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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Modomics Resource Report Resource Website 10+ mentions |
Modomics (RRID:SCR_007804) | data or information resource, database | A database of RNA modification pathways. The MODOMICS database contains the following types of items: * Modified Bases : Each modified base consists of a unique chemical structure. They are sorted by the regular RNA bases they originate from. The modified base queuosine is special, since it is synthesized first, and then attached to the ribose by a transglycosylation reaction. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). In the download section, the .mol structure files for alare available. * Modification Pathways : Here, we present four pathway graphs showing what modifications emerge from the different bases. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). All lines connecting two modifications are clickable, and show details on a particular reaction. * Enzymes : Lists enzymes that catalyse known reactions between modified bases. In the table, several alternatively used names for the enzymes are given, as well as a list of participating proteins. * Sequences : Shows sequences of RNAs with modifications highlighted. Currently, tRNAs and small and large subunit rRNAs are included in MODOMICS. * Publications : exactly that. | has parent organization: International Institute of Molecular and Cell Biology; Warsaw; Poland | nif-0000-03154 | SCR_007804 | Modomics | 2026-08-10 09:33:19 | 36 | ||||||||||
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Many Microbe Microarrays Database Resource Report Resource Website 10+ mentions |
Many Microbe Microarrays Database (RRID:SCR_007767) | data or information resource, database | M3D is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains Affymetrix expression compendia for Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis. M3D (Many Microbe Microarrays) was developed by the Gardner Lab at Boston University to facilitate the exchange and analysis of high quality, curated, microbial gene expression data. Currently, the database only includes data obtained using Affymetrix GeneChip technology, because the high quality of the platform facilitates cross-laboratory integration of data sets. The database allows downloading of raw data (CEL files) or preprocessed data that has been uniformly normalized with RMA. M3D also enables convenient web-based expression data exploration and visualization - accessable via the Analysis page. | has parent organization: Boston University; Massachusetts; USA | nif-0000-03091 | http://cgs.wustl.edu/~faithj/m3d_mirror/ | http://m3d.bu.edu/ | SCR_007767 | M3D | 2026-08-10 09:33:16 | 26 | ||||||||
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LumbriBASE Resource Report Resource Website 1+ mentions |
LumbriBASE (RRID:SCR_007766) | data or information resource, database | LumbriBASE is aa research tool for both Earthworm biology and environmental pollution monitoring.It provides a simple, easy-to-use access point to the publicly available Lumbricus rubellus sequence and functional data. It is a research tool for both Earthworm biology and environmental pollution monitoring. It is currently being developed by the Worm Consortium. | has parent organization: University of Edinburgh; Scotland; United Kingdom | nif-0000-03090 | SCR_007766 | LumbriBASE | 2026-08-10 09:33:19 | 4 | ||||||||||
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MolMovDB - Database of Macromolecular Movements Resource Report Resource Website 1+ mentions |
MolMovDB - Database of Macromolecular Movements (RRID:SCR_007801) | data or information resource, database | MolMovDB is a database that describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis. The morph server enables the automatic generation of 2D and 3D animations of a plausible or semi-plausible pathway between two static conformations of a protein subunit, such as those conventionally solved by x-ray crystallography. We believe these animations and associated interpolated pathways will become a valuable research and educational tool, allowing the researcher or educator to quickly visualize the chemical transformation of a protein subunit from one conformation into another. With the server, it is easy to determine quickly whether a valid chemical pathway exists between two protein conformations, as in a protein such as calmodulin, or whether, as is the case with diphtheria toxin, the two conformations have no clearly valid chemical pathway and therefore exist most likely as the result of other processes, such as domain swapping. | has parent organization: Yale University; Connecticut; USA | nif-0000-03157 | http://bioinfo.mbb.yale.edu/MolMovDB/ | SCR_007801 | MolMovDB | 2026-08-10 09:33:17 | 3 | |||||||||
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LPFC: A Library of Protein Family Cores Resource Report Resource Website 10+ mentions |
