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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PINT Resource Report Resource Website 100+ mentions |
PINT (RRID:SCR_007856) | PINT | data or information resource, database | A protein-protein interactions thermodynamic database which contains data of several thermodynamic parameters along with sequence and structural information experimental conditions and literature information. Each entry contains numerical data for features of the interacting proteins such as the free energy change, dissociation constant, association constant, enthalpy change, and heat capacity change. PINT includes: the name and source of the proteins involved in binding, SWISS-PROT and Protein Data Bank (PDB) codes, secondary structure and solvent accessibility of residues at mutant positions, measuring methods, and experimental conditions such as buffers, ions and additives, and literature information. PINT is cross-linked with other related databases such as PIR, SWISS-PROT, PDB and the NCBI PUBMED literature database. | database, protein protein interaction, thermodynamic, protein structure, protein database, FASEB list |
uses: UniProtKB uses: PubMed |
nif-0000-03291 | SCR_007856 | Protein-protein Interactions Thermodynamic Database | 2026-08-10 09:33:19 | 119 | ||||||||
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Phytome Resource Report Resource Website |
Phytome (RRID:SCR_007852) | data or information resource, database | An online comparative genomics resource that is built upon publicly available sequence and map information from a diverse set of plant species, with a focus on the angiosperms, or flowering plants. It provides an interface to the results from a variety of phylogenomic analyses. Phytome is designed to facilitate functional genomics, molecular breeding and evolutionary studies in model and non-model plant species. Currently, Phytome contains phylogenetic and functional information for predicted protein sequences ("Unipeptides"). Future development will incorporate data and tools for analysis of sequence-based comparative maps. | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | nif-0000-03284 | SCR_007852 | Phytome | 2026-08-10 09:33:20 | 0 | ||||||||||
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Plant Protein Phosphorylation Database Resource Report Resource Website 10+ mentions |
Plant Protein Phosphorylation Database (RRID:SCR_007841) | P3DB | data or information resource, database | It was established with an overall objective to provide a resource of protein phosphorylation data from multiple plants. P3DB was constructed with a dataset from oilseed rape. The data was obtained using a combination of data-dependent neutral loss and multistage activation mass spectrometry. The dataset includes 14,670 non-redundant phosphorylation sites from 8,894 phospho-peptides in 6,382 substrate proteins. | FASEB list | has parent organization: University of Missouri; Missouri; USA | nif-0000-03235 | SCR_007841 | Plant Protein Phosphorylation Database | 2026-08-10 09:33:20 | 34 | ||||||||
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ORENZA : a database of ORphan ENZyme Activities Resource Report Resource Website 1+ mentions |
ORENZA : a database of ORphan ENZyme Activities (RRID:SCR_007836) | data or information resource, database | ORENZA is a relational database of Orphan Enzyme Activities. ORENZA provides an accurate and up to date list of Enzyme Activities for which no sequences are available in the main sequence protein databases. Orphan enzyme activities correpond to the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), and which are not associated with any amino acid sequences in the major public databases. | nif-0000-03224 | SCR_007836 | ORENZA | 2026-08-10 09:33:18 | 3 | |||||||||||
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IRIS - International Rice Information System Resource Report Resource Website 1+ mentions |
IRIS - International Rice Information System (RRID:SCR_007755) | data or information resource, database | IRIS is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars. This includes germplasm pedigrees, field evaluations, structural and functional genomic data (including links to external plant databases) and environmental (GIS) data. | crop, rice, rice funcitonal genomics, rice genetics, rice germplasm | nif-0000-03048 | SCR_007755 | IRIS | 2026-08-10 09:33:16 | 8 | ||||||||||
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iProLINK Resource Report Resource Website 1+ mentions |
iProLINK (RRID:SCR_007752) | data or information resource, database | iProLINK (integrated Protein Literature, INformation and Knowledge) has been developed as a resource to facilitate text mining in the area of literature-based database curation, named entity recognition, and protein ontology development. The collection of data sources can be utilized by computational and biological researchers to explore literature information on proteins and their features or properties. The data sources for bibliography mapping and feature evidence attribution include mapped citations (PubMed ID to protein entry and feature line mapping) and annotation-tagged literature corpora. The latter includes several hundred abstracts and full-text articles tagged with experimentally validated post-translational modifications (PTMs) annotated in the PIR protein sequence database. | nif-0000-03045 | SCR_007752 | iProLINK | 2026-08-10 09:33:15 | 3 | |||||||||||
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L1Base Resource Report Resource Website 10+ mentions |
L1Base (RRID:SCR_007750) | data or information resource, database | L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included in the database. | fl-l1, flni-l1, full length l1, full length non-intact l1, l1, line, line-1, orf2-l1 | nif-0000-03076 | SCR_007750 | L1Base | 2026-08-10 09:33:18 | 23 | ||||||||||
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The Intronerator Resource Report Resource Website 1+ mentions |
The Intronerator (RRID:SCR_007745) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing. It includes: Tracks Display- View splicing diagrams for any gene in the Sanger C. elegans database alongside cDNA and EST alignments. Retrieve DNA sequences with the exons in upper case. Search the literature. Alt Splicing Catalog - As defined by Chuck's altGraphX process. A frames based viewer linking to the genome browser. Alt-Splicing Catalog - A catalog of genes for which the cDNA and EST evidence indicates alternative splicing. | has parent organization: University of California at Santa Cruz; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03037 | SCR_007745 | The Intronerator | 2026-08-10 09:33:16 | 1 | |||||||||
