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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Cell-PLoc
 
Resource Report
Resource Website
100+ mentions
Cell-PLoc (RRID:SCR_011966) Cell-PLoc data analysis service, production service resource, service resource, analysis service resource A package of web-servers for predicting subcellular localization of proteins in different organisms. subcellular localization, protein, gram-negative protein, gram-positive protein, virus is listed by: OMICtools
has parent organization: Shanghai Jiao Tong University; Shanghai; China
is parent organization of: Euk-mPLoc
PMID:18274516 OMICS_01617 SCR_011966 Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in different organisms 2026-08-05 10:45:38 203
CELLO
 
Resource Report
Resource Website
500+ mentions
CELLO (RRID:SCR_011968) CELLO data analysis service, production service resource, service resource, analysis service resource A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment. dna, protein, proteomic, genomic is used by: Cello2Go
is listed by: OMICtools
has parent organization: National Chiao Tung University; Hsinchu; Taiwan
PMID:15096640 Acknowledgement requested OMICS_01618 SCR_011968 CELLO: subCELlular LOcalization predictor 2026-08-05 10:45:38 957
Antibodypedia
 
Resource Report
Resource Website
10+ mentions
Antibodypedia (RRID:SCR_012782) data or information resource, database Open-access database of antibodies against human proteins developed through collaboration between Antibodypedia AB and the Nature Publishing Group. It aims to provide the scientific community and antibody distributors alike with information on the effectiveness of specific antibodies in specific applications--to help scientists select the right antibody for the right application. Antibodypedia's mission is to promote the functional understanding of the human proteome and expedite analysis of potential biomarkers discovered through clinical efforts. To this end, they have developed an open-access, curated, searchable database containing annotated and scored affinity reagents to aid users in selecting antibodies tailored to specific biological and biomedical assays. They envisage Antibodypedia as a virtual repository of validated antibodies against all human, and ultimately most model-organism, proteins. Such a tool will be exploitable to identify affinity reagents to document protein expression patterns in normal and pathological states and to purify proteins alone and in complex for structural and functional analyses. They hope to promote characterization of the roles and interplay of proteins and complexes in human health and disease. They encourage commercial providers to submit information regarding their inventory of antibodies with links to quality control data. Independent users can submit their own application-specific experimental data using standard validation criteria (supportive or non-supportive) developed with the assistance of an international advisory board recruited from academic research institutions. Users can also comment on specific antibodies without submitting validation data. cell biology, antibody, protein, human, reagent, model organism, non-human primate, FASEB list is listed by: 3DVC
is listed by: OMICtools
is related to: Nature Publishing Group
Antibodypedia AB ;
Nature Publishing Group ;
European Union 6th framework - ProteomeBinders ;
Human Antibody Initiative ;
HUPO - Human Proteome Organisation
PMID:18667413
PMID:18767878
The community can contribute to this resource nif-0000-22918, OMICS_01770 SCR_012782 Antibodypedia / Nature 2026-08-05 10:45:49 44
Mouse Genome Database
 
Resource Report
Resource Website
500+ mentions
Mouse Genome Database (RRID:SCR_012953) MGD data or information resource, database Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools is used by: DisGeNET
is listed by: Debian
is listed by: bio.tools
is related to: Mouse Genome Informatics (MGI)
has parent organization: Jackson Laboratory
NHGRI HG000330 PMID:21051359 biotools:mgi, biotools:mgd, nif-0000-10301 http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi SCR_012953 Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database 2026-08-05 10:45:54 502
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs
 
Resource Report
Resource Website
100+ mentions
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs (RRID:SCR_013182) SYFPEITHI data or information resource, database SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713. epitope, allele, allelic, amino acid, ape, bind, cattle, chicken, class i, class ii, human, immunological database, ligand, mhc, molecule, motif, mouse, natural, organism, peptide, product, protein, sequence, specie, t-cell, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: University of Tubingen; Tubingen; Germany
nif-0000-21383, biotools:syfpeithi https://bio.tools/syfpeithi SCR_013182 SYFPEITHI 2026-08-05 10:45:57 258
Cube-DB
 
Resource Report
Resource Website
1+ mentions
Cube-DB (RRID:SCR_013233) Cube-DB data or information resource, database Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioinformatics Institute; Singapore; Singapore
PMID:22139934 nlx_149432, biotools:cube-db https://bio.tools/cube-db SCR_013233 Cube-DB: Detection of Functional Divergence in Human Protein Families 2026-08-05 10:45:58 3
Alzforum Antibody Directory for Neuroscience Research
 
Resource Report
Resource Website
Alzforum Antibody Directory for Neuroscience Research (RRID:SCR_013601) data or information resource, database The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations. alzheimer, antibody, clinical trail, community, data, disease, disorder, molecule, neurodegenerative, protein, reagent, research, science, scientific, technology has parent organization: Alzheimer's Research Forum nif-0000-00129 SCR_013601 Alzforum Antibody Directory 2026-08-05 10:46:04 0
Glycosylation Pathways Database
 
