-10 09:33:18 | 23 | ||||||||||
|
The Intronerator Resource Report Resource Website 1+ mentions |
The Intronerator (RRID:SCR_007745) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing. It includes: Tracks Display- View splicing diagrams for any gene in the Sanger C. elegans database alongside cDNA and EST alignments. Retrieve DNA sequences with the exons in upper case. Search the literature. Alt Splicing Catalog - As defined by Chuck's altGraphX process. A frames based viewer linking to the genome browser. Alt-Splicing Catalog - A catalog of genes for which the cDNA and EST evidence indicates alternative splicing. | has parent organization: University of California at Santa Cruz; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03037 | SCR_007745 | The Intronerator | 2026-08-10 09:33:16 | 1 | |||||||||
|
IPD-HPA - Human Platelet Antigens Resource Report Resource Website 1+ mentions |
IPD-HPA - Human Platelet Antigens (RRID:SCR_007747) | data or information resource, database | A centralised repository for the data which define the human platelet antigens (HPA). Alloantibodies against human platelet antigens are involved in neonatal alloimmune thrombocytopenia, post-transfusion purpura and refractoriness to random donor platelets. The Human Platelet Antigen (HPA) nomenclature system was adopted in 1990 to overcome problems with the previous nomenclature. Since then more antigens have been described and meanwhile the molecular basis of many has been resolved, and the nomenclature was revised in 2003. | polymorphism, immuno-polymorphism, alloantigen |
is listed by: 3DVC has parent organization: European Bioinformatics Institute |
nif-0000-03040 | SCR_007747 | Immuno polymorphism database, IPD-HPA | 2026-08-10 09:33:18 | 5 | |||||||||
|
PLprot Resource Report Resource Website 10+ mentions |
PLprot (RRID:SCR_007864) | data or information resource, database | A plastid protein database. It integrates data from large scale proteome analyses of different plastid types.These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison allows establishing a core proteome that is common to all plastid types and provides furthermore information about plastid type-specific functions. | SCR_007864 | PLprot | 2026-08-10 09:33:19 | 10 | ||||||||||||
|
piRNABank Resource Report Resource Website 100+ mentions |
piRNABank (RRID:SCR_007858) | data or information resource, database | A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03293 | SCR_007858 | piRNABank | 2026-08-10 09:33:20 | 172 | ||||||||
|
MtbRegList Resource Report Resource Website 1+ mentions |
MtbRegList (RRID:SCR_007811) | data or information resource, database | A database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain most of the characterized transcription start sites and DNA binding sites cross-referenced with their respective transcription factor, along with some predicted regulatory motifs. | has parent organization: University of Sherbrooke; Quebec; Canada | nif-0000-03169 | SCR_007811 | MtbRegList | 2026-08-10 09:33:18 | 1 | ||||||||||
|
MegaMotifbase Resource Report Resource Website 1+ mentions |
MegaMotifbase (RRID:SCR_007775) | data or information resource, database | A database of structural motifs for protein structures related at the family and-or superfamily level. Such motifs among structurally aligned proteins are recognized by the conservation of amino acid preference and solvent inaccessibility and are examined for the conservation of other important structural features like secondary structural content, hydrogen bonding pattern and residue packing. These motifs may form the common core by maintaining a particular spatial orientation pattern when compared across different proteins belonging to the same family or superfamily. Such motifs can also be employed to design and rationalize protein engineering and folding experiments. Therefore, the MegaMotifbase can be a useful resource to gain knowledge about structure and functional relationship of proteins. Alignments are available for download. | protein families, protein superfamilies |
is listed by: 3DVC has parent organization: Tata Institute of Fundamental Research; Mumbai; India |
nif-0000-03108 | SCR_007775 | MegaMotifbase | 2026-08-10 09:33:19 | 1 | |||||||||
|
MPDB - Molecular Probe Database Resource Report Resource Website |
MPDB - Molecular Probe Database (RRID:SCR_007808) | MPDB | data or information resource, database | A database containing information on ca. 4300 synthetic oligonucleotides with a sequence of up to 100 nucleotides. Data are mainly taken from the literature and are encoded on the basis of controlled vocabularies. The probes target 821 different genes, of which 691 human and 112 viral. The probes can be used for genetic polymorphisms study (1944), human inherited disease diagnosis (834), cancer diagnosis (517), infectious disease diagnosis (517), neurologic disease diagnosis (72), autoimmune disease diagnosis (40). Oligonucleotides are described on the basis of: name, oligo type (primer, probe, antisense), nucleotide sequence, amino acid sequence (if part of a coding region), target gene and related infos (localization within the gene and recognized variants or specificities), applications, methods, technical notes, complementary primer (if used for PCR), primers for amplification (if probe), bibliographic references. At the moment MPDB is searchable through some SRS servers. MPDB can easily be retrieved from our FTP server, together with SRS syntax files. Typology * ca. 4300 oligonucleotides * 821 different genes, of which 691 human and 112 viral * ca. 3536 oligonucleotides are human gene specific * ca. 620 oligonucleotides are viral gene specific | molecular probe, synthetic oligonucleotide, molecule, probe, synthetic, oligonucleotide, nucleotide sequence, amino acid sequence, oligo probe, oligo dna, pcr primer, virus | has parent organization: IST National Institute for Cancer Research; Genoa; Italy | Genetic polymorphism, Inherited disease, Infectious disease, Neurologic disease, Autoimmune disease, Cancer | PMID:9399819 PMID:9016509 PMID:8594603 PMID:7937049 PMID:8332523 PMID:1598231 |
nif-0000-03165 | SCR_007808 | Molecular Probe Data Base (MPDB), Molecular Probe Data Base, Molecular Probe Database | 2026-08-10 09:33:18 | 0 | ||||||
|
MPIM - Mitochondrial Protein Import Machinery Resource Report Resource Website |
MPIM - Mitochondrial Protein Import Machinery (RRID:SCR_007809) | MPIM db | data or information resource, database | A database of Arabidopsis mitochondrial protein import components. Detailed information can be found in two main areas of the website, one of which contains a diagram detailing the plant mitochondrial import process which users can click on and interact with, and the other containing information about arabidopsis mitochondrial protein import components. | has parent organization: University of Washington; Seattle; USA | nif-0000-03166 | SCR_007809 | Mitochondrial Protein Import Machinery of Plants, Mitochondrial Protein Import Machinery | 2026-08-10 09:33:16 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
