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http://www.dddc.ac.cn/pdtd/

It is a dual function database that associates an informatics database to a structural database of known and potential drug targets. PDTD is a comprehensive, web-accessible database of drug targets, and focuses on those drug targets with known 3D-structures. PDTD contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank (PDB). Drug targets of PDTD were categorized into 15 and 13 types according to two criteria: therapeutic areas and biochemical criteria. The database supports extensive searching function using PDB ID, target name and category, related disease.

Proper citation: Potential Drug Target Database (RRID:SCR_007069) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/COG

A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be.

Proper citation: COG (RRID:SCR_007139) Copy   

•   Source: SciCrunch Registry

http://murphylab.web.cmu.edu/services/SLIF/

SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Images can be accessed via the SLIF Web database. SLIF takes on-line papers and scans them for figures that contain fluorescence microscope images (FMIs). Figures typically contain multiple FMIs, to SLIF must segment these images into individual FMIs. When the FMI images are extracted, annotations for the images (for instance, names of proteins and cell-lines) are also extracted from the accompanying caption text. Protein annotation are also used to link to external databases, such as the Gene Ontology DB. The more detailed process includes: segmentation of images into panels; panel classification, to find FMIs; segmentation of the caption, to find which portions of the caption apply to which panels; text-based entity extraction; matching of extracted entities to database entries; extraction of panel labels from text and figures; and alignment of the text segments to the panels. Extracted FMIs are processed to find subcellular location features (SLFs), and the resulting analyzed, annotated figures are stored in a database, which is accessible via SQL queries.

Proper citation: Subcellular Location Image Finder (RRID:SCR_006723) Copy   

•   Source: SciCrunch Registry

http://netage-project.org/

Database that contains gene sets and microRNA-regulated protein-protein interaction networks for longevity, age-related diseases and aging-associated processes.

Proper citation: NetAge Database (RRID:SCR_010224) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/tools/carp/

Service that generates Ramachandran-like plots of carbohydrate linkage torsions in pdb-files. The Ramachandran Plot, where backbone torsion angles are plotted against each other, is a frequently used tool to evaluate the quality of a protein 3D structure. For carbohydrate structures, linkage torsions can be evaluated in a similar way. Preferred Phi/Psi values of the torsion angles of glycosidic bonds depend strongly on the types of monosaccharides involved in the linkage, the kind of linkage (1-3, 1-4, etc) as well as the degree of branching of the structure. CARP analyses carbohydrate data given in PDB files using the pdb2linucs algorithm. For each different linkage type a separate plot is generated. The user can choose between two sources for plot background information for comparison: data obtained from PDB provided by GlyTorsion or from GlycoMapsDB. GlycoMapsDB provides calculated conformational maps, which show energetically preferred regions for a specific linkage, while PDB data are based on experimentally solved structures. For seldom occuring linkages, however, PDB data are often rare, so maybe not sufficient background information for comparison will be available from this source., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CARP (RRID:SCR_009021) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/sss/wublast/

Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity.

Proper citation: WU-BLAST (RRID:SCR_011824) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.biol.uoa.gr/ExTopoDB/

A publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins. Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein''s name and organism source. The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB''s protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction).

Proper citation: ExTopoDB (RRID:SCR_013143) Copy   

•   Source: SciCrunch Registry

http://omabrowser.org/cgi-bin/gateway.pl

A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed.

Proper citation: OMA Browser (RRID:SCR_011978) Copy   

•   Source: SciCrunch Registry

http://www.cdtdb.brain.riken.jp/CDT/Top.jsp

Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains.

Proper citation: Cerebellar Development Transcriptome Database (RRID:SCR_013096) Copy   

•   Source: SciCrunch Registry

http://proline.bic.nus.edu.sg/dedb/

Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.

Proper citation: Drosophila melanogaster Exon Database (RRID:SCR_013441) Copy   

•   Source: SciCrunch Registry

http://www.dbali.org

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali.

Proper citation: DBAli. A Database of Structure Alignments. (RRID:SCR_013418) Copy   

•   Source: SciCrunch Registry

http://tcm.lifescience.ntu.edu.tw/index.html

TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information collected from public databases are also available. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in deducing possible synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. TCMGeneDIT is a unique database of various association information about TCMs. The database integrating TCMs with life sciences and biomedical studies would facilitate the modern clinical research and the understanding of therapeutic mechanisms of TCMs and gene regulations.

Proper citation: TCMGeneDIT (RRID:SCR_013396) Copy   

•   Source: SciCrunch Registry

http://mordred.bioc.cam.ac.uk/bipa

A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces.
There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids.

Proper citation: Biological Interaction database for Protein-nucleic Acid (RRID:SCR_013371) Copy   

•   Source: SciCrunch Registry

http://rarge.psc.riken.jp/rartf/

Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available.

Proper citation: RARTF (RRID:SCR_013457) Copy   

•   Source: SciCrunch Registry

http://dorina.mdc-berlin.de/rbp_browser/dorina.html

In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.

Proper citation: doRiNA (RRID:SCR_013222) Copy   

•   Source: SciCrunch Registry

http://flytrap.med.yale.edu/

The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion.

Proper citation: FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) Copy   

•   Source: SciCrunch Registry

https://www.nist.gov/srd/nist-standard-reference-database-1a-v14

A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals.

Proper citation: Mass Spectral Library (RRID:SCR_014668) Copy   

•   Source: SciCrunch Registry

http://epsd.biocuckoo.org/

Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies.

Proper citation: EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) Copy   

•   Source: SciCrunch Registry

http://www.mrmatlas.org/

Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.

Proper citation: SRMAtlas (RRID:SCR_016996) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH

Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt.

Proper citation: Embassy-domsearch (RRID:SCR_016086) Copy   

•   Source: SciCrunch Registry