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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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trRosetta Resource Report Resource Website 100+ mentions |
trRosetta (RRID:SCR_021181) | service resource, simulation software, software application, software resource | Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets. | protein structure, restraint-guided structure generation, protein structure prediction | uses: Rosetta | China Scholarship Council ; Fok Ying-Tong Education Foundation ; Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin ; National Natural Science Foundation of China ; NIGMS R01 GM092802; NIH Office of the Director DP5 OD026389; Thousand Youth Talents Plan of China |
PMID:31896580 | Free, Freely available | https://github.com/gjoni/trRosetta | SCR_021181 | transformed restrained Rosetta | 2026-09-03 04:57:02 | 100 | ||||||
|
CAIRN Resource Report Resource Website |
CAIRN (RRID:SCR_019101) | data access protocol, data processing software, data visualization software, software application, software resource, web service | Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. | Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification | NCI CA102310; NCI CA107263; NCI CA177519; NCI CA207729; NCI P30 CA138313; NIA AG033082; NIGMS GM132055; Nine Girls Ask Foundation |
PMID:31923184 | Free, Available for download, Freely available | https://github.com/jrdelaney/CAIRN | SCR_019101 | Copy Alterations Intuitive Rendering Navigator | 2026-09-03 04:55:19 | 0 | |||||||
|
MolProbity Resource Report Resource Website 5000+ mentions |
MolProbity (RRID:SCR_014226) | software resource, web application | A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot. | web application, consultation, macromolecular structure, structure validation, macromolecular crystallography |
is listed by: SoftCite is related to: Phenix is related to: Coot has parent organization: Duke University; North Carolina; USA |
Howard Hughes Medical Institute Predoctoral Fellowship ; NIGMS GM-15000; NIGMS GM-61302 |
DOI:10.1107/S0907444909042073 | Acknowledgement requested, Requires Java and Javascript | https://www.phenix-online.org/documentation/reference/molprobity_tool.html | SCR_014226 | 2026-09-03 04:52:41 | 6711 | |||||||
|
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) Resource Report Resource Website |
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) | NUSDAT | data or information resource, database, image collection | A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data. | database, neuroimaging, clinical, cognitive, genetic, schizophrenia, longitudinal |
uses: CAWorks is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Northwestern University; Illinois; USA |
Schizophrenia | NIMH 1R01 MH084803; NIMH 1U01 MH097435; NIMH P50 MH071616; NIMH R01 MH056584; NCRR P41 RR15241; NIGMS U24 GM104203; NIH Bio-Informatics Research Network Coordinating Center |
Available to the research community | SCR_014153 | Northwestern University Schizophrenia Data and Software Tool | 2026-09-03 04:52:39 | 0 | ||||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, data processing software, software application, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-09-03 04:52:41 | 3874 | |||||
|
Yeast Resource Center Resource Report Resource Website 1+ mentions |
Yeast Resource Center (RRID:SCR_007942) | YRC | biomedical technology research center, training resource | Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology. | systems biology technology center, protein function, protein structure, mass spectrometry, protein, structure prediction, fluorescence microscopy, computational biology, sequence, function, phenotyping | has parent organization: University of Washington; Seattle; USA | NCRR ; NIGMS P41 GM103533 |
nif-0000-03650 | SCR_007942 | YRC | 2026-09-03 05:06:31 | 6 | |||||||
|
iPOP Resource Report Resource Website 10+ mentions |
iPOP (RRID:SCR_008991) | iPOP | data or information resource, data set | Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. | genomics, proteomics, transcriptional profiling, saliva, blood, maternal data, metabolomics, personalized medicine, adult human, genetics, transcriptome, male | has parent organization: Stanford University; Stanford; California | Healthy | Breetwor Family Foundation ; Korber Foundation ; Fundacion Marcelino Botin ; Fundacion Lilly ; NLM T15-LM007033; NIGMS R24-GM61374; NHLBI T32 HL094274; NHLBI KO8 HL083914; NIH New Investigator DP2 award OD004613; Spanish Ministry of Science and Innovation Projects ; Spanish Ministry of Science and Innovation Projects ; European Union FP7 Genica ; European Union FP7 TELOMARKER ; European Research Council Advanced Grant |
PMID:22424236 | Free for personal, Non-exclusive, Non-transferable, Non-commercial access., Please cite. | nlx_152492 | SCR_008991 | Snyderome, Integrated Personal Omics Profiling | 2026-09-03 05:06:08 | 14 | ||||
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Center for Computational Mass Spectrometry Resource Report Resource Website 1+ mentions |
