Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Thermo Fisher: Qubit fluorimeter Resource Report Resource Website 50+ mentions |
Thermo Fisher: Qubit fluorimeter (RRID:SCR_018095) | instrument resource | Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds. | Invitrogen, benchtop, fluorometer, DNA, RNA, protein, measurement, concentration, assay, instrument, equipment | Restricted | https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017209_Qubit_4_Fluorometer_UG.pdf | SCR_018095 | Qubit 4 Fluorometer | 2026-09-19 12:53:47 | 53 | |||||||||
|
DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-09-19 12:53:47 | 90 | ||||||
|
ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | analysis service resource, data analysis software, data processing software, production service resource, sequence analysis software, service resource, software application, software resource | Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. | Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal |
NHGRI U01 HG02712; Swiss Federal Government through Federal Office of Education and Science |
PMID:10027275 | Free, Freely available | biotools:protparam | https://bio.tools/protparam | SCR_018087 | ProtParam | 2026-09-19 12:53:47 | 7206 | |||||
|
SARS-CoV-2-Sequences Resource Report Resource Website 10+ mentions |
SARS-CoV-2-Sequences (RRID:SCR_018319) | data or information resource, data repository, data set, service resource, storage service resource | Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. | SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein |
works with: GenBank works with: NCBI Sequence Read Archive (SRA) |
COVID-19 | The Federal Government | Free, Available for download, Freely available | SCR_018319 | Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences | 2026-09-19 12:53:50 | 37 | |||||||
|
HPEPDOCK Server Resource Report Resource Website 50+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
Huazhong University of Science and Technology ; National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-09-19 12:53:53 | 73 | ||||||
|
GalaxyRefine Resource Report Resource Website 100+ mentions |
GalaxyRefine (RRID:SCR_018531) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. | Protein structure prediction, protein, structure prediction, protein structure, molecular dynamics simulation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Seoul National University. |
PMID:23737448 | biotools:galaxyrefine | https://bio.tools/galaxyrefine | SCR_018531 | 2026-09-19 12:53:53 | 316 | |||||||
|
ToxinPred Resource Report Resource Website 100+ mentions |
ToxinPred (RRID:SCR_018542) | analysis service resource, production service resource, service resource, software resource, software toolkit | Software package for peptides designing and prediction. In silico approach for predicting toxicity of peptides and proteins. Used for predicting peptide toxicity or non toxicity, minimum mutations in peptides for increasing or decreasing their toxicity, toxic regions in proteins. | Toxin, toxicity, toxicity prediction, peptide toxicity prediction, peptide design, protein, peptide mutation, toxic region, protein toxic region | Council of Scientific and Industrial Research Govt. of India ; Department of Biotechnology Govt. of India |
PMID:29300301 | Free, Freely available | SCR_018542 | 2026-09-19 12:53:53 | 244 | |||||||||
|
ProteinPilot Software Resource Report Resource Website 1000+ mentions |
ProteinPilot Software (RRID:SCR_018681) | data analysis software, data processing software, software application, software resource | Software tool for protein identification and relative protein expression analysis. Used in protein research to identify proteins and search large numbers of post translational modifications. Compatible with all proteomics MS/MS systems. | Protein identification, protein expression, protein expression analysis, protein, post translational modification, proteomics, mass spectrometry system | Restricted | SCR_018681 | Protein Pilot, Protein Pilot Software | 2026-09-19 12:53:56 | 1489 | ||||||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | data access protocol, software resource, software toolkit, web service | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-09-19 12:53:56 | 0 | ||||||
|
Batch Web CD-Search Tool Resource Report Resource Website 500+ mentions |
Batch Web CD-Search Tool (RRID:SCR_018756) | data access protocol, service resource, software resource, web service | Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence. | Functional domain detection, protein sequence, protein sequence domain, functional domain, protein, nucleotide sequence, conserved domain search, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIH Intramural Research Program | PMID:15215404 | Free, Freely available | biotools:cd-search | https://bio.tools/cd-search | SCR_018756 | NCBI Batch CD Search Tool, Batch conserved domain search, Conserved Domain Search service, CD-search | 2026-09-19 12:53:58 | 838 | |||||
|
PPA-Pred2 Resource Report Resource Website 1+ mentions |
PPA-Pred2 (RRID:SCR_018957) | data access protocol, simulation software, software application, software resource, web service | Web server for protein protein affinity prediction. Used for predicting binding affinity of protein protein complexes. | Protein, protein affinity, affinity prediction, predicting binding affinity, protein protein complex, binding affinity | Department of Science and Technology ; Government of India |
PMID:5172924 | Free, Freely available | SCR_018957 | Protein-Protein Affinity Predictor 2 | 2026-09-19 12:54:01 | 8 | ||||||||
|
Vesiclepedia Resource Report Resource Website 100+ mentions |
Vesiclepedia (RRID:SCR_019011) | data or information resource, data repository, database, service resource, storage service resource | Web based database of proteins, RNA, lipids and metabolites that are identified in extracellular vesicles. Compendium for extracellular vesicles with continuous community annotation and with manually curated data from published literature. | Extracellular vesicles, gene information, molecule information, protein, RNA, lipid, metabolite, gene ontology, annotation, external references, FASEB list | uses: Entrez Gene | Australian Research Council ; NHMRC project grant |
