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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Arizona Analytical and Biological Mass Spectrometry Core Facility Resource Report Resource Website 10+ mentions |
University of Arizona Analytical and Biological Mass Spectrometry Core Facility (RRID:SCR_023370) | ABMS | access service resource, core facility, service resource | Provides equipment and expertise for analysis of variety of biological and small molecules.Services include protein analysis encompassing protein identification, protein and peptide sequence confirmation, intact protein molecular weight determination, complex protein sample analysis, and protein/antibody drug interactions.Developed metabolomics library to support metabolomic and lipidomics analysis. Can identify range of post-translational modifications, determining their presence or absence, as well as quantitating PTMs.Proteomics and small molecule services include workflows for label free,chemical labeling (iTRAQ/TMT) and metabolic labeling (SILAC).Service for molecular synthesis, with monitoring reaction steps,calculating percentage of product, testing for purity, and molecule characterization with high resolution and high mass accuracy.Provides molecular weight and chemical composition determinations, structure elucidations and compound identification analysis or confirmation and accurate mass measurements of synthetic products, measurement of polymers, nucleic acids (DNA/RNA), peptides, proteins, natural products, and assistance with determination of unknowns. | USEDit, ABRF, small molecules, protein identification, protein and peptide sequence confirmation, intact protein molecular weight determination, complex protein sample analysis, protein, antibody, drug interactions, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Arizona; Arizona; USA |
ABRF_1698 | https://coremarketplace.org/?FacilityID=1698&citation=1 | SCR_023370 | UArizona Analytical & Biological Mass Spectrometry Facility, University of Arizona UArizona Analytical & Biological Mass Spectrometry Facility | 2026-09-12 01:04:24 | 10 | |||||||
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Nevada University Genomics Core Facility Resource Report Resource Website |
Nevada University Genomics Core Facility (RRID:SCR_018272) | access service resource, core facility, service resource | Provides development and support of genomics-based research, serving investigators in Nevada and beyond. Staff can be contracted for select services including ABI 3130 DNA sequencing, BD FACSCalibur flow cytometry, Affymetrix microarray processing, Agilent 2100 Bioanalyzer analysis and Qubit analysis. Facility also provides equipment and training for real-time PCR, Western blot/gel/microarray scanning, and analysis of DNA, RNA and protein samples. | Genomics, Nevada University, DNA sequencing, flow cytometry, microarray, analysis, RT PCR, Western Blotting, RNA, protein, core facility, USEDit, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit |
Open | ABRF_351 | https://coremarketplace.org/?FacilityID=351 | SCR_018272 | University of Nevada, Las Vegas - Genomics Core Facility, UNLV Genomics Core Facility | 2026-09-12 01:04:06 | 0 | |||||||
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Vilber: E-BOX CX5 TS gel imager Resource Report Resource Website |
Vilber: E-BOX CX5 TS gel imager (RRID:SCR_026106) | instrument resource | Stand alone gel imager for gel documentation. Provides high-resolution images of DNA, RNA or protein gels. Images can either be printed out directly or saved in internal storage. Transfer of data to PC is possible. | gel imager, gel documentation, images, DNA, RNA, protein, gels | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_026106.pdf | Model_Number_ E-BOX_CX5_TS | SCR_026106 | E-BOX CX5 TS imager | 2026-09-12 01:04:57 | 0 | |||||||||
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ALLSHENG: Nano100 Micro-specrophotometer Resource Report Resource Website |
ALLSHENG: Nano100 Micro-specrophotometer (RRID:SCR_026096) | instrument resource | Nano-100 microspectrophotometer to measure concentration of nucleic acid, protein and cell solution. 0.5 to 2μl of sample volume is required for each measurement. No cuvette is required. At the end of measurement, sample could be either wiped off directly or recovered with pipettor. | spectrophotometer, measure, absorbance, concentration, nucleic acid, protein, cell solution, | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_026096.pdf | Model_Number_Nano100 | SCR_026096 | , Nano100 Micro-specrophotometer, Nano-100 micro-spectrophotometer | 2026-09-12 01:04:57 | 0 | |||||||||
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BD Biosciences: Rhapsody Single-Cell Analysis System Resource Report Resource Website 1+ mentions |
