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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Molecular Connections NetPro Resource Report Resource Website 1+ mentions |
Molecular Connections NetPro (RRID:SCR_000395) | MolCon, NetPro | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references. The strength of NetPro lies in the complete manual curation of literature. It covers several entities other than proteins as interacting partners, like RNA, DNA, processes, etc. with well defined, exhaustive interaction terms. NetPro has received several accolades for the quality and quantity of data it contains. It has become an important resource for target identification, validation and pathway research and has subscribers from all over the globe including 3 of the top 5 pharmas. | drug, molecular, pharmaceutical, interaction, protein interaction, protein, protein-protein interaction, nucleic acid-protein, small molecule-protein, nucleic acid, small molecule |
is related to: IMEx - The International Molecular Exchange Consortium works with: IMEx - The International Molecular Exchange Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20877 | SCR_000395 | 2026-08-06 09:25:10 | 1 | ||||||||
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SynaptomeDB Resource Report Resource Website |
SynaptomeDB (RRID:SCR_000157) | SynaptomeDB | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Ontology-based knowledgebase for synaptic genes. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion / cytoskeletal proteins, scaffold proteins, transporters, and others. It integrates various and complex data sources for synaptic genes and proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, protein, pathway, synaptome, protein-protein interaction, synaptic gene, synapse, motif, presynaptic, postsynaptic, vesicle |
is related to: Gene Ontology has parent organization: Johns Hopkins University; Maryland; USA |
PMID:22285564 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157656 | SCR_000157 | 2026-08-06 09:25:07 | 0 | |||||||
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BindingDB Resource Report Resource Website 10+ mentions |
BindingDB (RRID:SCR_000390) | database, data or information resource | Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs . | drug, drug discovery, drug target, binding affinity, protein interaction, small molecule-protein interaction, interaction, protein, small molecule, FASEB list |
is related to: PSICQUIC Registry is related to: canSAR has parent organization: University of California at San Diego; California; USA |
NIGMS GM070064; NSF 9808318; National Institute of Standards and Technology ; NIGMS R24 GM144232 |
PMID:26481362 PMID:17145705 |
Free, Freely available | r3d100012074, nif-0000-02603 | https://doi.org/10.17616/R3ZS9T | SCR_000390 | BindingDB | 2026-08-06 09:25:10 | 41 | |||||
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Domain Interaction MAp Resource Report Resource Website |
Domain Interaction MAp (RRID:SCR_000731) | database, data or information resource | DIMA, the Domain Interaction Map, aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains. The scope of the resource comprises both experimental data and computational predictions. Several methods and datasets have been integrated, already and inclusion of others is under way. | protein, protein-protein interactions | PMID:21097782 PMID:17999995 |
nif-0000-02752 | http://mips.gsf.de/genre/proj/dima2 | SCR_000731 | DIMA | 2026-08-06 09:25:14 | 0 | ||||||||
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Smart Dictionary Lookup Resource Report Resource Website |
Smart Dictionary Lookup (RRID:SCR_000568) | Smart Dictionary Lookup | service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. System that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm. | gene, protein |
uses: UniProt uses: BioThesaurus is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
PMID:17698493 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01198 | SCR_000568 | 2026-08-06 09:25:12 | 0 | |||||||
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DNA-Protein Interaction Database Resource Report Resource Website |
DNA-Protein Interaction Database (RRID:SCR_000754) | database, data or information resource | The database NPIDB (Nucleic acid Protein Interaction DataBase) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from Protein Data Bank (PDB) (1932 complexes in the end of 2007). It is equipped with a web-interface and a set of tools for extracting biologically meaningful characteristics of complexes. They are committed to satisfy all potential database users in order to: 1. Provide an essential information on structural features of DNA-protein and RNA-protein interaction for the users who need to get acquainted with the problem. 2. Give an effective access to the reasonably structured information about all DNA-protein and RNA-protein complexes containing in PDB. 3. Allow all visitors a quick access to our own research. | complex, data bank, dna, nucleic acid, protein, rna | has parent organization: Moscow State University; Moscow; Russia | PMID:17977883 PMID:26656949 |
nif-0000-20838 | SCR_000754 | NPIDB | 2026-08-06 09:25:15 | 0 | ||||||||
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GlycoMod Resource Report Resource Website 100+ mentions |
GlycoMod (RRID:SCR_001602) | GlycoMod | data analysis service, production service resource, analysis service resource, service resource | A tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. This is done by comparing the mass of the glycan to a list of pre-computed masses of glycan compositions. The program can be used with free or derivatised glycans and for glycopeptides where the peptide mass or protein is known. Compositional constraints can be applied to the output. Note: You can use GlycanMass to calculate the mass of an oligosaccharide structure from its oligosaccharide composition. | predict, oligosaccharide structure, protein, mass, oligosaccharide, glycopeptide, glycoprotein, oligosaccharide composition, mass spectrometry, glycosylation, composition, glycan, structure, n-linked oligosaccharide, o-linked oligosaccharide, monosaccharide residue | has parent organization: ExPASy Bioinformatics Resource Portal | PMID:11680880 | Free, Freely available | nlx_153859 | SCR_001602 | GlycoMod Tool | 2026-08-06 09:25:25 | 109 | ||||||
