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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-02-14 02:06:25 | 740 | |||||
|
TopoSNP Resource Report Resource Website 1+ mentions |
TopoSNP (RRID:SCR_005572) | TopoSNP | data or information resource, database | A topographic database for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins. These include disease- associated nsSNPs derived from the Online Mendelian Inheritance in Man (OMIM) database and other nsSNPs derived from dbSNP, a resource at the National Center for Biotechnology Information that catalogs SNPs. TopoSNP further classifies each nsSNP site into three categories based on their geometric location: those located in a surface pocket or an interior void of the protein, those on a convex region or a shallow depressed region, and those that are completely buried in the interior of the protein structure. These unique geometric descriptions provide more detailed mapping of nsSNPs to protein structures. It also includes relative entropy of SNPs calculated from multiple sequence alignment as obtained from the Pfam database (a database of protein families and conserved protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW. These structural and conservational data can be useful for studying whether nsSNPs in coding regions are likely to lead to phenotypic changes. TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data. | visualization, disease, non-disease, non-synonymous single nucleotide polymorphism, topographic mapping, single nucleotide polymorphism, 3d structure, protein, protein structure, coding region, entropy |
is listed by: OMICtools is related to: OMIM is related to: dbSNP is related to: Pfam is related to: Clustal W2 has parent organization: University of Illinois at Chicago; Illinois; USA |
NSF DBI0133856; NSF DBI0078270; NSF MCB998008; NIGMS GM68958 |
PMID:14681472 | nif-0000-03570, OMICS_00191 | SCR_005572 | topographic mapping of Single Nucleotide Polymorphism | 2026-02-14 02:05:57 | 4 | ||||||
|
lapdftext Resource Report Resource Website |
lapdftext (RRID:SCR_006167) | lapdftext, LA-PDFText, | software resource, text extraction software, software application | Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise. | text mining, pdf, text extraction, natural language processing |
is listed by: FORCE11 has parent organization: University of Southern California; Los Angeles; USA |
NSF 0849977; NIGMS RO1-GM083871; NIMH 1R01MH079068-01A2; NCRR U24 RR025736-01 |
PMID:22640904 | Acknowledgement requested, GNU General Public License, v3 | nlx_151668 | SCR_006167 | Layout-Aware PDF Text Extraction, Layout-Aware Text Extraction from Full-text PDF of Scientific Articles, lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles | 2026-02-14 02:05:54 | 0 | |||||
|
BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | data or information resource, database | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | r3d100012402, nif-0000-10168 | http://biogps.gnf.org/ https://doi.org/10.17616/R33J20 |
SCR_006433 | 2026-02-14 02:06:00 | 725 | |||||
|
ESEfinder 3.0 Resource Report Resource Website 100+ mentions |
ESEfinder 3.0 (RRID:SCR_007088) | ESEfinder | data analysis service, production service resource, service resource, analysis service resource | A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. | exonic splicing enhancer, sr protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
NIGMS GM42699; NCI CA88351; NHGRI HG01696 |
PMID:12824367 | Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license | biotools:esefinder, nif-0000-30496 | http://rulai.cshl.edu/tools/ESE2/ https://bio.tools/esefinder |
http://exon.cshl.edu/ESE/ | SCR_007088 | 2026-02-14 02:06:02 | 211 | ||||
|
Proteomics Research Center for Integrative Biology Resource Report Resource Website |
Proteomics Research Center for Integrative Biology (RRID:SCR_001098) | Proteomics Resource for Integrative Biology | biomedical technology research center, training resource | Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use. | systems biology technology center, proteomics, mass spectrometry, data management, analysis | has parent organization: Pacific Northwest National Laboratory | NIGMS 4P41GM103493-14 | nlx_152684 | SCR_001098 | Proteomics Research Resource for Integrative Biology | 2026-02-14 02:07:17 | 0 | |||||||
|
Resource for Biocomputing Visualization and Informatics Resource Report Resource Website 100+ mentions |
Resource for Biocomputing Visualization and Informatics (RRID:SCR_001374) | RBVI | biomedical technology resource center, training resource | Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas. | training resource, molecular modeling, software, molecular graphics, visualization, modeling, molecular structure, analysis, computation, computing and informatics technology center, FASEB list |
is listed by: 3DVC has parent organization: University of California at San Francisco; California; USA is parent organization of: Structure-function linkage database is parent organization of: UCSF Chimera |
NIGMS | nlx_152531 | SCR_001374 | 2026-02-14 02:07:48 | 154 | ||||||||
|
GeneWays Resource Report Resource Website |
GeneWays (RRID:SCR_000572) | Geneways | service resource | System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information. | pathway, molecule, literature, natural language processing, gene, protein, interaction, database |
is listed by: OMICtools has parent organization: Argonne National Laboratory has parent organization: Columbia University; New York; USA |
NSF ; DOE ; NIGMS GM61372 |