BD Biosciences: Rhapsody Single-Cell Analysis System (RRID:SCR_027096) | instrument resource | System allows high-throughput capture of multiomic information from single cells using cartridge workflow and multitier barcoding system. Used for high-throughput, multiomic profiling of single cells. Allows to analyze gene expression at both mRNA and protein levels, as well as other cellular characteristics, using microwell-based system with multitiered barcoding approach.This enables the generation of various next-generation sequencing (NGS) libraries for deeper analysis. | profiling of single cells, analyze gene expression, mRNA, protein, multitiered barcoding, generation of next-generation sequencing libraries, | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_027096.pdf | SCR_027096 | 2026-09-12 01:05:18 | 8 | |||||||||||
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COACH Resource Report Resource Website 1+ mentions |
COACH (RRID:SCR_027684) | data access protocol, software resource, web service | Web application for protein-ligand binding site prediction. Starting from given structure of target proteins, COACH will generate complementray ligand binding site predictions using two comparative methods, TM-SITE and S-SITE, which recognize ligand-binding templates from the BioLiP protein function database by binding-specific substructure and sequence profile comparisons. | protein-ligand binding site prediction, protein, ligand, binding site prediction, | NIGMS GM083107; NIGMS GM084222; NSF Career Award |
PMID:23975762 | Free, Freely available | http://zhanglab.ccmb.med.umich.edu/COACH/ | SCR_027684 | , COACH server | 2026-09-12 01:05:33 | 7 | |||||||
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Azure Biosystems: c600 Imaging System Resource Report Resource Website |
Azure Biosystems: c600 Imaging System (RRID:SCR_027952) | AZURE c600 | instrument resource | Benchtop instrument designed for life science research, specifically for imaging, detecting, and quantifying protein and nucleic acids on gels and blots. It enables multi-channel analysis, including laser infrared (IR) fluorescence, RGB visible fluorescence, and chemiluminescence, allowing for multiplexed Western blots. | imaging, detecting, quantifying, protein, nucleic acids, gels, blots | is related to: Azure Biosystems: 600 Western Blot Imaging System | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_027952.pdf | Model_Number_Azure_c600 | SCR_027952 | , Azure c600 Imaging System, Azure c600 Western Blot Imaging System | 2026-09-12 01:05:40 | 0 | |||||||
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University of Oklahoma Protein Production and Characterization Core Facility Resource Report Resource Website |
University of Oklahoma Protein Production and Characterization Core Facility (RRID:SCR_028067) | access service resource, core facility, service resource | Offers access to instrumentation, training, and services for protein expression, purification, and biophysical characterization. In addition to instrument access, PPCC personnel offer advice, hands-on training, education, and collaboration. Provides a range of protein purification and characterization equipment. | ABRF, protein, expression, purification, biophysical characterization, |
is listed by: ABRF CoreMarketplace has parent organization: University of Oklahoma; Oklahoma; USA |
NIH P20GM103640; NIH P30GM145423 |
ABRF_5816 | https://coremarketplace.org/RRID:SCR_028067/?citation=1 | SCR_028067 | 2026-09-12 01:05:42 | 0 | ||||||||
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Allsheng: Nano-400A spectrophotometer Resource Report Resource Website |
Allsheng: Nano-400A spectrophotometer (RRID:SCR_028470) | instrument resource | Ultra-micro UV spectrophotometer used in life science and biology labs to measure the concentration and purity of DNA, RNA, and protein samples. Measures DNA and RNA concentrations at a fixed wavelength of 260 nm.Measures purified protein concentration at 280 nm. Requires only 1 to 2 ul of sample, eliminating the need for cuvettes or capillaries. | Hangzhou Allsheng Instruments, Ultra-micro UV spectrophotometer, spectrophotometer, protein, DNA, RNA, measurement | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028470.pdf | Model_Number_Nano-400A | SCR_028470 | , Nano-400A spectrophotometer, Nano-400A ultra-micro spectrophotometer | 2026-09-12 01:05:52 | 0 | ||||||||
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NetNGlyc Resource Report Resource Website 1000+ mentions |
NetNGlyc (RRID:SCR_001570) | NetNGlyc | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. | predict, n-glycosylation site, human, protein, neural network, sequence, asn-xaa-ser/thr sequon, glycoprotein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Free, Freely available | nlx_153863, biotools:netnglyc | https://bio.tools/netnglyc | SCR_001570 | NetNGlyc Server | 2026-09-12 12:55:27 | 1828 | ||||||
