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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SitEx Resource Report Resource Website 1+ mentions |
SitEx (RRID:SCR_006122) | SitEx | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms. | projection, protein, functional site, exon, blast, structure, function, gene, amino acid, encoding gene, proteome, ligand, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Ministry of Science and Education 14.740.11.0001; Ministry of Science and Education 07.514.11.4003; Interdisciplinary Integrative Project 35 of SB RAS ; Russian Foundation for Basic Research 11-04-92712; EU-FP7 260429; Program of RAS ; DAAD Leonard Euler Program Grant |
PMID:22139920 | THIS RESOURCE IS NO LONGER IN SERVICE. | biotools:sitex, nlx_151602 | https://bio.tools/sitex | SCR_006122 | SitEx Database | 2026-02-13 10:55:46 | 1 | ||||
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CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | data or information resource, database | Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site. | carbohydrate, carbohydrate-binding, carbohydrate binding module, carbohydrate esterase, catalytic binding, glycosidic bond, glycosidic hydrolase, glycosyl transferase, polysaccharide lyase, enzyme class, enzyme, module, genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
PMID:24270786 | biotools:cazy, OMICS_01677, nif-0000-02642, SCR_012935 | https://bio.tools/cazy | SCR_012909 | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-02-11 10:58:41 | 2045 | ||||||
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PTMcode Resource Report Resource Website 10+ mentions |
PTMcode (RRID:SCR_002046) | PTMCode | data or information resource, database | Database of known and predicted functional associations between protein posttranslational modifications (PTMs) within proteins. In its first release it contains 13 different PTM types. PTM types are abbreviated in a two letter code as: Ph (phosphorylation), NG (N-linked glycosylation), Ac (acetylation), OG (O-linked glycosylation), Ub (ubiquitination), Me (methylation), SM (SUMOylation), Hy (hydroxylation), Ca (carboxylation), Pa (palmitoylation), Su (sulfation), Ni (nitrosylation) and CG (C-linked glycosylation). These PTMs are present in 25,765 proteins of 8 different eukaryotes. The database is focused on the exploration of the global post-translational regulation of proteins, not only by describing the set of its modifications, but by identifying the functional associations among the PTMs present in the protein. To do that, they combine five different evidence channels based on a literature survey, the modified residue co-evolution, their structural proximity, their competition for the same residue and the location within PTM highly-enriched protein regions (hotspots) and show the functional associations within the context of the protein architecture. | protein posttranslational modification, protein, function, phosphorylation, n-linked glycosylation, acetylation, o-linked glycosylation, ubiquitination, methylation, sumoylation, hydroxylation, carboxylation, palmitoylation, sulfation, nitrosylation, c-linked glycosylation |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
PMID:23193284 | Free, Freely available | OMICS_01915 | SCR_002046 | 2026-02-11 10:56:22 | 13 | |||||||
|
ChIPBase Resource Report Resource Website 100+ mentions |
ChIPBase (RRID:SCR_005404) | ChIPBase | data or information resource, database | A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chip-seq, gene, rna, microrna, long non-coding rna, non-coding, transcription factor binding site, protein, transcriptional regulation, annotation, regulatory element, transcription factor, genome, network, FASEB list |
is listed by: OMICtools has parent organization: Sun Yat-sen University; Guangdong; China |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00527 | SCR_005404 | 2026-02-11 10:57:08 | 145 | ||||||||
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Genomicus Resource Report Resource Website 50+ mentions |
Genomicus (RRID:SCR_011791) | Genomicus | data or information resource, database | A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. | genome, gene, synteny, browser, FASEB list | is listed by: OMICtools | PMID:23193262 | OMICS_00914 | SCR_011791 | 2026-02-11 10:58:30 | 52 | ||||||||
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QuartetS-DB Resource Report Resource Website |