PMID:15016385 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30019, SCR_008368, OMICS_01182 | http://anya.igsb.anl.gov/genewaysApp | SCR_000572 | GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data, GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data | 2026-02-14 02:07:26 | 0 | ||||
|
National Center for Macromolecular Imaging Resource Report Resource Website 1+ mentions |
National Center for Macromolecular Imaging (RRID:SCR_001445) | NCMI | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods. | cryo-electron microscopy, structure determination, structure, macromolecule, assembly, model, reconstruction, subcellular complex, electron cryo-microscopy, 3d spatial image, structural biology technology center |
is related to: EMDataResource.org has parent organization: Baylor University; Texas; USA |
NIGMS 3R01GM079429-05S1 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152670 | SCR_001445 | 2026-02-14 02:07:49 | 1 | |||||||
|
National Biomedical Computation Resource Resource Report Resource Website 10+ mentions |
National Biomedical Computation Resource (RRID:SCR_002656) | NBCR | biomedical technology research center, training resource | Biomedical technology research center that conducts, catalyzes and enables multiscale biomedical research, focusing on four key activities: 1) integrating computational, data and visualization resources in a transparent, advanced grid environment to enable better access to distributed data, computational resources, instruments and people; 2) developing and deploying advanced computational tools for modeling and simulation, data analysis, query and integration, three-dimensional image processing and interactive visualization; 3) delivering and supporting advanced grid/cyberinfrastructure for biomedical researchers; and 4) training a cadre of new researchers to have an interdisciplinary, working knowledge of computational technology relevant to biomedical scientists. NBCR enables biomedical scientists to address the challenge of integrating detailed structural measurements from diverse scales of biological organization that range from molecules to organ systems in order to gain quantitative understanding of biological function and phenotypes. Predictive multi-scale models and their driving biological research problems together address issues in modeling of sub-cellular biophysics, building molecular modeling tools to accelerate discovery, and defining tools for patient-specific multi-scale modeling. NBCR furthers these driving problems by developing tools and models based on rapid advances in mathematics and information technology, incorporating them into NBCR pipelines or problem solving environments, and addressing the inevitable changes in the underlying cyber-infrastructure technologies and continually adapting codes over time. Their technology focus integrates both the biological applications and the underlying support software into reproducible science workflows that can function across a number of physical infrastructures. | computation, molecule, visualization, software, cyberinfrastructure, biomedical, computing, informatics, computational tool, modeling, simulation, data analysis, query, integration, image processing, grid computing, cluster, computing and informatics technology center |
has parent organization: University of California at San Diego; California; USA is parent organization of: MEME Suite - Motif-based sequence analysis tools is parent organization of: Grid Enabled Molecular Science Through Online Networked Environments |
NIGMS GM103426; NCRR P41 RR08605 |
Free, Available for download, Freely available | nif-0000-22270 | SCR_002656 | NBCR - National Biomedical Computation Resource | 2026-02-14 02:07:19 | 15 | ||||||
|
National Center for Microscopy and Imaging Research Resource Report Resource Website 100+ mentions |
National Center for Microscopy and Imaging Research (RRID:SCR_002655) | NCMIR | biomedical technology research center, training resource | Biomedical technology research center that develops computer-aided, advanced microscopy for the acquisition of structural and functional data in the dimensional range of 1 nm to 100 um, a range encompassing macromolecules, subcellular structures and cells. Novel specimen-staining methods, imaging instrumentsincluding intermediate high-voltage transmission electron microscopes (IVEMs) and high-speed, large-format laser-scanning light microscopesand computational capabilities are available for addressing mesoscale biological microscopy of proteins and macromolecular complexes in their cellular and tissue environments. These technologies are developed to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed. NCMIR fulfills its mission through technology development, collaboration, service, training, and dissemination. It aims to develop preparative methods and analytical approaches to 3D microscopy applicable to neurobiology and cell biology, incorporating equipment and implementing software that expand the analysis of 3D structure. The core research activities in the areas of specimen development, instrument development, and software infrastructures maximize the advantages of higher voltage electron microscopy and correlated light microscopies to make ambitious imaging studies across scales routine, and to facilitate the use of resources by biomedical researchers. NCMIR actively recruits outside users who will not only make use of these resources, but who also will drive technology development and receive training. | microscopy, electron microscopy, electron tomography, 3d imaging, instrumentation, intermediate voltage electron microscopy, light microscopy, specimen preparation, telemicroscopy, image, software, tissue, cell, macromolecular complex, macromolecule, subcellular structure, 3d microscopy, neurobiology, cell biology, 3d structure, imaging technology center |
