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http://www.syfpeithi.de/

SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713.

Proper citation: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs (RRID:SCR_013182) Copy   

•   Source: SciCrunch Registry

http://www.phosphonet.ca/

PhosphoNET is an open-access, online knowledgebase developed by Kinexus Bioinformatics Corporation to foster the study of cell signaling systems to advance biomedical research in academia and industry. PhosphoNET is the world''s largest repository of known and predicted information on human phosphorylation sites, their evolutionary conservation and the identities of protein kinases that may target these sites. Search by protein name, UniProt number, IPI number, or 15 AA P-site sequence. PhosphoNET presently holds data on over 650,000 known and putative phosphorylation sites (P-sites) in over 23,000 human proteins that have been collected from the scientific literature and other reputable websites. Over 14% of these phospho-sites have been experimentally validated. The rest have been predicted with a novel P-Site Predictor algorithm developed at Kinexus with academic partners at the University of British Columbia and Simon Fraser University. With the PhosphoNET Evolution module, this website also provides information about cognate proteins in over 20 other species that may share these human phospho-sites. This helps to define the most functionally important phospho-sites as these are expected to be highly conserved in nature. With the Kinase Predictor module, listings are provided for the top 50 human protein kinases that are likely to phosphorylate each of these phospho-sites using another proprietary kinase substrate prediction algorithm developed at Kinexus. Our kinase substrate predictions are based on deduced consensus phosphorylation site amino acid frequency scoring matrices that we have determined for each of ~500 different human protein kinases. The specificity matrices are generated directly from the primary amino acid sequences of the catalytic domains of these kinases, and when available, have proven to correlate strongly with substrate prediction matrices based on alignment of known substrates of these kinases. The higher the score, the better the prospect that a kinase will phosphorylate a given site. Over 30 million kinase-substrate phospho-site pairs are quantified in PhosphoNET. Kinexus Bioinformatics Corporation has the capability to test most of these putative interactions in vitro for our clients.

Proper citation: PhosphoNET (RRID:SCR_013070) Copy   

•   Source: SciCrunch Registry

http://www.hgsc.bcm.tmc.edu/

Center for high-throughput DNA sequence generation and the accompanying analysis. The sequence data generated by the center's machines are analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI).

Proper citation: Baylor College of Medicine Human Genome Sequencing Center (RRID:SCR_013605) Copy   

•   Source: SciCrunch Registry

http://www.dna.affrc.go.jp/PLACE/

A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained.

Proper citation: PLACE- A Database of Plant Cis-acting Regulatory DNA Elements (RRID:SCR_013428) Copy   

•   Source: SciCrunch Registry

http://data.kew.org/cvalues/

The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for 7058 plant species. It combines data from the Angiosperm DNA C-values Database, Gymnosperm DNA C-values Database, the Pteridophyte DNA C-values Database, the Bryophyte DNA C-values Database, together with the addition of the Algae DNA C-values database.

Proper citation: Plant DNA C-values Database (RRID:SCR_013434) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

http://www.cyverse.org/

A google drive interface for scientific big data. CyVerse cyberinfrastructure is applicable to all life sciences disciplines and works equally well on data from plants, animals, or microbes. It provides life scientists with computational infrastructure to handle large datasets and complex analyses. Its extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, and APIs.

Proper citation: CyVerse (RRID:SCR_014531) Copy   

•   Source: SciCrunch Registry

https://tcia.at/

A database which provides results of comprehensive immunogenomic analyses of next generation sequencing data for 19 solid cancers from The Cancer Genome Atlas and other datasources. The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). It also provides survival analyses for different types immunological parameters.

Proper citation: The Cancer Immunome Database (RRID:SCR_014508) Copy   

•   Source: SciCrunch Registry

https://xcmsonline.scripps.edu

Cloud-based mass spectrometry data processing platform for metabolomics and lipidomics.

Proper citation: XCMS (RRID:SCR_015538) Copy   

•   Source: SciCrunch Registry

http://gnomad.broadinstitute.org/

Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects.

Proper citation: Genome Aggregation Database (RRID:SCR_014964) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/ExaML

Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers.

Proper citation: Examl (RRID:SCR_016087) Copy   

•   Source: SciCrunch Registry

https://www.mzcloud.org

A mass spectral database that assists in identifying compunds in life sciences, matabolomics, pharmaceutical research, toxicology, forensic investigations, environemnta analysis, food control, and industry.

Proper citation: mzCloud (RRID:SCR_014669) Copy   

•   Source: SciCrunch Registry

http://predictsite.com

Patient database that contains EEG data sets, executable tasks, and computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PREDiCT (RRID:SCR_015517) Copy   

•   Source: SciCrunch Registry

http://www.apa.org/pubs/databases/psycinfo/

Database for published, indexed resources pertaining to psychological, psychiatric and other behavioral and social science research. Users can search for resources by document type, research methodology, and funding source.

Proper citation: PsycINFO (RRID:SCR_014799) Copy   

•   Source: SciCrunch Registry

http://www.massbank.jp/?lang=en

Public repository of mass spectral data which allows users to search similar spectra on a peak-to-peak basis, on a neutral loss-to-neutral loss basis, or by the m/z value and molecular formula, search chemical compounds by substructures, and keyword search chemical compounds

Proper citation: MassBank (RRID:SCR_015535) Copy   

•   Source: SciCrunch Registry

http://www.lncrnadb.org/

Searchable database of comprehensive annotations of eukaryotic long non-coding RNAs. Entries are manually curated from referenced literature.

Proper citation: lncRNAdb (RRID:SCR_015491) Copy   

•   Source: SciCrunch Registry

http://www.regulomedb.org/

Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.

Proper citation: RegulomeDB (RRID:SCR_017905) Copy   

•   Source: SciCrunch Registry

http://mirtarbase.mbc.nctu.edu.tw/

Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.

Proper citation: miRTarBase (RRID:SCR_017355) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/pubs/MitoCarta/

Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.

Proper citation: MitoCarta (RRID:SCR_018165) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/gsea/msigdb/index.jsp

Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.

Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy   

•   Source: SciCrunch Registry