DOI:10.1371/journal.pbio.1001450 DOI:10.1093/nar/gky1029 |
Free, Freely available | SCR_019011 | Vesiclepedia 2019 | 2026-09-19 12:54:01 | 214 | |||||||
|
FGENESH Plus Resource Report Resource Website 1+ mentions |
FGENESH Plus (RRID:SCR_018937) | data access protocol, simulation software, software application, software resource, web service | Web tool as HMM plus similar protein based gene prediction. Used for multiple gene prediction in genomic DNA with using information from similar protein. Used if you know protein sequence similar with protein which is encoded by gene in your sequence. | HMM, gene prediction, protein, multiple gene prediction, genomic DNA, similar protein, protein sequence, Softberry | is related to: Fgenesh plus plus | Free, Freely available | SCR_018937 | Fgenesh plus | 2026-09-19 12:54:00 | 6 | |||||||||
|
MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. | Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide |
uses: Mascot is listed by: SoftCite |
Free, Available for download | http://msquant.alwaysdata.net/ | SCR_019206 | 2026-09-19 12:54:04 | 4 | |||||||||
|
Moffitt Cancer Center Proteomics and Metabolomics Core Facility Resource Report Resource Website |
Moffitt Cancer Center Proteomics and Metabolomics Core Facility (RRID:SCR_012168) | access service resource, core facility, service resource | Provides instrumentation for proteomics and metabolomics studies, including protein, peptide and metabolite separations, MS instrumentation for protein, peptide and metabolite analysis, and data systems, software, and bioinformatics tools for data archiving and analysis. Proteomics Core performs routine analytical proteomics services, including target discovery, identification and quantitation, and also provides platforms for functional proteomics using variety of strategies for protein separation, sub-proteome enrichment, post-translational modification analysis, and quantitation. | protein, peptide and metabolite separations, peptide and metabolite analysis, data systems, |
is listed by: ScienceExchange is listed by: ABRF CoreMarketplace has parent organization: Moffitt Cancer Center |
SciEx_10069, ABRF_2761 | https://coremarketplace.org/?FacilityID=2761&citation=1 | http://www.scienceexchange.com/facilities/proteomics-core-facility-moffitt | SCR_012168 | H. Lee Moffitt Cancer Center and Research Institute Proteomics and Metabolomics Core Facility, Moffitt Proteomics Core Facility | 2026-09-19 12:59:04 | 0 | |||||||
|
CGDB Resource Report Resource Website 10+ mentions |
CGDB (RRID:SCR_011959) | CGDB | data or information resource, data set | A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations. | protein, image, coarse-grained, molecular dynamics, membrane protein |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
BBSRC | PMID:18937097 PMID:18208379 |
Acknowledgement requested | OMICS_01608 | SCR_011959 | Coarse Grained Database, Coarse-Grained Database, CG Database | 2026-09-19 12:59:03 | 32 | |||||
|
UniProt Chordata protein annotation program Resource Report Resource Website |
UniProt Chordata protein annotation program (RRID:SCR_007071) | Chordata protein annotation program | data or information resource, data set | Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms. | chordata, protein, protein annotation, functional annotation, human, non-human vertebrate, xenopus laevis, xenopus tropicalis, zebrafish, protein sequence, protein sequencing, nucleotide sequence, sequence, annotation, sequence variant, disease, proteome, gold standard |
is related to: Human Proteomics Initiative is related to: UniProtKB has parent organization: UniProt |
nlx_143879 | SCR_007071 | 2026-09-19 12:58:39 | 0 | |||||||||
|
National Resource for the Mass Spectrometric Analysis of Biological Macromolecules Resource Report Resource Website |
National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) | National Resource for the Mass Spectrometric Analysis of Biological Macromolecules | biomedical technology research center, training resource | Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available. | systems biology technology center, mass spectrometric, analysis, peptide, protein, software, proteomic, cellular function | has parent organization: Rockefeller University; New York; USA | NIGMS | nlx_152683 | SCR_009007 | 2026-09-19 12:58:41 | 0 | ||||||||
|
CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | software resource, source code | CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | CUDASW++ (Smith Waterman) | 2026-09-19 12:58:40 | 5 | |||||
|
McGill Cell Imaging and Analysis Network Core Facility Resource Report Resource Website 1+ mentions |
McGill Cell Imaging and Analysis Network Core Facility (RRID:SCR_012623) | McGill CIAN | access service resource, core facility, service resource | Core facility at Biology Department in McGill Faculty of Science. Expertise in Light Microscopy and Image Analysis. Provides light microscopes, ranging from Point Scanning and Spinning Disc Confocals to Multi-Photon, TIRF, Light Sheet and Super-Resolution microscopes. Provides services in Automation/High throughput screening (liquid handler, pinning robot), Protein expression and antibody production. Users get training. | Light, microscopy, image, analysis, service, automation, high, throughput, screening, protein, expression, antibody, production, training |
is listed by: ScienceExchange is related to: McGill University Labs and Facilities has parent organization: McGill University; Montreal; Canada |
Restricted | SciEx_569 | http://www.scienceexchange.com/facilities/cell-imaging-and-analysis-network-cian | SCR_012623 | McGill University Cell Imaging and Analysis Network, McGill Cell Imaging and Analysis Network (CIAN), McGill University Cell Imaging and Analysis Network (CIAN) | 2026-09-19 12:59:11 | 1 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
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.
Email: info_at_ dknet.org