has parent organization: University of California at San Diego; California; USA is parent organization of: XFido is parent organization of: Xvoxtrace is parent organization of: National Center for Microscopy and Imaging Research: SAGE is parent organization of: Combine RTS2000 is parent organization of: Montage RTS2000 is parent organization of: Manual Align RTS2000 |
NIGMS ; NCRR P41 GM103412 |
Free, Available for download, Freely available | nif-0000-22234, SCR_016627 | SCR_002655 | National Center for Microscopy and Imaging Research | 2026-02-14 02:07:51 | 252 | ||||||
|
MacCHESS Resource Report Resource Website 1+ mentions |
MacCHESS (RRID:SCR_001443) | MacCHESS | access service resource, service resource | MacCHESS Synchrotron Source for Structural Biology advances structural characterization of proteins and biomolecules critical for understanding key biological processes and properties through leveraging both established and emerging X-ray synchrotron technologies. Used to collect data that comprises all or part of research programs. | structure, macromolecule, crystallography, beamlne, x-ray, bending magnet, unit-cell diffraction, ultra-high-resolution diffraction, dispersion phasing, drug design, structural genomics, microdiffraction, cryo-cooling, high pressure cooling, diffraction, software, synchrotron, cryo-crystallography, small-angle x-ray solution scattering, microcrystallography, structural biology, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS GM103485 | Free, Freely Available | nlx_152668 | SCR_001443 | MacCHESS Synchrotron Source for Structural Biology | 2026-02-14 02:07:45 | 9 | ||||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-02-14 02:07:19 | 35 | ||||||
|
National Center for X-ray Tomography Resource Report Resource Website 1+ mentions |
National Center for X-ray Tomography (RRID:SCR_001433) | NCXT | biomedical technology research center, training resource | Biomedical technology research center that develops novel cellular imaging technologies, specifically soft X-ray tomography, for visualizing and quantifying the internal structure of whole, hydrated cells, and high-numerical aperture fluorescence microscopy for locating the position of specific cellular molecules. Data from these two imaging modalities can be combined to form a single, correlated imaging view of a cell. | x-ray tomography, cell, imaging, microscopy, x-ray, tomography, imaging technology center |
has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at San Francisco; California; USA |
NIGMS ; DOE |
Free, Freely Available | nlx_152657 | http://ncxt.lbl.gov/ | SCR_001433 | National Center for X-ray Tomography: Cellular imaging at the mesoscale | 2026-02-14 02:07:18 | 6 | |||||
|
Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-02-14 02:07:20 | 3 | |||||||
|
Ultrafast Optical Processes Laboratory Resource Report Resource Website 1+ mentions |
Ultrafast Optical Processes Laboratory (RRID:SCR_006582) | Ultrafast Optical Processes Laboratory | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center and training resource that develops time-resolved laser technologies and instrumentation, with a focus on 2-D IR spectroscopy. The technologies enable atomic-level measurements of the fastest steps in biological processes to elucidate structure and dynamics in biological macromolecules, assemblies and cells. The Center makes most of its instrumentation available for service research projects to outside users nation-wide. | spectroscopy, structure, dynamics, macromolecule, assembly, cell, optical and laser technology center, laser spectroscopy, biochemical, biophysical, biomedical, laser, biological process | has parent organization: University of Pittsburgh; Pennsylvania; USA | NIGMS 9P41GM104605; NCRR P41RR001348 |
nlx_152664 | SCR_006582 | Laser and Biomedical Technology Laboratories | 2026-02-14 02:07:52 | 1 | |||||||
|
VU National Research Resource for Imaging Mass Spectrometry Resource Report Resource Website |
VU National Research Resource for Imaging Mass Spectrometry (RRID:SCR_006904) | National Research Resource for Imaging Mass Spectrometry | biomedical technology research center, training resource | Biomedical technology research center that advances the technology of Imaging Mass Spectrometry, facilitates the application of this novel imaging modality to problems of biological and clinical significance, and promotes the adoption of these technologies by a larger community of scientists and clinicians. Technical innovations include next-generation hardware, software and methods. Technology development is conducted by an interdisciplinary team of scientists and engineers, both within the Resource and through collaborative relationships with other universities, research institutes, and private industry. Development milestones are guided by Driving Biological Projects that require specific advancements in Imaging Mass Spectrometry in order to address biological problems. By working together, they anticipate new insights into these biological systems and a better understanding of health and disease at the molecular level that translates to improved patient care. The training mission of the Resource is accomplished through a variety of educational programs where Resource scientists and collaborators share their knowledge and experience with those interested in learning more about the technology. | imaging, mass spectrometry, imaging technology center | has parent organization: Vanderbilt University; Tennessee; USA | NIGMS | nlx_152658 | SCR_006904 | Vanderbilt University National Research Resource for Imaging Mass Spectrometry | 2026-02-14 02:07:23 | 0 | |||||||
