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http://sarst.life.nthu.edu.tw/cpdb/

A database of circular permutation (CP) in proteins that provides resources for studying circular permutation (CP) and circular permutation relationships among protein structures. This site also offers viable CP site predictions in order to facilitate the application of CP in academic researches and biotechnological developments.

Proper citation: CPDB - the Circular Permutation Database (RRID:SCR_002261) Copy   

•   Source: SciCrunch Registry
  

http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/

Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.

Proper citation: COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) Copy   

•   Source: SciCrunch Registry
  

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

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http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17493288

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. LinkHub is a software system using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. It leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data. For efficiency, it is also provided with relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; LinkHub was used to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as connecting glue between different identifier spaces. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code. Sponsors: Funding for this work comes from NIH/NIGMS grant P50 GM62413-01, NIH grant K25 HG02378, and NSF grant DBI-0135442.

Proper citation: LinkHub: A Semantic Web System that facilitates cross-database queries and information retrieval in proteomics (RRID:SCR_001844) Copy   

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http://mech.ctb.pku.edu.cn/protisa/

Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq.

Proper citation: ProTISA (RRID:SCR_002138) Copy   

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http://django.nubic.northwestern.edu/fundo/

Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods.

Proper citation: FunDO (RRID:SCR_001725) Copy   

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https://epd.expasy.org/epd/

Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

Proper citation: Eukaryotic Promoter Database (RRID:SCR_002132) Copy   

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http://caps.ncbs.res.in/stifdb2/

Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.

Proper citation: STIFDB (RRID:SCR_002131) Copy   

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http://www.ebi.ac.uk/swissprot/hpi/hpi.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals.

Proper citation: Human Proteomics Initiative (RRID:SCR_002373) Copy   

•   Source: SciCrunch Registry
  

http://www.cisreg.ca/tfe

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.

Proper citation: Transcription Factor encyclopedia (RRID:SCR_002130) Copy   

•   Source: SciCrunch Registry
  

http://megasun.bch.umontreal.ca/ogmpproj.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP.

Proper citation: Organelle Genomics (RRID:SCR_002137) Copy   

•   Source: SciCrunch Registry
  

https://ictv.global

International Committee on Taxonomy of Viruses (ICTV) is charged by the Virology Division of the International Union of Microbiological Societies (IUMS) with developing, refining, and maintaining the official, universal taxonomy of all viruses. The goal is to classify and name all known viruses into a single taxonomy that reflects their evolutionary relationships. It provides a variety of resources in support of that goal including online and downloadable versions of current and historical releases of the virus taxonomy.

Proper citation: International Committee on Taxonomy of Viruses (RRID:SCR_002377) Copy   

•   Source: SciCrunch Registry
  

http://wikipathways.org/

Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.

Proper citation: WikiPathways (RRID:SCR_002134) Copy   

•   Source: SciCrunch Registry
  

http://www.iconbazaar.com/molecules/

This website contains animated 3D molecular models for amino acids, carbohydrates, and drugs. The amino acids listed are: -Alanine -Arginine -Asparagine -Aspartate -Cysteine -Glutamine -Glutamate -Glycine -Histidine -Isoleucine -Leucine -Lysine -Methionine -Phenylalanine -Proline -Serine -Threonine -Tryptophan -Tyrosine -Valine The categories of drugs included are: -Analgesics -Mood Elevators -Antacids -Psychedelics -Aphrodisiacs -Depressants -Stimulants -Intoxicants The carbohydrates listed are: -Fructose -Glucosamine -Glucose -Glyceraldehyde -Glycerol -Lactose -Maltose -Mannitol -Ribose -Ribulose -Sorbitol -Sucrose

Proper citation: IconBAZAAR (RRID:SCR_002376) Copy   

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http://magi.cs.brown.edu/

A tool for annotating, exploring, and analyzing gene sets that may be associated with cancer.

Proper citation: Mutation Annotation and Genomic Interpretation (RRID:SCR_002800) Copy   

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http://pathway.gramene.org/gramene/ricecyc.shtml

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP.

Proper citation: Rice Metabolic Pathway Database (RRID:SCR_002128) Copy   

•   Source: SciCrunch Registry
  

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry
  

http://pstiing.icr.ac.uk/

A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.

Proper citation: pSTIING (RRID:SCR_002045) Copy   

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http://pallab.serc.iisc.ernet.in/gester/

Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed.

Proper citation: WebGeSTer DB (RRID:SCR_002165) Copy   

•   Source: SciCrunch Registry
  

http://www.ddg-pharmfac.net/antijen/AntiJen/antijenhomepage.htm

Database with quantitative binding data for peptides binding to various cells including MHC Ligand, TCR-MHC complexes, T-cell epitopes, TAP, B-cell, and immunological protein-protein interactions. Information in each entry includes peptide libraries, copy numbers, and diffusion coefficient data.

Proper citation: AntiJen (RRID:SCR_001750) Copy   

•   Source: SciCrunch Registry