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AMPDB: Arabidopsis Mitochondrial Protein Database Resource Report Resource Website |
AMPDB: Arabidopsis Mitochondrial Protein Database (RRID:SCR_000758) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The Arabidopsis Mitochondrial Protein Database is an Internet-accessible relational database containing information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. This database, and the proteomic data contained in it for Arabidopsis mitochondria, have been accepted for publication in The Plant Cell. | arabidopsis, cell, mitochondria, mitochondrial, model, plant, protein, proteomic, thaliana | has parent organization: University of Western Australia; Perth; Australia | PMID:15608271 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21026 | SCR_000758 | AMPDB | 2026-08-06 09:25:17 | 0 | |||||||
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GlyProt Resource Report Resource Website 10+ mentions |
GlyProt (RRID:SCR_001560) | GlyProt | data analysis service, production service resource, analysis service resource, service resource | Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php | glycosylation, protein, in silico, 3d structure, protein structure, glycan, n-glycan, glycoprotein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: SWEET-DB has parent organization: glycosciences.de |
DFG | PMID:15980456 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:glyprot, nlx_152875 | https://bio.tools/glyprot | http://www.glycosciences.de/glyprot/ | SCR_001560 | GlyProt - In Silico Glycosylation of Proteins | 2026-08-06 09:25:24 | 39 | |||
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Bio Resource for Array Genes Database Resource Report Resource Website |
Bio Resource for Array Genes Database (RRID:SCR_000748) | database, data or information resource | Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona. | drug, experiment, expression, fly, functional, gene, array, biological, biology, c. elegans, cluster, database, disease, human, microarray, mouse, protein, rat, target, tissue | has parent organization: University of Arizona; Arizona; USA | nif-0000-10165 | SCR_000748 | BioRag | 2026-08-06 09:25:17 | 0 | |||||||||
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MitoMiner Resource Report Resource Website 50+ mentions |
MitoMiner (RRID:SCR_001368) | database, data or information resource | A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. | mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list |
uses: HomoloGene uses: UniProt uses: KEGG uses: OMIM uses: The Human Protein Atlas uses: Gene Ontology |
MRC | PMID:22121219 PMID:19208617 |
Public, Acknowledgement requested, Code: | nlx_152504 | SCR_001368 | MitoMiner - A database of the mitochondrial proteome | 2026-08-06 09:25:23 | 76 | ||||||
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big-PI Predictor Resource Report Resource Website 50+ mentions |
big-PI Predictor (RRID:SCR_001599) | big-PI Predictor | data analysis service, production service resource, analysis service resource, service resource | Prediction tool locating potential GPI-modification sites in precursor sequences applied for large-scale protein sequence database searches. The composite prediction function (with separate parametrization for metazoan and protozoan proteins) consists of terms evaluating both amino acid type preferences at sequence positions near a supposed omega-site as well as the concordance with general physical properties encoded in multi-residue correlation within the motif sequence. The latter terms are especially successful in rejecting non-appropriate sequences from consideration. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set of fully annotated sequences from the SWISS-PROT database as well as with a newly created database big-Pi (more than 300 GPI-motif mutations extracted from original literature sources). The accuracy of predicting the effect of mutations in the GPI sequence motif was above 83 %. | prediction, glycoprotein, protein, glycosylphosphatidylinositol, genome annotation, target selection, FASEB list | has parent organization: University of Vienna; Vienna; Austria | PMID:10497036 PMID:10871885 |
Free, Freely available | nlx_153855 | http://www.embl.de/beisenha/gpi/gpi_p%20rediction.html | SCR_001599 | big-PI Predictor: GPI Modification Site Prediction | 2026-08-06 09:25:25 | 50 | |||||
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A Classification of Mobile genetic Elements Resource Report Resource Website 10+ mentions |
A Classification of Mobile genetic Elements (RRID:SCR_001694) | ACLAME | database, data or information resource | A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME. | mobile genetic element, phage genome, plasmid, virus, prophage, transposon, protein, gene, classification, data analysis service, prophage prediction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Free University of Brussels; Brussels; Belgium is parent organization of: MeGO |
ESTEC contract ESTEC 16370/02/NL/CK | PMID:19933762 PMID:14681355 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02533, OMICS_01528, biotools:aclame | https://bio.tools/aclame | SCR_001694 | ACLAME: A CLAssification of Mobile genetic Elements | 2026-08-06 09:25:27 | 31 | ||||
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Spliceosome Database Resource Report Resource Website 10+ mentions |
