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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ORFprimer Resource Report Resource Website 1+ mentions |
ORFprimer (RRID:SCR_003269) | ORFprimer | software resource | An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. | java, java swing, open reading frame, protein, high throughput sequencing, primer, primer design, pcr, pcr primer design |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02331 | SCR_003269 | ORFprimer - primer design for ORFs | 2026-02-14 02:00:44 | 1 | |||||||
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NESbase Resource Report Resource Website 1+ mentions |
NESbase (RRID:SCR_003268) | NESbase | data repository, storage service resource, data or information resource, service resource, database | Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature. Each NESbase entry contains information of whether NES was shown to be necessary and/or sufficient for export, and whether the export was shown to be mediated by the export receptor CRM1. The compiled information was used to make a sequence logo of the Leucine-rich NESs, displaying the conservation of amino acids within a window of 25 residues. Error reports and submissions of new data are most welcome! | nuclear export signal, protein, leucine | has parent organization: DTU Center for Biological Sequence Analysis | Danish National Research Foundation ; John and Birthe Meyer Foundation |
PMID:12520031 | Free, Available for download, Freely available | nif-0000-03188 | https://services.healthtech.dtu.dk/datasets/NESbase-1.0/ | SCR_003268 | 2026-02-14 02:00:24 | 7 | |||||
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BrainTrap: Fly Brain Protein Trap Database Resource Report Resource Website 1+ mentions |
BrainTrap: Fly Brain Protein Trap Database (RRID:SCR_003398) | BrainTrap | d spatial image, data or information resource, database | This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download. | brain, exon, expression, 3d confocal, affinity, antibody, dataset, immunohistochemical, microscopy, image, protein, protein-trap, gene | has parent organization: University of Edinburgh; Scotland; United Kingdom | EPSRC ; British society for Developmental Biology ; Society for Experimental Biology ; Virtual Fly Brain e-Science Institute Theme ; BBSRC ; MRC |
PMID:20624714 | Free, Freely available | nif-0000-32989 | http://fruitfly.inf.ed.ac.uk/braintrap/ | SCR_003398 | Fly Brain Protein Trap Database, Brain Trap | 2026-02-14 02:00:32 | 1 | ||||
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Rockland Immunochemicals Resource Report Resource Website 50+ mentions |
Rockland Immunochemicals (RRID:SCR_003278) | Rockland | commercial organization | A global biotechnology company manufacturing research tools, antibodies, and cGMP grade protein. | cancer, cardiovascular, cell biology, chromatin, nuclear signaling, developmental biology, epigenetics, immunology, protein, peptide, blood, blood product, cell lysate, stem cell, assay | Free, Freely available | nlx_152452, nif-0000-31467 | SCR_003278 | Rockland Immunochemicals Inc., Rockland antibodies & assays, Rockland antibodies and assays | 2026-02-14 02:00:31 | 54 | ||||||||
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Glioma Molecular Dignostic Initiatives Resource Report Resource Website 10+ mentions |
Glioma Molecular Dignostic Initiatives (RRID:SCR_003329) | GMDI | data repository, storage service resource, data or information resource, service resource, controlled vocabulary, narrative resource, standard specification | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. An initiative to develop a molecular classification schema that is both clinically and biologically meaningful, based on gene expression and genomic data from tumors (Gliomas) of patients who will be prospectively followed through natural history and treatment phase of their illness. The study will also explore gene expression profiles to determine the responsiveness of the patients and correlate with discrete chromosomal abnormalities. The initiative was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. The sample collection is accompanied by careful and prospective clinical data acquisition, allowing a variety of matched molecular and clinical data permitting a wide variety of analyses. GMDI has accrued fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and fresh frozen tumors in the prospective phase (from a variety of institutions). In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory. | molecular neuroanatomy resource, molecular data, clinical data, genomic analyses, genomics, gene, expression array, snp array, gene expression, microarray, glioma initiating cell, glioma stem cell, protein, glioma, molecular, diagnostic, dna, rna, tumor, tissue, blood, plasma, data repository |
is listed by: One Mind Biospecimen Bank Listing is related to: Repository of molecular brain neoplasia data has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31950 | http://search.engrant.com/project/NxvG9G/the_glioma_molecular_diagnostic_initiative_characterizing_brain_tumor_data | SCR_003329 | Glioma Molecular Diagnostic Initiative: Characterizing Brain Tumor Data | 2026-02-14 02:00:32 | 17 | ||||
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Nuclear Receptor Resource Resource Report Resource Website 1+ mentions |