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YinOYang Resource Report Resource Website 100+ mentions |
YinOYang (RRID:SCR_001605) | YinOYang | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. | neural network, prediction, o-beta-glcnac attachment site, protein sequence, protein, sequence, glycosylation site, proteome, post-translational modification, protein function, glycoprotein, bio.tools |
uses: NetPhos is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Danish National Research Foundation | PMID:11928486 | Free, Freely available | nlx_153865, biotools:yinoyang | https://bio.tools/yinoyang | SCR_001605 | 2026-09-12 12:55:28 | 118 | |||||
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Clustal Omega Resource Report Resource Website 10000+ mentions |
Clustal Omega (RRID:SCR_001591) | Clustal Omega, Clustalo | alignment software, data processing software, image analysis software, service resource, software application, software resource | Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF. | multiple, sequence, alignment, DNA, RNA, protein, generate, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clustal W2 is related to: Clustal W2 is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:21988835 PMID:20439314 DOI:10.1038/msb.2011.75 |
Free, Available for download, Freely available | OMICS_00972, SCR_016062, biotools:clustalo, nlx_153836 | https://sources.debian.org/src/clustalo/, http://www.clustal.org/omega/, http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-multialign, https://bio.tools/clustalo, https://sources.debian.org/src/clustalo/ | SCR_001591 | 2026-09-12 12:55:27 | 10580 | |||||
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MatrixDB Resource Report Resource Website 50+ mentions |
MatrixDB (RRID:SCR_001727) | MatrixDB | data or information resource, database, production service resource, service resource | Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. | extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: Gene Ontology is related to: PSI-MI is related to: HPRD - Human Protein Reference Database is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: Claude Bernard University Lyon 1; Lyon; France |
European Union contract FP7-HEALTH-2007-223411 | PMID:20852260 PMID:19147664 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:matrixdb, r3d100010672, nif-0000-10226 | https://bio.tools/matrixdb, https://doi.org/10.17616/R3M03H | http://matrixdb.ibcp.fr/ | SCR_001727 | MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database | 2026-09-12 12:55:30 | 95 | |||
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Kidney and Urinary Pathway Knowledge Base Resource Report Resource Website 1+ mentions |
Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) | KUPKB | analysis service resource, data analysis service, data or information resource, data repository, data set, production service resource, service resource, storage service resource | A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made. | kidney, urinary, urine, pathway, molecule, visualizer, gene, protein, mirna, metabolite, mrna, microarray, ortholog, rdf, renal cell, anatomy, animal model, disease, sparql, proteomics, ontology, biomarker, gene expression, physiology, pathology |
is related to: NIDDK Information Network (dkNET) is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: KEGG has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: National Institute of Health and Medical Research; Rennes; France |
Kidney disease | European Union ; FP7 ; ICT-2007.4.4 e-LICO project |
PMID:21624162 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_154134 | http://www.e-lico.eu/kupkb | SCR_001746 | Kidney & Urinary Pathway Knowledge Base | 2026-09-12 12:55:30 | 2 | |||
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TANGO Resource Report Resource Website 100+ mentions |
TANGO (RRID:SCR_001770) | TANGO | software resource | A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions. | polypeptide chain, polypeptide, peptide, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:15361882 | Free, Freely available | biotools:tango, OMICS_03859 | https://bio.tools/tango | SCR_001770 | 2026-09-12 12:55:31 | 136 | ||||||
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BLASTX Resource Report Resource Website 10000+ mentions |
BLASTX (RRID:SCR_001653) | BLASTX | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level. | protein, translated nucleotide, blast, nucleotide, expressed sequence tag, sequence, genome, wgs, peptide, alignment, dna |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
PMID:28902395 PMID:8485583 |