Center for Computational Mass Spectrometry (RRID:SCR_008161) | CCMS | biomedical technology research center, training resource | Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications. | systems biology technology center, mass spectrometry, algorithm, computational proteomics, proteomics |
is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA is parent organization of: NeuroPedia |
NCRR ; NIGMS |
nlx_152677 | https://api.datacite.org/dois?prefix=10.25345 | SCR_008161 | UCSD Center for Computational Mass Spectrometry | 2026-09-03 05:06:22 | 7 | ||||||
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NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis Resource Report Resource Website 1+ mentions |
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) | Mass Spectrometry Resource, WU Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry | systems biology technology center, mass spectrometry, protein, lipid, metaboilite, biomarker, isotope, analysis | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIGMS ; NCRR 2P41RR00954 |
nlx_152688 | SCR_009009 | Mass Spectrometry Resource at Washington University in St. Louis, Washington University Mass Spectrometry Resource | 2026-09-03 05:06:13 | 1 | |||||||
|
Resource for Integrated Glycotechnology Resource Report Resource Website |
Resource for Integrated Glycotechnology (RRID:SCR_009008) | Resource for Integrated Glycotechnology | biomedical technology research center, training resource | Biomedical technology research center that develops technologies to increase understanding of the molecular basis of the involvement of carbohydrates in protein-carbohydrate interactions in disease and to develop more powerful technologies necessary to achieve this goal. Complex carbohydrates play an important role in many biomedically important processes, including inflammatory response, hormone action, malignancy, viral and bacterial infections and cell differentiation. The resource combines complimentary technologies: synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression and cell-based assays. As new technologies are developed, application to these processes will be pursued through collaborative and service projects. | systems biology technology center, protein-carbohydrate interaction, disease, synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression, cell-based assay, glycan, enzyme, carbohydrate | has parent organization: University of Georgia; Georgia; USA | NIGMS 8 P41 GM103390-23; NCRR 5P41RR005351-23 |
nlx_152685 | SCR_009008 | 2026-09-03 05:06:34 | 0 | ||||||||
|
National Resource for Biomedical Accelerator Mass Spectrometry Resource Report Resource Website |
National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) | Resource for Biomedical AMS | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers. | systems biology technology center, accelerator mass spectrometry, radioisotope, isotope | has parent organization: Lawrence Livermore National Laboratory | NCRR ; NIGMS |
nlx_152682 | SCR_009006 | 2026-09-03 05:06:09 | 0 | ||||||||
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Integrated Technology Resource for Biomedical Glycomics Resource Report Resource Website 1+ mentions |
Integrated Technology Resource for Biomedical Glycomics (RRID:SCR_009003) | Integrated Technology Resource for Biomedical Glycomics | biomedical technology research center, training resource | Biomedical technology research center that develops and implements new technologies to investigate the glycome of cells, including glycoproteomics and glycoconjugate analysis, transcript analysis and bioinformatics. It develops the tools and technology to analyze in detail the glycoprotein and glycolipid expression of mouse embryonic stem cells and the cells into which they differentiate. The technology developed in the Center will allow an understanding of how glycosylation is controlled during differentiation and will allow the development of tools to promote the use of stem cells to treat human disease. In addition, the technology developed will be applicable to the study of other cell types, including cancer cells that are progressing to a more invasive phenotype. The technology developed will also allow others in the scientific community to participate in glycomics research through dissemination of the new methods developed and through the analytical services provided by the resource to other scientists requesting assistance in glycomic analyses. | systems biology technology center, glycome, cell, glycoproteomics, glycoconjugate analysis, transcript analysis, bioinformatics, glycoprotein, glycolipid, embryonic stem cell, glycosylation, stem cell, glycomics | has parent organization: University of Georgia; Georgia; USA | NCRR ; NIGMS |
nlx_152678 | SCR_009003 | NCRR Integrated Technology Resource for Biomedical Glycomics | 2026-09-03 05:06:09 | 1 | |||||||
|
SSRL Structural Molecular Biology Resource Report Resource Website 1+ mentions |