LPFC: A Library of Protein Family Cores (RRID:SCR_007765) | data or information resource, database | LPFC is a database of structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | has parent organization: Stanford University; Stanford; California | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03089 | SCR_007765 | LPFC | 2026-08-10 09:33:15 | 21 | |||||||||
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Legume Information System Resource Report Resource Website 10+ mentions |
Legume Information System (RRID:SCR_007761) | data or information resource, database | LIS is a publicly accessible legume resource that integrates genetic and molecular data from multiple legume species and enables cross-species genomic, transcript and map comparisons. The intent of the LIS is to help researchers leverage data-rich model plants to fill knowledge gaps across crop plant species and provide the ability to traverse between interrelated data types. LIS, a component of the Model Plant Initiative (MPI), is being developed as part of a cooperative research agreement between the National Center for Genome Resources (NCGR) and the USDA Agricultural Research Service (ARS). | FASEB list | nif-0000-03078 | SCR_007761 | LIS | 2026-08-10 09:33:16 | 32 | ||||||||||
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KinMutBase: A registry of disease-causing mutations in protein kinase domains Resource Report Resource Website 1+ mentions |
KinMutBase: A registry of disease-causing mutations in protein kinase domains (RRID:SCR_007759) | data or information resource, database | KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. The current release of the database contains 582 mutations in 20 tyrosine kinase domains and 13 serine/threonine kinase domains. The database refers 1790 cases from 1322 families. KinMutBase is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signaling molecules, in which mutations can lead to diseases, including immunodeficiencies, cancers and endocrine disorders. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme patterns. | has parent organization: University of Tampere; Tampere; Finland | nif-0000-03071 | SCR_007759 | KinmutBase | 2026-08-10 09:33:15 | 1 | ||||||||||
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Systematic Platform for Identifying Mutated Proteins (SysPIMP) Resource Report Resource Website 1+ mentions |
Systematic Platform for Identifying Mutated Proteins (SysPIMP) (RRID:SCR_007954) | SysPIMP | data or information resource, database | A database ofhuman disease-related mutated proteins identified by mass-spectrometry (MS). For achieving this goal, we collected human mutated sequences known to be related to diseases till now. After surveying mutated sequence sources: PMD, OMIM, SwissProt polymorphism, HGMD, etc, we found that currently HGMD contains the largest human gene mutation information. However, because, for academic users, HGMD does not provide with whole data download service, we decided to systematically extract and curate mutation information from PMD, OMIM, SwissProt, MSIPI database to form SysPIMP and provide it free for academic users. | human disease, mutation, protein |
has parent organization: Shanghai Jiao Tong University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
nif-0000-03527 | SCR_007954 | Systematic Platform for Identifying Mutated Proteins | 2026-08-10 09:33:22 | 2 | ||||||||
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SYSTERS Resource Report Resource Website 1+ mentions |
SYSTERS (RRID:SCR_007955) | data or information resource, database | SYSTERS is a database of protein sequences grouped into homologous families and superfamilies. The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Gene, Human, Vertebrate, Genome, Human ORFs | family, gene, genome, human, human orfs, protein, superfamily, vertebrate | has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany | nif-0000-03528 | SCR_007955 | SYSTERS | 2026-08-10 09:33:22 | 7 | |||||||||
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SUPERFAMILY Resource Report Resource Website 100+ mentions |
SUPERFAMILY (RRID:SCR_007952) | data or information resource, database | SUPERFAMILY is a database of structural and functional protein annotations for all completely sequenced organisms. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 1,700 completely sequenced genomes against the hidden Markov models. | protein, hmm, hidden markov model, genome, structure, homology, model, FASEB list |
is listed by: 3DVC is related to: DBD: Transcription factor prediction database has parent organization: University of Bristol; Bristol; United Kingdom |
PMID:11697912 | nif-0000-03511 | http://supfam.org, http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY | SCR_007952 | Superfamily - HMM library and genome assignments server | 2026-08-10 09:33:22 | 345 | |||||||
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