Nuclear Receptor Resource (RRID:SCR_003285) | NRR | data or information resource, database, resource | Collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily. NRR Components: Androgen receptor, Estrogen receptor, Glucocorticoid receptor, Peroxisome proliferator, Steroid receptor protein, Thyroid receptor, Vitamin D receptor. | nuclear receptor, androgen receptor, estrogen receptor, glucocorticoid receptor, peroxisome proliferator, steroid receptor protein, thyroid receptor, vitamin d receptor, androgen, estrogen, glucocorticoid, peroxisome, steroid, thyroid hormone, vitamin d, mineralocorticoid receptor, mineralocorticoid, protein, structure, function |
is related to: NIDDK Information Network (dkNET) has parent organization: Georgetown University; Washington D.C.; USA |
NIDDK R01DK43382; NIDDK K04 DK02105 |
PMID:9471621 PMID:9016529 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03205 | http://nrr.georgetown.edu/NRR/nrrhome.htm | SCR_003285 | Nuclear Receptor Resource Project, NRR Project, Nuclear Receptor Resource (NRR) Project | 2026-02-14 02:00:25 | 1 | ||||
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ProbeMatchDB 2.0 Resource Report Resource Website |
ProbeMatchDB 2.0 (RRID:SCR_003433) | ProbeMatchDB | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. | experiment, human, microarray, mouse, oligo, operon, platform, probe, protein, proteomic, rate, sequence, study, gene, est, cdna, sts marker, orthologous gene, ortholog, microarray probe, nucleotide sequence |
is related to: UniGene is related to: HomoloGene has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan Microarray Network ; Nancy Pritzker Depression Research Network ; Department of Psychiatry pilot study ; NIMH L99 MH60398; NIDA R21 DA13754-01 |
PMID:11934751 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33156 | SCR_003433 | 2026-02-14 02:00:33 | 0 | ||||||
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PROSITE Resource Report Resource Website 1000+ mentions |
PROSITE (RRID:SCR_003457) | PROSITE | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP. | protein domain, protein family, functional site, protein, structure, function, pattern, profile |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Federal government through the Federal Office of Education and Science ; European Union contract FELICS 021902RII3; European Union contract IMPACT 213037; FNS 315200-116864 |
PMID:23161676 PMID:19858104 PMID:12230035 |
Free, Freely available | nif-0000-03351, OMICS_01699 | http://www.expasy.org/prosite, http://www.expasy.ch/prosite/ | SCR_003457 | PROSITE - Database of protein domains families and functional sites | 2026-02-14 02:00:49 | 2165 | ||||
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Protein Structure Initiative Resource Report Resource Website |
Protein Structure Initiative (RRID:SCR_002161) | data or information resource, portal, topical portal | The Structural Genomics Project aims at determination of the 3D structure of all proteins. It also aims to reduce the cost and time required to determine three-dimensional protein structures. It supports selection, registration, and tracking of protein families and representative targets. This aim can be achieved in four steps : -Organize known protein sequences into families. -Select family representatives as targets. -Solve the 3D structure of targets by X-ray crystallography or NMR spectroscopy. -Build models for other proteins by homology to solved 3D structures. PSI has established a high-throughput structure determination pipeline focused on eukaryotic proteins. NMR spectroscopy is an integral part of this pipeline, both as a method for structure determinations and as a means for screening proteins for stable structure. Because computational approaches have estimated that many eukaryotic proteins are highly disordered, about 1 year into the project, CESG began to use an algorithm. The project has been organized into two separate phases. The first phase was dedicated to demonstrating the feasibility of high-throughput structure determination, solving unique protein structures, and preparing for a subsequent production phase. The second phase, PSI-2, has focused on implementing the high-throughput structure determination methods developed in PSI-1, as well as homology modeling and addressing bottlenecks like modeling membrane proteins. The first phase of the Protein Structure Initiative (PSI-1) saw the establishment of nine pilot centers focusing on structural genomics studies of a range of organisms, including Arabidopsis thaliana, Caenorhabditis elegans and Mycobacterium tuberculosis. During this five-year period over 1,100 protein structures were determined, over 700 of which were classified as unique due to their < 30% sequence similarity with other known protein structures. The primary goal of PSI-1 was to develop methods to streamline the structure determination process, resulted in an array of technical advances. Several methods developed during PSI-1 enhanced expression of recombinant proteins in systems like Escherichia coli, Pichia pastoris and insect cell lines. New streamlined approaches to cell cloning, expression and protein purification were also introduced, in which robotics and software platforms were integrated into the protein production pipeline to minimize