SSRL Structural Molecular Biology (RRID:SCR_009000) | SSRL SMB | biomedical technology research center, training resource | Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis. | synchrotron, radiation, structural biology, structural biology technology center, macromolecular crystallography, x-ray absorption spectroscopy, small-angle x-ray scattering, diffraction | has parent organization: Stanford University; Stanford; California | DOE ; NIGMS ; NCRR P41RR001209 |
nlx_152676 | SCR_009000 | Stanford Synchrotron Radiation Lightsource Structural Molecular Biology, Synchrotron Radiation Structural Biology Resource | 2026-09-03 05:06:25 | 1 | |||||||
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Rhode Island INBRE Molecular Informatics Core Facility Resource Report Resource Website 10+ mentions |
Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) | access service resource, core facility, service resource | Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research. | Analysis, interpretation, nucleotide, amino acid, sequence, protein, domain, structure, service, 3D visualization, modeling, USEDit |
has parent organization: University of Rhode Island; Rhode Island; USA has parent organization: USEDit |
NIGMS P20 GM103430 | Open | ABRF_3 | SCR_017685 | Rhode Island INBRE Molecular Informatics, RI-INBRE Bioinformatics Core; RI Genomics and Sequencing Center | 2026-09-03 05:08:25 | 16 | |||||||
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University of Delaware CBCB Bioinformatics Data Science Core Facility Resource Report Resource Website 10+ mentions |
University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) | access service resource, core facility, service resource | CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis. | ABRF, USEDit, CBCB, Bioinformatics, core, Delaware, Biotechnology, Institute, data, analyzing, service, data science |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Delaware; Delaware; USA |
NIGMS P20GM103446; NIH Office of the Director S10OD028725 |
Open | SCR_017712, ABRF_82 | SCR_017696 | Center for Bioinformatics and Computational Biology Bioinformatics Core, CBCB Bioinformatics Core | 2026-09-03 05:07:56 | 46 | |||||||
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University of North Dakota School of Medicine and Health Sciences Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of North Dakota School of Medicine and Health Sciences Imaging Core Facility (RRID:SCR_017733) | access service resource, core facility, service resource | Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school. | Light, electron, microscopy, imaging | NIGMS P20 GM113123; NIGMS U54 GM128729; UNDSMHS fund |
Open | ABRF_184 | SCR_017733 | Imaging Core | 2026-09-03 05:08:14 | 1 | ||||||||
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University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility (RRID:SCR_024793) | HSTRI Core | access service resource, core facility, service resource | Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies. | ABRF, Image acquisition and analysis, high spatial and temporal resolution imaging, |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20GM130459 | Open | ABRF_2596 | https://coremarketplace.org/?FacilityID=2596&citation=1 | SCR_024793 | , University of Nevada High Spatial and Temporal Resolution Imaging Core | 2026-09-03 05:09:39 | 2 | |||||
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SomaticSeq Resource Report Resource Website 1+ mentions |
SomaticSeq (RRID:SCR_024891) | software resource, software toolkit | Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification. | NGS variant calling and classification, somatic mutation detection, somatic mutation calls, single nucleotide variants, detect somatic mutations, | NHGRI R01 HG007834; NIGMS R01 GM109836 |
PMID:26381235 | SCR_024891 | 2026-09-03 05:09:43 | 6 | ||||||||||
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PEPhub Resource Report Resource Website 1+ mentions |
PEPhub (RRID:SCR_024892) | data access protocol, data or information resource, database, software resource, web service | Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end. | Portable Encapsulated Projects, biological metadata server, sharing, retrieving, validating, sample metadata, | NHGRI R01 HG012558; NIGMS R35 GM128636 |
PMID:37645717 | Free, Available for download, Freely available | https://github.com/pepkit/pephub | SCR_024892 | Portable Encapsulated Projects hub | 2026-09-03 05:09:14 | 2 | |||||||
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PLAAC Resource Report Resource Website 10+ mentions |
PLAAC (RRID:SCR_024973) | data access protocol, software resource, web service | Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm. | protein sequences search, identify proteins with prion-like amino acid composition, identify proteins, identify probable prion subsequences, | G. Harold and Leila Y. Mathers Foundation ; Howard Hughes Medical Institute ; NIGMS GM025874 |
PMID:24825614 | Free, Freely available | SCR_024973 | Prion Like Amino Acid Composition | 2026-09-03 05:09:07 | 49 |
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