QuartetS-DB (RRID:SCR_011981) | QuartetS-DB | data or information resource, database | A large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. Contnet includes orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic), covering >7 million proteins and 4 million pairwise orthologs; Orthologous groups, comprising >300000 groups of orthologous proteins and >236000 corresponding gene trees; and inparalog groups, comprising >500000 groups of inparalogs. |
is listed by: OMICtools has parent organization: BHSAI; Maryland; USA |
PMID:22726705 | OMICS_01693 | SCR_011981 | 2026-02-11 10:58:31 | 0 | |||||||||
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ProRepeat Resource Report Resource Website 1+ mentions |
ProRepeat (RRID:SCR_006113) | ProRepeat | data or information resource, database | ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats' corresponding codons. | amino acid, tandem, repeat, protein, sequence, nucleotide sequence, repeat fragment, protein repeat, proteome, sequence length, gene, taxon, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB is related to: RefSeq has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
PMID:22102581 | nlx_151587, biotools:prorepeat | https://bio.tools/prorepeat | SCR_006113 | 2026-02-11 10:57:16 | 1 | |||||||
|
SILVA Resource Report Resource Website 10000+ mentions |
SILVA (RRID:SCR_006423) | data or information resource, database | High quality ribosomal RNA databases providing comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Supplementary services include a rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Alignment tool, SINA, is available for download as well as available for use online. | ribosomal rna, gene sequence, gene, sequence, alignment, taxonomy, 16s, 18s, 23s, 28s, phylogeny, probe, primer, alignment service, fish, arb, ribocon, geoblast, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: RNAcentral is related to: ARB project is related to: SINA is related to: European ribosomal RNA database has parent organization: German Collection of Microorganisms and Cell Cultures |
German Collection of Microorganisms and Cell Cultures | PMID:23193283 PMID:24293649 PMID:17947321 |
biotools:silva, OMICS_01514, nif-0000-03464, r3d100011323, rid_000103 | https://bio.tools/silva https://doi.org/10.17616/R3FP60 |
SCR_006423 | SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-02-11 10:57:24 | 13429 | ||||||
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Cell Cycle Ontology Resource Report Resource Website |
Cell Cycle Ontology (RRID:SCR_007085) | CCO | data or information resource, ontology, controlled vocabulary | An application ontology integrating knowledge about the eukaryotic cell cycle. | obo | is listed by: BioPortal | nlx_157355 | http://www.semantic-systems-biology.org/cco/ | SCR_007085 | 2026-02-12 09:44:22 | 0 | ||||||||
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YinOYang Resource Report Resource Website 100+ mentions |
YinOYang (RRID:SCR_001605) | YinOYang | data analysis service, analysis service resource, production service resource, service resource, software application, software resource | Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. | neural network, prediction, o-beta-glcnac attachment site, protein sequence, protein, sequence, glycosylation site, proteome, post-translational modification, protein function, glycoprotein, bio.tools |
uses: NetPhos is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Danish National Research Foundation | PMID:11928486 | Free, Freely available | nlx_153865, biotools:yinoyang | https://bio.tools/yinoyang | SCR_001605 | 2026-02-13 10:54:53 | 111 | |||||
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JGI Genome Portal Resource Report Resource Website 500+ mentions |
JGI Genome Portal (RRID:SCR_002383) | data or information resource, organization portal, portal, department portal | Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. | gene, computation, genome, genomics, model organism, assembly, annotation, sequenced genome, metagenome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute is parent organization of: Takifugu rubripes Genome |
Department of Energy | PMID:24225321 PMID:22110030 |
nif-0000-21230, SCR_004706, OMICS_01654, biotools:jgi_genome_portal, nlx_69965 | http://genome.jgi-psf.org https://bio.tools/jgi_genome_portal |
http://genome.jgi-psf.org/ | SCR_002383 | JGI Genome Portal, DOE Joint Genome Institute Genome Portal | 2026-02-13 10:55:01 | 865 | |||||
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Eukaryotic Linear Motif Resource Report Resource Website 100+ mentions |