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IPD-HPA - Human Platelet Antigens Resource Report Resource Website 1+ mentions |
IPD-HPA - Human Platelet Antigens (RRID:SCR_007747) | data or information resource, database | A centralised repository for the data which define the human platelet antigens (HPA). Alloantibodies against human platelet antigens are involved in neonatal alloimmune thrombocytopenia, post-transfusion purpura and refractoriness to random donor platelets. The Human Platelet Antigen (HPA) nomenclature system was adopted in 1990 to overcome problems with the previous nomenclature. Since then more antigens have been described and meanwhile the molecular basis of many has been resolved, and the nomenclature was revised in 2003. | polymorphism, immuno-polymorphism, alloantigen |
is listed by: 3DVC has parent organization: European Bioinformatics Institute |
nif-0000-03040 | SCR_007747 | Immuno polymorphism database, IPD-HPA | 2026-08-10 09:33:18 | 5 | |||||||||
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PLprot Resource Report Resource Website 10+ mentions |
PLprot (RRID:SCR_007864) | data or information resource, database | A plastid protein database. It integrates data from large scale proteome analyses of different plastid types.These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison allows establishing a core proteome that is common to all plastid types and provides furthermore information about plastid type-specific functions. | SCR_007864 | PLprot | 2026-08-10 09:33:19 | 10 | ||||||||||||
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piRNABank Resource Report Resource Website 100+ mentions |
piRNABank (RRID:SCR_007858) | data or information resource, database | A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03293 | SCR_007858 | piRNABank | 2026-08-10 09:33:20 | 172 | ||||||||
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MtbRegList Resource Report Resource Website 1+ mentions |
MtbRegList (RRID:SCR_007811) | data or information resource, database | A database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain most of the characterized transcription start sites and DNA binding sites cross-referenced with their respective transcription factor, along with some predicted regulatory motifs. | has parent organization: University of Sherbrooke; Quebec; Canada | nif-0000-03169 | SCR_007811 | MtbRegList | 2026-08-10 09:33:18 | 1 | ||||||||||
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MegaMotifbase Resource Report Resource Website 1+ mentions |
MegaMotifbase (RRID:SCR_007775) | data or information resource, database | A database of structural motifs for protein structures related at the family and-or superfamily level. Such motifs among structurally aligned proteins are recognized by the conservation of amino acid preference and solvent inaccessibility and are examined for the conservation of other important structural features like secondary structural content, hydrogen bonding pattern and residue packing. These motifs may form the common core by maintaining a particular spatial orientation pattern when compared across different proteins belonging to the same family or superfamily. Such motifs can also be employed to design and rationalize protein engineering and folding experiments. Therefore, the MegaMotifbase can be a useful resource to gain knowledge about structure and functional relationship of proteins. Alignments are available for download. | protein families, protein superfamilies |
is listed by: 3DVC has parent organization: Tata Institute of Fundamental Research; Mumbai; India |
nif-0000-03108 | SCR_007775 | MegaMotifbase | 2026-08-10 09:33:19 | 1 | |||||||||
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MPDB - Molecular Probe Database Resource Report Resource Website |
MPDB - Molecular Probe Database (RRID:SCR_007808) | MPDB | data or information resource, database | A database containing information on ca. 4300 synthetic oligonucleotides with a sequence of up to 100 nucleotides. Data are mainly taken from the literature and are encoded on the basis of controlled vocabularies. The probes target 821 different genes, of which 691 human and 112 viral. The probes can be used for genetic polymorphisms study (1944), human inherited disease diagnosis (834), cancer diagnosis (517), infectious disease diagnosis (517), neurologic disease diagnosis (72), autoimmune disease diagnosis (40). Oligonucleotides are described on the basis of: name, oligo type (primer, probe, antisense), nucleotide sequence, amino acid sequence (if part of a coding region), target gene and related infos (localization within the gene and recognized variants or specificities), applications, methods, technical notes, complementary primer (if used for PCR), primers for amplification (if probe), bibliographic references. At the moment MPDB is searchable through some SRS servers. MPDB can easily be retrieved from our FTP server, together with SRS syntax files. Typology * ca. 4300 oligonucleotides * 821 different genes, of which 691 human and 112 viral * ca. 3536 oligonucleotides are human gene specific * ca. 620 oligonucleotides are viral gene specific | molecular probe, synthetic oligonucleotide, molecule, probe, synthetic, oligonucleotide, nucleotide sequence, amino acid sequence, oligo probe, oligo dna, pcr primer, virus | has parent organization: IST National Institute for Cancer Research; Genoa; Italy | Genetic polymorphism, Inherited disease, Infectious disease, Neurologic disease, Autoimmune disease, Cancer | PMID:9399819 PMID:9016509 PMID:8594603 PMID:7937049 PMID:8332523 PMID:1598231 |
nif-0000-03165 | SCR_007808 | Molecular Probe Data Base (MPDB), Molecular Probe Data Base, Molecular Probe Database | 2026-08-10 09:33:18 | 0 | ||||||
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MPIM - Mitochondrial Protein Import Machinery Resource Report Resource Website |
MPIM - Mitochondrial Protein Import Machinery (RRID:SCR_007809) | MPIM db | data or information resource, database | A database of Arabidopsis mitochondrial protein import components. Detailed information can be found in two main areas of the website, one of which contains a diagram detailing the plant mitochondrial import process which users can click on and interact with, and the other containing information about arabidopsis mitochondrial protein import components. | has parent organization: University of Washington; Seattle; USA | nif-0000-03166 | SCR_007809 | Mitochondrial Protein Import Machinery of Plants, Mitochondrial Protein Import Machinery | 2026-08-10 09:33:16 | 0 | |||||||||
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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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