|
NRCAM Resource Report Resource Website 50+ mentions |
NRCAM (RRID:SCR_006134) | NRCAM | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center that develops new technologies for modeling cell biological processes. The technologies are integrated through Virtual Cell, a problem-solving environment built on a central database and disseminated as a Web application for the analysis, modeling and simulation of cell biological processes. NRCAM resides at the Center for Cell Analysis and Modeling, CCAM, and provides a vast array of laboratory equipment that can be used for obtaining experimental data needed to create and enhance Virtual Cell models. Microscopy instrumentation includes three confocal laser scanning microscopes including UV excitation, nonlinear optical microscopy utilizing a titanium sapphire pulsed laser, confocal-based fluorescence correlation spectroscopy, wide-field imaging workstation with cooled CCD and rapid excitation filter wheel, and dual-wavelength spectrofluorometer. Access to the facilities and technical staff is open to all researchers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | modeling, simulation, cell, microscopy, software, biological process, model, cell model, informatics, computing and informatics technology center, FASEB list |
is listed by: 3DVC has parent organization: University of Connecticut; Connecticut; USA is parent organization of: Virtual Cell at the National Resource for Cell Analysis and Modeling |
NIGMS ; NCRR ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03953 | SCR_006134 | The National Resource for Cell Analysis and Modeling, National Resource of Cell Analysis and Modeling, National Resource of Cell Analysis and Modeling (NRCAM), National Resource for Cell Analysis and Modeling, National Resource of Cell Analysis & Modeling (NRCAM) | 2026-02-14 02:07:52 | 76 | ||||||
|
Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING Resource Report Resource Website 1+ mentions |
Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING (RRID:SCR_007412) | data or information resource, data set | Data sets, tools and computational techniques for modeling of protein interactions, including docking benchmarks, docking decoys and docking templates. Adequate computational techniques for modeling of protein interactions are important because of the growing number of known protein 3D structures, particularly in the context of structural genomics. The first release of the DOCKGROUND resource (Douguet et al., Bioinformatics 2006; 22:2612-2618) implemented a comprehensive database of cocrystallized (bound) protein-protein complexes in a relational database of annotated structures. Additional releases added features to the set of bound structures, such as regularly updated downloadable datasets: automatically generated nonredundant set, built according to most common criteria, and a manually curated set that includes only biological nonobligate complexes along with a number of additional useful characteristics. Also included are unbound (experimental and simulated) protein-protein complexes. Complexes from the bound dataset are used to identify crystallized unbound analogs. If such analogs do not exist, the unbound structures are simulated by rotamer library optimization. Thus, the database contains comprehensive sets of complexes suitable for large scale benchmarking of docking algorithms. Advanced methodologies for simulating unbound conformations are being explored for the next release. The Dockground project is developed by the Vakser lab at the Center for Bioinformatics at the University of Kansas. Parts of Dockground were co-developed by Dominique Douguet from the Center of Structural Biochemistry (INSERM U554 - CNRS UMR5048), Montpellier, France. | protein 3d structure, protein interaction, protein interface, protein model, structural genomics, co-crystallized, protein complex, protein recognition, protein modeling, structure prediction, protein-protein complex, benchmark |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Kansas; Kansas; USA |
NIH ; NIGMS R01 GM074255; NIGMS R01 GM61889 |
PMID:17803215 PMID:16928732 |
nif-0000-02757 | SCR_007412 | Dockground, Dockground: Benchmarks Docoys Templates other knowledge resources for DOCKING, Dockground: Benchmarks Docoys Templates and other knowledge resources for DOCKING | 2026-02-14 02:07:31 | 8 | |||||||
|
Northeastern Collaborative Access Team Resource Report Resource Website 10+ mentions |
Northeastern Collaborative Access Team (RRID:SCR_008999) | NE-CAT, NECAT | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center for macromolecular crystallography at Sector 24 of the Advanced Photon Source at Argonne National Laboratory. The macromolecules studied by resource users often involve large unit cells, small crystals, weakly diffracting crystals and crystals with weak anomalous scattering. Technological research includes use of silicon monochromators, focusing optics, methods of phase determination, radiation damage, X-ray detectors, automated sample mounting, microdiffraction and crystallographic software. | synchrotron, x-ray, beamline, structural biology, macromolecular crystallography, macromolecule, crystallography, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS | nlx_152674 | SCR_008999 | Northeastern CAT, Northeastern Collaborative Access Team Undulator Resource for Structural Biology | 2026-02-14 02:07:56 | 16 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