required manpower, increase speed, and lower costs. The goal of the second phase of the Protein Structure Initiative (PSI-2) is to use methods introduced in PSI-1 to determine a large number of proteins and continue development in streamlining the structural genomics pipeline. Currently, the third phase of the PSI is being developed and will be called PSI: Biology. The consortia will propose work on substantial biological problems that can benefit from the determination of many protein structures Sponsors: PSI is funded by the U.S. National Institute of General Medical Sciences (NIGMS), | elegans, escherichia, eukaryotic, expression, arabidopsis, biology, bottleneck, caenorhabditis, cell, clone, coli, crystallography, genomic, homology, insect, membrane, myobacterium, nmr, organism, pastoris, pichia, protein, purification, sequence, spectroscopy, structural, structure, thaliana, tuberculosis, x-ray | nif-0000-20950 | SCR_002161 | PSI | 2026-02-14 02:00:22 | 0 | ||||||||||
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PROVEAN Resource Report Resource Website 1000+ mentions |
PROVEAN (RRID:SCR_002182) | PROVEAN | data analysis service, analysis service resource, production service resource, service resource, software resource | A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. | amino acid substitution, indel, function, protein, amino acid, substitution, protein variant, genome variant, next-generation sequencing, insertion, deletion |
is listed by: OMICtools has parent organization: J. Craig Venter Institute |
NIH ; NHGRI 5R01HG004701-04 |
PMID:23056405 | Free, Available for download, Freely available | OMICS_01849 | SCR_002182 | Protein Variation Effect Analyzer | 2026-02-14 02:00:15 | 2231 | |||||
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Autosomal Recessive Polycystic Kidney Disease Mutation Database Resource Report Resource Website 10+ mentions |
Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) | data repository, storage service resource, data or information resource, service resource, database | Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges. | clinical, gene, genetic, mutation, protein, recessive, renal | has parent organization: RWTH Aachen University; Aachen; Germany | Autosomal recessive polycystic kidney disease, Polycystic kidney disease | PMID:16199545 PMID:11919560 |
Permission required, Terms of use | nif-0000-21038 | http://www.humgen.rwth-aachen.de/index.asp?subform=database.html&nav=database_nav.html | SCR_002290 | Mutation Database Autosomal Recessive Polycystic Kidney Disease (ARPKD/PKHD1) | 2026-02-14 02:00:22 | 14 | |||||
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Community Structure-Activity Resource Resource Report Resource Website 10+ mentions |
Community Structure-Activity Resource (RRID:SCR_002206) | CSAR | data repository, storage service resource, data set, data or information resource, service resource | Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data. | crystal structure, binding affinity, protein-ligand complex, protein, small molecule, ligand, compound |
is used by: NIF Data Federation is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Michigan; Ann Arbor; USA |
NIGMS | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154720 | SCR_002206 | 2026-02-14 02:00:20 | 15 | |||||||
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ConSurf Database Resource Report Resource Website 100+ mentions |
ConSurf Database (RRID:SCR_002320) | ConSurfDB | data or information resource, service resource, database | Provides pre-calculated evolutionary conservation profiles for proteins of known structure in the PDB. Enables flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation of conservation profiles. | PDB, Protein DataBase, evolution, conservation, protein, structure, pre-calculated, profile, FASEB list |
is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Tel Aviv University; Ramat Aviv; Israel | PMID:20478830 PMID:15980475 PMID:12499312 PMID:11243830 |
Free, Freely available | nif-0000-21098, SCR_007609, BioTools:consurf-db, nif-0000-02685 | http://bental.tau.ac.il/new_ConSurfDB/ https://bio.tools/consurf-db |
http://consurf-hssp.tau.ac.il | SCR_002320 | , consurf-db, ConSurf-DataBase, ConSurf-DB, ConSurfDB, ConSurf Server Database, ConSurfDataBase, ConSurf- Data Base | 2026-02-14 02:00:22 | 311 | |||
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glycosciences.de Resource Report Resource Website 10+ mentions |
glycosciences.de (RRID:SCR_002324) | GLYCOSCIENCES.de | data or information resource, portal, database, topical portal | Portal of glycoinformatics resources including databases and bioinformatics tools for glycobiology and glycomics research. Databases include a bibliography, structure, nuclear magnetic resonance (NMR), mass spectroscopy (ms) and a PDB search. | glycoinformatics, glycobiology, glycomics, carbohydrate, 3d structure, data analysis service, modeling, structure, nuclear magnetic resonance, mass spectroscopy, protein, glycan |
lists: LiGraph lists: pdb-data lists: PDB2MultiGif is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Giessen; Hesse; Germany is parent organization of: GlyProt is parent organization of: Distance Mapping is parent organization of: pdb-care is parent organization of: pdb2linucs is parent organization of: GlyVicinity is parent organization of: GlyTorsion is parent organization of: GlySeq is parent organization of: LINUCS is parent organization of: sumo is parent organization of: GlycoFragment is parent organization of: Glyco-CD is parent organization of: GlycoMapsDB is parent organization of: SWEET-DB is parent organization of: CARP |