Resource Report
Resource Website
500+ mentions
Glycosylation Pathways Database (RRID:SCR_013486) data or information resource, database A pathway-based graphical interface for navigating the glycoenzyme database. The goal of the project is to define the paradigms by which carbohydrate binding proteins function in cellular communication. These pages are divided into six categories: -Glycosphingolipid: Sub-categories are Isogloboseries, Globoseries, Neo-lactoseries, Lactoseries and Ganglioseries - N-linked: Sub-categories are High-mannose, Hybrid and Complex -Mucin -Terminal Core 1 -Other O-linked -Terminal All: Includes all potential terminal structures for each glycan category binding, carbohydrate, glycoenzyme, glycosylation, pathway, protein NIGMS nif-0000-20850 SCR_013486 GTDB 2026-08-05 10:46:01 683
Therapeutically Relevant Multiple Pathways Database
 
Resource Report
Resource Website
1+ mentions
Therapeutically Relevant Multiple Pathways Database (RRID:SCR_013471) data or information resource, database The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore. drug, gene, condition, disease, intermolecular interactions and signaling pathways databases, ligand, literature, location, pathway, protein, sequence, specie, target, therapeutic, therapy nif-0000-21402 SCR_013471 TRMP 2026-08-05 10:46:02 2
iPTMnet
 
Resource Report
Resource Website
10+ mentions
iPTMnet (RRID:SCR_014416) data or information resource, database A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies. database, protein, phosphorylation, bioinformatics, text mining, ontology NSF ABI-1062520 Available to the research community SCR_014416 2026-08-05 10:46:09 30
PHAROS
 
Resource Report
Resource Website
PHAROS (RRID:SCR_016258) TCRD data or information resource, database Database of ligands and diseases. Its goal is to develop a knowledge-base for the Druggable Genome (DG) in order to illuminate the uncharacterized and/or poorly annotated portion of the genome. DG, focusing on four of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs); nuclear receptors (NRs); ion channels (ICs); and kinases. protein, target, disease, ligand, phenotype, drug, medication, pharmacology, gpcr, nuclear, receptor, ion, channel, kinase Novo Nordisk Foundation NNF14CC0001;
NCATS ;
NCI U24 CA224370;
NCI CA189205;
NCI CA189201
PMID:27903890 Freely available, Free, Available for download SCR_016258 Target Central Resource Database 2026-08-05 10:46:36 0
p300db
 
Resource Report
Resource Website
1+ mentions
p300db (RRID:SCR_017063) data or information resource, database Data collection of CBP/p300 regulated acetylome, proteome, and transcriptome in murine embryonic fibroblasts. Composed of Symbol search for quantified acetylation sites, proteins and transcripts abundance in CBP/p300, Domain search for batch query of proteins by specific domain and Conserved sites for acetylation sites that are conserved between mouse and human, and their regulation in KATi treated cells. data, collection, CBP, p300, regulated, acetylome, proteome, transcriptome, murine, embryonic, fibroblast, domain, protein, acetylation, site, dataset is related to: Ensembl
is related to: UniProt
has parent organization: University of Copenhagen; Copenhagen; Denmark
Free, Available for download, Freely available SCR_017063 2026-08-05 10:46:47 1
MitoCarta
 
Resource Report
Resource Website
100+ mentions
MitoCarta (RRID:SCR_018165) data or information resource, database Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria. Gene, protein, mitochondrial protein, protein expression, data, human, mouse, RefSeq protein, analysis, mammalian mitochondra, FASEB list NIGMS GM0077465;
NIDDK DK43351;
NIDDK DK57521;
Australian NHMRC ;
Burroughs Wellcome Fund Career Award in the Biomedical Sciences ;
Howard Hughes Medical Institute ;
Charles E. Culpeper Scholarship in Medical Science
PMID:26450961
PMID:18614015
Free, Freely available SCR_018165 MitoCarta2.0 2026-08-05 10:47:00 183
UniProtKB/Swiss-Prot
 
Resource Report
Resource Website
500+ mentions
UniProtKB/Swiss-Prot (RRID:SCR_021164) data or information resource, database Curated component of UniProtKB (produced by the UniProt consortium). It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants. protein descriptions, protein function, protein, domain structure, subcellular location, post-translational modifications, functionally characterized variants is related to: UniProtKB SIB Swiss Institute of Bioinformatics DOI:10.1093/nar/26.1.38 Free, Freely available r3d100010677 https://doi.org/10.17616/R33314 SCR_021164 Swiss-Prot, SwissProt 2026-08-05 10:47:22 601
Liver cell atlas
 