Eukaryotic Linear Motif (RRID:SCR_003085) | ELM | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive. | linear motif, regulatory protein, motif, protein sequence, functional site, prediction, disease, virus, cell compartment, phylogeny, globular domain clash, structure, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: SMART is related to: Pfam has parent organization: European Molecular Biology Laboratory |
EMBL international PhD program ; EMBL Interdisciplinary PostDoc fellowship ; Federal Government Department of Education and Science FKZ01GS0862; European Community Seventh Framework Programme FP7/2009 241955; European Community Seventh Framework Programme FP7/2009 242129; Polish Ministry of Science and Higher Education IP2010-0483-70; Biotechnology and Biological Sciences Research Council BB/F010486/1; Region Alsace and College Doctoral Europeen ; Science Foundation Ireland 08/IN.1/B1864; BBSRC BB/I006230/1; German Research Foundation SFB796; Swiss National Science Foundation |
PMID:22110040 | Free, Available for download, Freely available | biotools:elm, nif-0000-30486 | https://bio.tools/elm | SCR_003085 | Eukarotic Linear Motif resource for Functional Sites in Proteins | 2026-02-13 10:55:11 | 296 | ||||
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JASPAR Resource Report Resource Website 1000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Novo Nordisk Foundation ; European Union ; EMBRACEa Sixth Framework Network of Excellence ; Sars Centre ; Carlsberg Foundation |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-02-13 10:55:09 | 4766 | |||
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mGOASVM Resource Report Resource Website 1+ mentions |
mGOASVM (RRID:SCR_013098) | mGOASVM | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available. | subcellular localization, gram-negative protein, virus, protein |
is listed by: OMICtools has parent organization: Hong Kong Polytechnic University; Hong Kong; China |
PMID:23130999 | OMICS_01627 | SCR_013098 | 2026-02-13 10:57:04 | 4 | ||||||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | data repository, storage service resource, image collection, d spatial image, data or information resource, service resource, database | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-02-13 10:56:04 | 7 | |||||
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AutoPrime Resource Report Resource Website 1+ mentions |
AutoPrime (RRID:SCR_000097) | AutoPrime | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Server to rapidly design primers for real-time PCR measurement of eukaryotic expression. | primer, real-time pcr, primer design |
is listed by: OMICtools has parent organization: German Cancer Research Center |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02333 | SCR_000097 | 2026-02-13 10:54:36 | 7 | ||||||||
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KnowPredsite Resource Report Resource Website 1+ mentions |
KnowPredsite (RRID:SCR_011974) | KnowPredsite | data analysis service, production service resource, service resource, analysis service resource | A knowledge-based data analysis service to predict the localization site(s) of both single-localized and multi-localized proteins. | homolog, protein, subcellular localization |
is listed by: OMICtools has parent organization: Academia Sinica; Taipei; Taiwan |
PMID:19958518 | OMICS_01625 | SCR_011974 | KnowPredsite: A web server for predicting single and multiple subcellular localization sites, KnowPred site, KnowPredsite: A general protein subcellular localization predictor for eukaryotes and prokaryotes | 2026-02-13 10:56:50 | 1 | |||||||
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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 | 2026-02-13 10:56:50 | 203 | |||||||
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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 | 2026-02-13 10:56:50 | 957 | ||||||
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Euk-mPLoc Resource Report Resource Website 50+ mentions |
Euk-mPLoc (RRID:SCR_011971) | Euk-mPLoc | data analysis service, production service resource, service resource, analysis service resource | Data analysis service for predicting subcellular localization of eukaryotic proteins including those with multiple sites. Euk-mPLoc covers 22 eukaryotic subcellular locations. | subcellular location |
is listed by: OMICtools has parent organization: Cell-PLoc |
PMID:17397210 | Acknowledgement requested | OMICS_01621 | SCR_011971 | Euk-mPLoc 2.0: Predicting subcellular localization of eukaryotic proteins including those with multiple sites | 2026-02-13 10:56:50 | 75 |
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