NIGMS GM076990; Canadian Foundation for Innovation ; Michael Smith Foundation for Health Research ; Canadian Institutes for Health Research |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/, https://doi.org/10.17616/R36R54, https://doi.org/10.17616/R36R54 | SCR_008007 | 2026-08-10 09:33:23 | 1145 | |||||
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Search Tool for Interactions of Chemicals Resource Report Resource Website 1000+ mentions |
Search Tool for Interactions of Chemicals (RRID:SCR_007947) | STITCH | data or information resource, database | Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. | drug-target relationship, chemical, chemical-protein interaction, chemical relationship, crystal structure, metabolic pathway interaction, protein, interaction, small molecule, drug, interaction network, FASEB list |
is listed by: OMICtools is related to: Integrated Molecular Interaction Database has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 EMBO ; ProBioC |
PMID:22075997 PMID:19897548 PMID:18084021 |
r3d100012165, OMICS_01589, nif-0000-03499 | https://doi.org/10.17616/R3606X, https://doi.org/10.17616/R3606X | SCR_007947 | STITCH: Chemical-Protein Interactions | 2026-08-10 09:33:21 | 1054 | |||||
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spliceNest Resource Report Resource Website 1+ mentions |
spliceNest (RRID:SCR_007946) | data or information resource, database | A web based graphical tool for exploring gene structure of the human genome, including alternative splicing. It is based on a mapping of the EST consensus sequences (contigs) from GeneNest to the complete human genome. SpliceNest is integrated with GeneNest and the SYSTERS protein sequence cluster set in one framework, permitting an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. Users can search for alignments by browsing, utilizing the graphical chromosome display feature, or performing a cluster, keyword or BLAST search. | est consensus sequence, gene structure, alternative splicing, human genome | has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany | nif-0000-03489 | SCR_007946 | spliceNest | 2026-08-10 09:33:22 | 3 | |||||||||
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SNPSTR Resource Report Resource Website 1+ mentions |
SNPSTR (RRID:SCR_007945) | data or information resource, database | A database containing compound microsatellite-SNP markers in human, dog, mouse, rat and chicken. SNPSTRs are a relatively new type of compound genetic marker which combines a STR marker with one or more tightly linked SNPs. This combination of co-inherited markers evolving at different rates may offer the possibility of gaining better resolved insights into population genetic processes compared to when these different marker types are used separately. SNPSTRs were first described by Mountain et al (2002) who developed experimental protocols for autosomal SNPSTRs which contain a SNP and a microsatellite within 500 base pairs apart. microsatellite-SNP, dog microsatellite-SNP, mouse microsatellite-SNP, rat microsatellite-SNP, chicken microsatellite-SNP | chicken microsatellite-snp, dog microsatellite-snp, human microsatellite-snp, microsatellite-snp, mouse microsatellite-snp, rat microsatellite-snp | has parent organization: Imperial College London; London; United Kingdom | nif-0000-03482 | http://www3.imperial.ac.uk/theoreticalgenomics/data-software | SCR_007945 | SNPSTR | 2026-08-10 09:33:20 | 1 | ||||||||
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snoRNABase- a comprehensive database of human H/ACA and C/D box snoRNAs. Resource Report Resource Website 50+ mentions |
snoRNABase- a comprehensive database of human H/ACA and C/D box snoRNAs. (RRID:SCR_007939) | data or information resource, database | This is a database of human C/D box and H/ACA modification guide RNAs. Information on a particular snoRNA can be accessed by three ways: 1- On the Search page, just type the name of the snoRNA (for example ACA17) in the Id window. 2- The Find guide RNA contains the sequences of the human ribosomal rRNAs 28S, 18S and 5.8S, and of the snRNAs U1, U2, U4, U5 and U6, with the positions of modified (2''O-ribose methylated or pseudo-uridinylated) nucleotides, and the identity of the corresponding modification guide RNAs. You can click on the name of the relevant snoRNA. 3- By utilizing the link to the UCSC Human Genome Browser. | human c/d box, human h/aca, human rna, human snorna | has parent organization: Paul Sabatier University - Toulouse III; Toulouse; France | nif-0000-03476 | SCR_007939 | snoRNABase | 2026-08-10 09:33:20 | 60 | |||||||||
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Sno/scaRNAbase Resource Report Resource Website 1+ mentions |
Sno/scaRNAbase (RRID:SCR_007938) | data or information resource, database | A curated database for small nucleolar RNAs and small cajal body-specific RNAs. It presents sno/scaRNA-associated genetic and functional data and provides access to several other database sources via web-accessible search interfaces. Consisting of 1979 sno/scaRNA records obtained from 85 organisms, sno/scaRNAbase is a combination of systematic literature curation and annotation effort. small nucleolar RNA, small cajal body-specific RNA | scarna, small cajal body-specific rna, small nucleolar rna, snorna | has parent organization: Fudan University; Shanghai; China | nif-0000-03475 | http://bioinfo.fudan.edu.cn/snoRNAbase.nsf | SCR_007938 | Sno/scaRNAbase | 2026-08-10 09:33:21 | 4 | ||||||||