DFG | PMID:16239495 | Free, Public | nif-0000-21103 | SCR_002324 | Glycosciences | 2026-02-14 02:00:22 | 23 | |||||
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Pharmabase - an open content cheminformatics resource linking physiology with pharmacology Resource Report Resource Website |
Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) | Pharmabase | data or information resource, image collection, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research. | function, cell, compound, graphic, illustration, membrane, molecular, pharmacological, pharmacology, protein, transport, metabolism, intracellular messenger, cell signaling, disease, tissue, cell type, pathway, pharmacology, channel, pump, carriers, protein transporter, membrane transport | has parent organization: BioCurrents Research Center | NCRR P41 RR001395 | PMID:18428760 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21324 | SCR_002462 | 2026-02-14 02:00:24 | 0 | ||||||
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Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl https://sources.debian.org/src/ensembl/ https://doi.org/10.17616/R39K5B |
SCR_002344 | ENSEMBL | 2026-02-14 02:00:23 | 11652 | ||||||
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DBSubLoc - Database of protein Subcellular Localization Resource Report Resource Website 1+ mentions |
DBSubLoc - Database of protein Subcellular Localization (RRID:SCR_002339) | DbSubLoc | web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | A database of protein subcellular localization containing proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross references to taxonomies and Gene Ontology database. Annotations were taken from primary protein databases, model organism genome projects and literature texts, and then were analyzed to dig out the subcellular localization features of the proteins. The proteins are also classified into different categories. Based on sequence alignment, nonredundant subsets of the database have been built, which may provide useful information for subcellular localization prediction. The database now contains >60 000 protein sequences including 30 000 protein sequences in the nonredundant data sets. Online download, SOAP server, Blast tools and prediction services are also available. | protein, protein database, protein subcellular localization, blast, prediction, subcellular | has parent organization: National Tsing Hua University; Hsinchu; Taiwan | National Key Foundational Research of China 863-2002AA23/03/; National Key Foundational Research of China 2002AA234041; National Key Foundational Research of China 973-2003CB715900; National Key Foundational Research of China NSF-90303017 |
PMID:14681374 | nif-0000-02735 | SCR_002339 | 2026-02-14 02:00:23 | 2 | |||||||
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Reflect Resource Report Resource Website 50+ mentions |
Reflect (RRID:SCR_002714) | Reflect | data access protocol, software resource, web service, software application | Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community. | text mining, semantic mark up, gene, protein, computational linguistics, small molecule, domain structure, sub-cellular localization, 3d structure, interaction, chemical structure |
is listed by: OMICtools is listed by: FORCE11 has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: European Bioinformatics Institute |
PMID:19513049 | nif-0000-23349, OMICS_01196 | http://reflect.ws/ | SCR_002714 | Reflect: Protein small molecules | 2026-02-14 02:00:26 | 87 | ||||||
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EMBL - Bork Group Resource Report Resource Website |
EMBL - Bork Group (RRID:SCR_000810) | EMBL - Bork Group | portal, laboratory portal, data or information resource, organization portal, service resource | The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin. | computational biology, gene, protein, protein network, cellular process, phenotype, environment, gene, genome, metagenome, analysis, interaction, pathway, temporal, spatial, network, genotype, phenotype, molecular process |
has parent organization: European Molecular Biology Laboratory is parent organization of: SMART is parent organization of: SmashCommunity is parent organization of: Candidate Genes to Inherited Diseases |
European Molecular Biology Laboratory ; Max-Delbruck Center for Molecular Medicine ; European Union ; BMBF ; IBM |
nlx_149173 | SCR_000810 | Bork Group - Comparative Systems Analysis (EMBL) | 2026-02-14 01:59:50 | 0 | |||||||
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Abazyme Resource Report Resource Website |
Abazyme (RRID:SCR_001139) | commercial organization | Commercial antibody supplier that provides reagents such as immunoassay kits, antibodies, and proteins as well as custom services such as antigen preparation, sequencing and engineering. | antibody, immunoassay, protein, antigen, commercial, biomaterial supply resource | nlx_152242 | SCR_001139 | 2026-02-14 02:00:00 | 0 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
