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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PRED-TMR2 Resource Report Resource Website 1+ mentions |
PRED-TMR2 (RRID:SCR_006205) | PRED-TMR2 | data analysis service, analysis service resource, production service resource, service resource | A web server that classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF''s) identified in complete genomes and, especially, those ORF''s that correspond to proteins with unknown function. The network has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF''s of several complete genomes. The neural network developed was associated with the PRED-TMR algorithm (Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J., 1999) in a new application package called PRED-TMR2. | prediction, transmembrane, protein, algorithm, neural network, classification, transmembrane protein, protein classification, membrane protein, protein structure |
is related to: DAM-Bio has parent organization: PRED-TMR |
European Union ERBFMRXCT960019 | PMID:10469822 | nlx_151766 | SCR_006205 | PRED-TMR2: Prediction of Transmembrane regions in proteins | 2026-08-04 09:41:33 | 1 | ||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | data analysis service, analysis service resource, production service resource, service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-08-04 09:41:34 | 3 | |||||
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PRED-TMR Resource Report Resource Website 1+ mentions |
PRED-TMR (RRID:SCR_006203) | PRED-TMR | data analysis service, analysis service resource, production service resource, service resource | A web server that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini (edges, starts and ends) of transmembrane regions. This allows both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non homologous transmembranes proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35). | predict, transmembrane segment, protein, algorithm, sequence, membrane protein, protein structure, transmembrane region, hydrophobicity analysis |
is related to: waveTM is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory is parent organization of: PRED-TMR2 |
European Union ERBFMRXCT960019 | PMID:10360978 | nlx_151765 | SCR_006203 | PRED-TMR: A novel method for predicting transmembrane segment in proteins based on a statistical analysis of the SwissProt database | 2026-08-04 09:41:32 | 7 | ||||||
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VirusMINT Resource Report Resource Website 10+ mentions |
VirusMINT (RRID:SCR_005987) | VirusMINT | database, data or information resource | A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome. | protein interaction, virus, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PSI-MI is related to: VirHostNet: Virus-Host Network is related to: MINT has parent organization: University of Rome Tor Vergata; Rome; Italy |
Papilloma virus, Human immunodeficiency virus, Epstein-Barr virus, Hepatitis B virus, Hepatitis C virus, Herpes virus, Simian virus 40 | PMID:18974184 | nif-0000-03636, OMICS_01909, biotools:virusmint, r3d100010685 | https://bio.tools/virusmint, https://doi.org/10.17616/R3F890 | SCR_005987 | 2026-08-04 09:41:29 | 16 | ||||||
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Kabat Database of Sequences of Proteins of Immunological Interest Resource Report Resource Website 1+ mentions |
Kabat Database of Sequences of Proteins of Immunological Interest (RRID:SCR_006465) | database, data or information resource | The Kabat Database determines the combining site of antibodies based on the available amino acid sequences. The precise delineation of complementarity determining regions (CDR) of both light and heavy chains provides the first example of how properly aligned sequences can be used to derive structural and functional information of biological macromolecules. The Kabat database now includes nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. The Kabat Database searching and analysis tools package is an ASP.NET web-based portal containing lookup tools, sequence matching tools, alignment tools, length distribution tools, positional correlation tools and much more. The searching and analysis tools are custom made for the aligned data sets contained in both the SQL Server and ASCII text flat file formats. The searching and analysis tools may be run on a single PC workstation or in a distributed environment. The analysis tools are written in ASP.NET and C# and are available in Visual Studio .NET 2003/2005/2008 formats. The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that time. Bence Jones proteins, mostly from human, were aligned, using the now-known Kabat numbering system, and a quantitative measure, variability, was calculated for every position. Three peaks, at positions 24-34, 50-56 and 89-97, were identified and proposed to form the complementarity determining regions (CDR) of light chains. Subsequently, antibody heavy chain amino acid sequences were also aligned using a different numbering system, since the locations of their CDRs (31-35B, 50-65 and 95-102) are different from those of the light chains. CDRL1 starts right after the first invariant Cys 23 of light chains, while CDRH1 is eight amino acid residues away from the first invariant Cys 22 of heavy chains. During the past 30 years, the Kabat database has grown to include nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules and other proteins of immunological interest. It has been used extensively by immunologists to derive useful structural and functional information from the primary sequences of these proteins. | functional, align, alignment, amino acid, antibody, antigen, biological, cdr, chain, class i, class ii, combining, complementarity, complex, delineation, heavy, histocompatibility, human, immunological, immunological database, light, macromolecule, mhc, molecule, nucleotide, position, protein, receptor, region, sequence, structural, t cell | has parent organization: Northwestern University; Illinois; USA | nif-0000-21233 | SCR_006465 | Kabat Database | 2026-08-04 09:41:36 | 2 | |||||||||