Free, Freely Available | nlx_153933, OMICS_00992 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001653 | Translated BLAST, Translated BLAST: blastx | 2026-09-12 12:55:28 | 10411 | |||||
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International Union of Physiological Sciences: Physiome Project Resource Report Resource Website 1+ mentions |
International Union of Physiological Sciences: Physiome Project (RRID:SCR_001760) | data or information resource, portal, topical portal | The Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. Additionally, an important goal of the project is to develop applications for teaching physiology. Current projects include the development of: - ontologies to organize biological knowledge and access to databases - markup languages to encode models of biological structure and function in a standard format for sharing between different application programs and for re-use as components of more comprehensive models - databases of structure at the cell, tissue and organ levels - software to render computational models of cell function such as ion channel electrophysiology, cell signaling and metabolic pathways, transport, motility, the cell cycle, etc. in 2 & 3D graphical form - software for displaying and interacting with the organ models which will allow the user to move across all spatial scales Sponsors: This project is supported by the International Union of Physiological Sciences (IUPS), the IEEE Engineering. in Medicine and Biology (EMBS), and the International Federation for Medical and Biological Engineering (IFMBE) | electrophysiology, eukaryotic, framework, function, gene, 3d form, biological, cell, cell cycle, channel, computational, human, ion, metabolic, model, motility, network, organ, organism, pathway, physiology, physiome, protein, public domain, regulatory, signaling, software, structure, tissue, transport | is related to: Physiome Model Repository | Free, Freely available | nif-0000-10266 | http://www.physiome.org.nz/ | SCR_001760 | IUPS Physiome | 2026-09-12 12:55:30 | 2 | |||||||
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Dynamic Brain Platform Resource Report Resource Website 1+ mentions |
Dynamic Brain Platform (RRID:SCR_001754) | DBPF | atlas, bibliography, data or information resource, data repository, data set, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19. 2022. Platform to promote studies on dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Provides services such as data sets, popular research findings and articles and current developments in field. This site has been archived since FY2019 and is no longer updated. | collaboration, glial cell, interaction, model, network, neuron, neuron-glia network, numerical tool, paper, protein, publish, tool, book, neural dynamics, brain, stimulus, book, conference, presentation, simulation, paper, simulator, experimental stimuli, poster, data sharing |
is related to: INCF Japan Node has parent organization: RIKEN Brain Science Institute |
Free, Freely available | SCR_001812, nif-0000-10262, nif-0000-10377 | https://nimg.neuroinf.jp/ | SCR_001754 | Neuro-Imaging Platform, Dynamic Brain PF | 2026-09-12 12:55:30 | 1 | ||||||
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Homology Maps Page Resource Report Resource Website 1+ mentions |
Homology Maps Page (RRID:SCR_001666) | data or information resource, portal, topical portal | This page provides quick access to the Comparative mapping functions available in the Map Viewer. Currently, comparative maps are calculated using HomoloGene orthology predictions. Once the gene pairs have been established, blocks of conserved syteny can be established using the positions of each gene object in their respective builds. Sponsors: This resource is supported by NCBI. | function, gene, comparative, homology, map, mapping, orthology, protein | has parent organization: NCBI | Free, Freely Available | nif-0000-25559 | SCR_001666 | Homology | 2026-09-12 12:55:29 | 2 | ||||||||
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Chilibot: Gene and Protein relationships from MEDLINE Resource Report Resource Website 10+ mentions |
Chilibot: Gene and Protein relationships from MEDLINE (RRID:SCR_001705) | Chilibot | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation | drug, gene, literature, natural language processing, protein, text-mining, network, keyword, biological concept, graph, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: PubMed has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PHS DA-03977 | PMID:15473905 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01176, nif-0000-10196, biotools:chilibot | https://bio.tools/chilibot | SCR_001705 | Chilibot - Mining PubMed for relationships | 2026-09-12 12:55:29 | 33 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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