Spliceosome Database (RRID:SCR_002097) | Spliceosome Database | database, data or information resource | A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes. | splicing, mass spectrometry, protein, rna, complex, spliceosome, small nuclear rna, structure, dynamics, ortholog, gene |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:23118483 | Free, Freely available | OMICS_01891 | SCR_002097 | Spliceosome Database - A source of information for the SLPICEOSOME: The large ribonucleoprotein complex responsible for pre-mRNA splicing, Spliceosome Component Database | 2026-08-06 09:25:34 | 11 | ||||||
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PTMcode Resource Report Resource Website 10+ mentions |
PTMcode (RRID:SCR_002046) | PTMCode | database, data or information resource | 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 | 2026-08-06 09:25:33 | 13 | |||||||
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WD repeat Family of Proteins Resource Report Resource Website |
WD repeat Family of Proteins (RRID:SCR_002160) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. This website contains a library of WD-repeat containing proteins in which the repeats appear as multi-aligned sets. WD-repeat-containing proteins are those that contain 4 or more copies of the WD-repeat (tryptophan-aspartate repeat), a sequence motif approximately 31 amino acids long, that encodes a structural repeat. This repeat is described by the following profile, where x is ANY amino acid. By clicking on each high-lighted character you will obtain the distribution of amino acids found at that position of the repeat among an aligned set of WD-repeat containing proteins. The tertiary structure of only one member of this family has been determined, that of the G protein beta subunit, which contains 7 WD-repeats. Each of the 7 repeats folds into a small antiparallel beta-sheet. The over-lines above indicate the position of these strands, with a being the strand closest to the central pore and d at the external surface of the folded protein. These sheets are arranged around a central pseudosymmetry axis into a beta propeller. The WD-repeat-containing proteins form a very large family that is diverse in both its function and domain structure. Within all these proteins the WD-repeat domains are thought to have two common features: the domain folds into a beta propeller; and the domains form a platform without any catalytic activity on which multiple protein complexes assemble reversibly. The fact that these proteins play such key roles in the formation of protein-protein complexes in nearly all the major pathways and organelles unique to eukaryotic cells has two important implications. It supports both their ancient and proto eukaryotic origins and supports a likely association with many genetic diseases. | eukaryotic, function, genetic, align, amino acid, ancient, antiparallel, aspartate, beta, cell, disease, domain, g protein, multi-aligned, organelle, origin, pathway, propeller, protein, proto, pseudosymmetry, sheet, structural, tertiary, tryptophan, wd-repeat | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20949 | SCR_002160 | WD repeat Family of Proteins | 2026-08-06 09:25:36 | 0 | |||||||||
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TcoF Resource Report Resource Website 10+ mentions |
TcoF (RRID:SCR_002158) | TcoF | database, data or information resource | Database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors). | protein, regulation, transcription, transcription factor, transcription co-factor, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:20965969 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tcof-db, OMICS_01865 | https://bio.tools/tcof-db | SCR_002158 | Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins, TcoF-DB, TcoF - Dragon database of transcription co-factors and transcription factor interacting proteins | 2026-08-06 09:25:33 | 10 | |||||
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Genome Network Platform Resource Report Resource Website 10+ mentions |
Genome Network Platform (RRID:SCR_001737) | GNP | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed. | gene, genome, chip, human, interaction, micro array, protein, protein-protein interaction, qrt-pcr, rat, rna, sequence, short rna, tiling array, transcription, transcription control, transcription factor, transcription starting position, yeast two hybrid, data set, cage, data analysis service |
is listed by: 3DVC has parent organization: National Institute of Genetics; Shizuoka; Japan |
PMID:24927841 | Free, Freely Available | nif-0000-10237 | http://genomenetwork.nig.ac.jp/index_e.html | SCR_001737 | 2026-08-06 09:25:27 | 20 | ||||||
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ASPicDB Resource Report Resource Website 1+ mentions |
ASPicDB (RRID:SCR_002102) | ASPicDB | database, data or information resource | A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation. | annotation, splicing pattern, gene, transcript, intron, protein, variant, alternative splicing, splicing, blast, exon, u2, u12, isoform |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bari; Bari; Italy |
Normal, Cancer | PMID:21051348 PMID:18388144 |
Free, Freely available | OMICS_01882 | http://srv00.ibbe.cnr.it/ASPicDB/ | SCR_002102 | Alternative Splicing Prediction Data Base, ASPicDB - A Database tool for alternative splicing analysis | 2026-08-06 09:25:32 | 7 | ||||
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AutoPSI database of predicted SCOP classifications Resource Report Resource Website |
AutoPSI database of predicted SCOP classifications (RRID:SCR_001923) | database, data or information resource | Searchable database for predicted protein sequences and structures. It has the ability to search through PDB ID, UniProt ID, and descriptive classifiers. | protein, structure, sequence, database, search, uniprot | has parent organization: Ludwig-Maximilians-University; Munich; Germany | Ludwig Maximilians Universitat Munchen | PMID:17932066 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02588 | SCR_001923 | Automated Protein Structure Identification (AutoPSI) database, AutoPSI, AutoPSI Database, Automated Protein Structure Identification database | 2026-08-06 09:25:31 | 0 |
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