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Protein Ligand Database Resource Report Resource Website |
Protein Ligand Database (RRID:SCR_006980) | PLD | database, data or information resource | It is a publicly available web-based database that aims to provide further understanding of protein-ligand interactions. It''s a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design. | binding energy, biomolecular, interaction, ligand, protein, protein sequence | nif-0000-20902 | http://www-mitchell.ch.cam.ac.uk/pld/ | SCR_006980 | Protein Ligand Database | 2026-08-04 09:41:45 | 0 | ||||||||
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Dali database Resource Report Resource Website 1+ mentions |
Dali database (RRID:SCR_006974) | database, data or information resource | Resource out of service. Documented on May, 5th, 2021.The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighborhoods and alignments are automatically maintained and regularly updated using the Dali search engine. The Dali Database contains structural alignments of PDB90 versus the full PDB using DaliLite. The data can be viewed interactively here, or downloaded in its entirety Users may search by PDB identifier or keyword. | protein, protein 3d structure, protein structure | has parent organization: University of Helsinki; Helsinki; Finland | PMID:20457744 | nif-0000-02719 | SCR_006974 | Dali Database | 2026-08-04 09:41:45 | 4 | ||||||||
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Consensus CDS Resource Report Resource Website 100+ mentions |
Consensus CDS (RRID:SCR_006729) | CCDS | database, data or information resource | Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly. | human genome sequence, human protein, mouse genome sequence, mouse protein, protein coding region, gene, genome sequence, genome, sequence, gene annotation, protein, gold standard |
is listed by: OMICtools is related to: Entrez Gene is related to: HomoloGene is related to: MapViewer is related to: VEGA has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: University of California at Santa Cruz; California; USA |
PMID:24217909 PMID:22434842 PMID:19498102 |
The community can contribute to this resource, Acknowledgement requested | nif-0000-02645, OMICS_01535 | http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi | SCR_006729 | CCDS Database, NCBI Consensus CDS protein set, NCBI CCDS Database | 2026-08-04 09:41:41 | 230 | |||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 100+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | data analysis service, analysis service resource, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-08-04 09:41:42 | 492 | |||||
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HIV-1 Human Protein Interaction Database Resource Report Resource Website 10+ mentions |
HIV-1 Human Protein Interaction Database (RRID:SCR_006879) | HIV-1 Human Protein Interaction Database | database, data or information resource | A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication. | protein-protein interaction, protein, interaction, cellular protein |
is related to: VirHostNet: Virus-Host Network has parent organization: NCBI |
Human immunodeficiency virus, Type 1 | NIAID contract N01-AI-05415; NIAID N01-AI-70042 |
PMID:18927109 PMID:19025396 PMID:19262354 |
Acknowledgement requested | nif-0000-02964 | SCR_006879 | HIV-1: Human Protein Interaction Database, Human immunodeficiency virus type 1 human protein interaction database at NCBI | 2026-08-04 09:41:43 | 13 | ||||
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MyHits Resource Report Resource Website 10+ mentions |
MyHits (RRID:SCR_006757) | database, data or information resource | Database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. | protein, domain, motif, sequence, predictor, markov, model, gene, expression, mysql, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:17545200 | Free | nif-0000-02962, biotools:myhits | https://bio.tools/myhits | SCR_006757 | MyHit | 2026-08-04 09:41:41 | 39 | ||||||
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Rice Kinase Database Resource Report Resource Website |
Rice Kinase Database (RRID:SCR_006990) | RKD | database, data or information resource | It was created to host functional genomic information gathered as part of a large NSF funded rice kinase proteomics project. The goal is to integrate disparate data sets into a logical, user friendly format. To accomplish this, they have developed a platform to display user selected functional genomic data on a phylogenetic tree. The RKD also includes an interactive chromosomal map showing the positions of all rice kinases and an interactive protein-protein interaction maps. | chromosomal map, genomic data, genomic information, phylogenetic tree, protein, proteomic, rice kinase | nif-0000-20910 | SCR_006990 | Rice Kinase Database | 2026-08-04 09:41:45 | 0 | |||||||||
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UCSD-Nature Signaling Gateway Molecule Pages Resource Report Resource Website 10+ mentions |
UCSD-Nature Signaling Gateway Molecule Pages (RRID:SCR_006907) | SGMP | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Relational database of all significant published qualitative and quantitative information on cell signaling proteins. The Molecule Pages database was developed with the specific aim of allowing interactions, and indeed whole pathways, to be modeled. The goal is to filter the data to present only validated information. In addition, the Gateway is the home of Signaling Update, which provides a one-stop overview of the latest and hottest research in cell signaling for both the specialist and non-specialist alike. | database, data model, cell signaling pathway, molecule, protein, signal transduction |