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SNAPPI Resource Report Resource Website 1+ mentions |
SNAPPI (RRID:SCR_007937) | data or information resource, database | An object-oriented database of domain-domain interactions observed in structural data. SNAPPI-DB is a useful resource for any analysis of structures but has been opitmised for analysis on domain-domain interactions and domain-ligand interactions. The database has already been employed for 3 studies on the properties of domain-domain interactions and is currently being employed to train a protein-protein interaction predictor and a functional residue predictor. SNAPPI-DB has several features which are not available in other databases, including links to the MSD, speed, being object oriented, storage of multiple domain definitions, and storage of Protein Quaternary Structures (PQS). | domain-domain interactions, domain interactions, domain-ligand interaction, interaction structure, protein-protein interaction, structure database | has parent organization: University of Dundee; Scotland; United Kingdom | SCR_007937 | SNAPPI | 2026-08-10 09:33:21 | 2 | ||||||||||
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YDPM - Yeast Deletion Project Resource Report Resource Website 10+ mentions |
YDPM - Yeast Deletion Project (RRID:SCR_007977) | data or information resource, database | This database contains different yeast strains searchable by ORF and gene name, and serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The database is hyperlinked with other public databases. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. 5791 heterozygous diploid and 4706 homozygous diploid deletion strains were monitored in parallel using molecular barcodes on fermentable (YPD, YPDGE) and non-fermentable substrates (YPG, YPE, YPL). The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. Strains can be searched by ORF or Gene name to access growth measurements and data plots for each strain. Category: Genomics Databases (non-vertebrate) Subcategory: Fungal genome databases Category: Organelle databases Subcategory: Mitochondrial genes and proteins | has parent organization: Stanford University; Stanford; California | nif-0000-03648 | SCR_007977 | YDMP | 2026-08-10 09:33:22 | 13 | ||||||||||
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Vir-Mir Resource Report Resource Website 1+ mentions |
Vir-Mir (RRID:SCR_007971) | data or information resource, database | A database containing predicted viral miRNA candidate hairpins. Users may query the putative miRNA hairpins of a specific viral species by the hierarchical menu or by search function using the GenBank Identifier or RefSeq accession number. In addition, users can also search for the putative target genes of a particular viral miRNA hairpins by a RNAhybrid service link. We have previously identified human intronic microRNA as well as zebrafish microRNA. The microRNA hairpin discovery pipeline was also applied to discover viral encoded microRNAs. All viral genomes were obtain from NCBI. The classification of virus is based on the taxonomy table of NCBI (Jun, 2006). Totally, the genomes of 2266 viruses were analyzed. The 3’-UTR regions of human, mouse, rat, zebrafish, arabidopsis and rice genes are available for search. | hairpin, microrna, mirna, viral genome, viral mirna | nif-0000-03631 | SCR_007971 | Vir-Mir | 2026-08-10 09:33:22 | 7 | ||||||||||
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Unigene MicroSatellite database Resource Report Resource Website |
Unigene MicroSatellite database (RRID:SCR_007968) | data or information resource, database | This is a database of microsatellite sequences (short tandem repeats useful in gene comparison and kinship studies) present in 80 genomes. Users can search the database by microsatellite type, repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. They can also search by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. Microsatellites, also known as simple sequence repeats (SSRs) or simple tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications including genome characterization and mapping. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type simple (perfect) and compound (perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar) and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of any desired microsatellite. | has parent organization: Guru Gobind Singh Indraprastha University; Delhi; India | nif-0000-03605 | http://veenuash.info/web1/index.htm | SCR_007968 | UgMicroSatdb : Database for mining microsatellites from Unigenes, UgMicroSatdb | 2026-08-10 09:33:22 | 0 |
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