Resource Report
Resource Website
10+ mentions
Liver cell atlas (RRID:SCR_023627) data or information resource, atlas Portal to search liver single cell RNA-sequencing datasets. Datasets for expression of genes or proteins (when CITE-seq was performed). To search for gene enter the official gene name. To search for protein please click to see specific names to use for different markers included. liver single cell RNA-sequencing data, liver cell, RNA-sequencing data, gene expression, protein, dataset, has parent organization: Ghent University; Ghent; Belgium Free, Freely available SCR_023627 2026-08-05 10:47:53 24
AlphaFold Protein Structure Database
 
Resource Report
Resource Website
1000+ mentions
AlphaFold Protein Structure Database (RRID:SCR_023662) AlphaFold DB data or information resource, database Database of protein structure predictions by AlphaFold that are freely and openly available to global scientific community. Included are nearly all catalogued proteins known to science. Provides programmatic access to and interactive visualization of predicted atomic coordinates, per residue and pairwise model confidence estimates and predicted aligned errors. EMBL-EBI, protein structure predictions, AlphaFold, catalogued proteins, protein, programmatic access, interactive visualization, PMID:34791371 Free, Freely available r3d100013615 https://doi.org/10.17616/R31NJMZZ SCR_023662 2026-08-05 10:47:53 1055
UniProtKB
 
Resource Report
Resource Website
5000+ mentions
UniProtKB (RRID:SCR_004426) data or information resource, data repository, database, storage service resource, service resource Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway. protein, annotation, amino acid sequence, taxonomy, proteome uses: UniportKB
is used by: NIF Data Federation
is used by: PINT
is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is related to: ESTHER
is related to: PIRSF
is related to: AmiGO
is related to: UniSave
is related to: ProRepeat
is related to: UniProt Chordata protein annotation program
is related to: neXtProt
is related to: TopFIND
is related to: UniPathway
is related to: NCBI Protein Database
is related to: Biomine
is related to: Gene Ontology
is related to: UniProt DAS
is related to: FunTree
is related to: ConceptWiki
is related to: InterProScan
is related to: UniProtKB/Swiss-Prot
is related to: FuzDrop
has parent organization: UniProt
is parent organization of: UniProtKB Keywords
is parent organization of: UniProtKB Subcellular Locations
works with: PremierBiosoft Proteo IQ Software
works with: Cello2Go
works with: UniprotR
works with: Kinase Associated Neural Phospho Signaling
PMID:15888679
PMID:18287689
Available to the research community, The community can contribute to this resource r3d100011521, nlx_53981 https://doi.org/10.17616/R3NK9Z SCR_004426 UniProtKB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, UniProt Knowledgebase 2026-08-05 10:44:02 6654
MetaMorph Microscopy Automation and Image Analysis Software
 
Resource Report
Resource Website
5000+ mentions
MetaMorph Microscopy Automation and Image Analysis Software (RRID:SCR_002368) MetaMorph data processing software, data acquisition software, image acquisition software, software application, image analysis software, software resource Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression. automated, microscope, acquisition, device, control, image, analysis, fluorescent, cell, signaling, counting, protein, expression, Molecular Devices PMID:18367250 Commercially available SciRes_000136 SCR_002368 MetaMorph version 7.8.0.0, Molecular Devices Metamorph Premier Software, MetaMorph image analysis software, MetaMorph Microscopy Automation and Image Analysis Software 2026-08-05 10:43:38 8275
COnsensus-DEgenerate Hybride Oligonucleotide Primers
 
Resource Report
Resource Website
1+ mentions
COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) data processing software, software application, data analysis software, software resource, data analysis service, production service resource, service resource, analysis service resource This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. fractionation, gel, 3', amplification, clone, dna, genome, homolog, human, hybrid, molecule, oligonucleotide, pcr, plant, primer, protein, sequence, transcriptase-methyltransferase is related to: OMICtools
has parent organization: University of Washington; Seattle; USA
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25557 SCR_002875 CODEHOP 2026-08-05 10:43:42 8
MOPED - Model Organism Protein Expression Database
 
Resource Report
Resource Website
1+ mentions
MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) MOPED data or information resource, database, data analysis service, resource, production service resource, service resource, analysis service resource An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. protein expression, gene expression, model organism, gene, protein, pathway, proteomics, transcriptomics, data visualization, overlap plot, heatmap, dot plot, data sharing, protein localization, gene localization is related to: GeneCards
is related to: UniProt
is related to: KEGG
is related to: Reactome
Robert B McMillen Foundation ;
NSF DBI0544757;
NIGMS 5R01GM076680;
NIDDK UO1DK072473;
NIDDK 1U01DK089571
PMID:24350770
PMID:22139914
nlx_151470 SCR_006065 Multi-Omics Profiling Expression Database 2026-08-05 10:44:25 2

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