is listed by: 3DVC has parent organization: University of California at San Diego; California; USA |
Genentech Inc ; National Institute of General Medical Sciences |
PMID:21505029 PMID:17965093 PMID:12478304 |
THIS RESOURCE IS NO LONGER IN SERVICE | r3d100011690, nif-0000-03604, SCR_013230, nif-0000-20810 | https://doi.org/10.17616/R3V343 | SCR_006907 | Molecule Pages: A comprehensive signaling database, UCSD - Signaling Gateway Molecule Pages, Alliance for Cellular Signaling Molecule Pages Database | 2026-08-04 09:41:44 | 12 | ||||
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HOMSTRAD - Homologous Structure Alignment Database Resource Report Resource Website 10+ mentions |
HOMSTRAD - Homologous Structure Alignment Database (RRID:SCR_006544) | HOMSTRAD | database, data or information resource | A curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually. | homologous structure, protein, protein family, protein structure, align, 3d structure, structure-based alignment |
is listed by: OMICtools has parent organization: National Institute of Biomedical Innovation; Osaka; Japan |
PMID:14681395 | nif-0000-02977, OMICS_00976 | http://www-cryst.bioc.cam.ac.uk/homstrad | SCR_006544 | HOMologous STRucture Alignment Database | 2026-08-04 09:41:37 | 22 | ||||||
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Subcellular Location Image Finder Resource Report Resource Website 1+ mentions |
Subcellular Location Image Finder (RRID:SCR_006723) | SLIF | database, data or information resource, image | 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. | fluorescence, annotation, cell, journal, microscope, protein, subcellular, image, cell line, fluorescence microscope, information retrieval, data mining |
is listed by: Biositemaps has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Commonwealth of Pennsylvania Tobacco Settlement Fund ; National Center for Integrative Biomedical Informatics ; NIGMS R01 GM078622; NIDA U54 DA021519 |
PMID:17990497 | nif-0000-10308 | SCR_006723 | SLIF - Subcellular Location Image Finder | 2026-08-04 09:41:41 | 1 | ||||||
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Worldwide Protein Data Bank (wwPDB) Resource Report Resource Website 1000+ mentions |
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) | wwPDB | database, data or information resource | Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. | 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard |
is used by: Ligand Expo is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Proteopedia - Life in 3D is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: PDBj - Protein Data Bank Japan is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDB Validation Server is related to: Structural Antibody Database is parent organization of: PDB-Dev works with: PDB-REDO |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NINDS ; NIDDK ; European Molecular Biology Laboratory ; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; NBDC - National Bioscience Database Center ; Japan Science and Technology Agency |
PMID:14634627 | Free, Freely available | nif-0000-23903, r3d100011104 | https://doi.org/10.17616/R3462V | SCR_006555 | World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank | 2026-08-04 09:41:38 | 1215 | ||||
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GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | database, data or information resource | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | Generic Genome Browser | 2026-08-04 09:41:41 | 43 | ||||
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Artificial Selected Proteins/Peptides Database Resource Report Resource Website 1+ mentions |
Artificial Selected Proteins/Peptides Database (RRID:SCR_007557) | ASPD | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 04, 2014. Curated database on selected from randomized pools proteins and peptides designed for accumulation of experimental data on protein functionality obtained by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, etc). The database also contains modules for pairwise correlation analysis and BLAST search. | amino acid, ligand, nucleotide sequence database, peptide, phage, protein, ribosome, transcriptional regulator site, transcription factor, blast, pairwise correlation analysis |
is listed by: 3DVC has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
Russian Foundation for Basic Research and INTAS 00-04-49229; Russian Foundation for Basic Research and INTAS YSF 00-177 |
PMID:11752292 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02576 | http://www.sgi.sscc.ru/mgs/gnw/aspd/ | SCR_007557 | Artificial Selected Proteins Peptides Database | 2026-08-04 09:41:54 | 3 | ||||
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Biomolecular Object Network Databank Resource Report Resource Website 10+ mentions |
Biomolecular Object Network Databank (RRID:SCR_007433) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.BOND, which requires registration of a free account, is a resource used to perform cross-database searches of available sequence, interaction, complex and pathway information. BOND integrates a range of component databases including GenBank and BIND, the Biomolecular Interaction Network Database. BOND contains 70+ million biological sequences, 33,000 structures, 38,000 GO terms, and over 200,000 human curated interactions contained in BIND, and is open access. BOND serves the interests of the developing global interactome effort encompassing the genomic, proteomic and metabolomic research communities. BOND is the first open access search resource to integrate sequence and interaction information. BOND integrates BLAST functionality, and contains a well-documented API. BOND also stores annotation links for sequences, including links to Genome Ontology descriptions, MedLine abstracts, taxon identifiers, associated structures, redundant sequences, sequence neighbors, conserved domains, data base cross-references, Online Mendalian Inheritance in Man identifiers, LocusLink identifiers and complete genomes. BIND on BOND The Biomolecular Interaction Network Database (BIND), a component database of BOND, is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.Interactions A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction. Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways. The BIND interaction viewer is a tool to visualize and analyze molecular interactions, complexes and pathways. The BIND interaction viewer uses Ontoglyphs to display information about a protein via attributes such as molecular function, biological process and sub-cellular localization. Ontoglyphs allow to graphically and interactively explore interaction networks, by visualizing interactions in the context of 34 functional, 25 binding specificity and 24 sub-cellular localization Ontoglyphs categories. We will continue to provide an open access version of BOND, providing its subscribers with free, unlimited access to a core content set. But we are confident you will soon want to upgrade to BONDplus. | gene, genes, genome, annotation, binding specificity, biological process, complex, dna, genomes, genomic, human, interaction, interactome, ligand, metabolomic, molecular, molecular complex, molecular function, molecular interaction, mouse, ontoglyphs, ontology terms, pathway, photon, protein, protein-protein interactions, proteomic, rna, sequence, structure, sub-cellular localization, taxonomy, unclassified biological entity | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00571 | SCR_007433 | BOND | 2026-08-04 09:41:52 | 17 | |||||||||
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Alternative Splicing Database Resource Report Resource Website |
Alternative Splicing Database (RRID:SCR_007555) | database, data or information resource |
It has been established with the intention of assembling in a central, publicly accessible site information about alternatively spliced genes, their products and expression patterns. Version 2.1 of ASDB consists of two divisions, ASDB(proteins) , which contains amino acid sequences, and ASDB(nucleotides) with genomic sequences. SWISS-PROT uses two formats for description of alternative splicing Thus the protein sequences were selected from SWISS-PROT using full text search for both the words alternative splicing (usually in the CC lines) and varsplic (in the FT lines). In order to group proteins that could arise by alternative splicing of the same gene, we developed the clustering procedure. Two proteins were linked if they had a common fragment of at least 20 amino acids, and clusters were initially defined as maximum connected groups of linked proteins. It turned out that some clusters were chimeric, in the sense that they contained members of multi-gene families, but not alternatively spliced variants of one gene. Therefore the multiple alignments were subject to additional analysis aimed at detection of chimeric clusters. Each cluster is represented by multiple alignment of its members constructed using CLUSTALW. The distribution of cluster size, representation of species and other relevant statistics of ASDB(proteins) can be accessed through the links below. This processing covers the cases when alternatively spliced variants are described in separate SWISS-PROT entries. The other kinds of ASDB records, originating from the SWISS-PROT entries with the varsplic field in the feature table, usually describe the proteins that are not part of any cluster. In these cases, the information on the variable fragments of the several proteins which result from the alternative splicing of a single gene is contained in the entry itself. ASDB(proteins) entries are marked with different symbols to allow for easy differentiation among the three types: those proteins which are part of the ASDB clusters and the corresponding multialignments, those which have the information on different variants in the associated SWISS-PROT entries, and those for which the information on the variants is not available at the present time. ASDB contains internal links between entries and/or clusters, as well as external links to Medline, GenBank and SWISS-PROT entries. The ASDB(nucleotides) division was generated by collecting all GenBank entries containing the words alternative splicing and further selection of those entries that contain complete gene sequences (all CDS fields are complete, i.e. they do not have continuation signs). Sponsors: This work was supported by the Director, Office of Energy Research, Office of Biological and Environmental Research, of the US Department of Energy under Contract No. DE-ACO3-76SF00098. Additional support came from grants from the Russian Fund of Basic Research (99-04-48347), the Russian State Scientific Program Human Genome (65/99), and the Merck Genome Research Institute (244). |
exon, exon splice site, gene expression, gene structure, alternative splicing, amino acid, amino acid sequence, genomic sequence, human genome, human orf, intron, intron splice site, nucleotide, nucleotide sequence, protein, protein sequence, vertebrate genome | has parent organization: Lawrence Berkeley National Laboratory | nif-0000-02574 | http://hazelton.lbl.gov/~teplitski/alt/ | SCR_007555 | ASDB | 2026-08-04 09:41:53 | 0 |
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