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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.
http://glycotech.ccrc.uga.edu/
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.
Proper citation: Resource for Integrated Glycotechnology (RRID:SCR_009008) Copy
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.
Proper citation: National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) Copy
http://cell.ccrc.uga.edu/world/glycomics/glycomics.php
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.
Proper citation: Integrated Technology Resource for Biomedical Glycomics (RRID:SCR_009003) Copy
http://www-ssrl.slac.stanford.edu/content/science/ssrl-smb-program
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.
Proper citation: SSRL Structural Molecular Biology (RRID:SCR_009000) Copy
https://prokoplab.com/vistedd/
Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein.
Proper citation: Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) Copy
http://www.sci.utah.edu/cibc/software/131-shapeworks.html
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.
Proper citation: ShapeWorks (RRID:SCR_000424) Copy
http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml
Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits.
Proper citation: MORGAN (RRID:SCR_006906) Copy
http://www.mirtoolsgallery.org/miRToolsGallery/node/1055
Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: miRanda (RRID:SCR_017496) Copy
Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.
Proper citation: CIS-BP (RRID:SCR_017236) Copy
Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.
Proper citation: SRMAtlas (RRID:SCR_016996) Copy
Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.
Proper citation: Gemma (RRID:SCR_008007) Copy
bNAber is the Broadly Neutralizing Antibody E-Resource Database, analysis, visualization, and data discovery tool for broadly neutralizing HIV-1 antibodies (bNAbs). bNAber seeks to be a vital tool in the search for an AIDS vaccine.
Proper citation: bNAber (RRID:SCR_010510) Copy
https://bioinformatics.sdstate.edu/idep/
Integrated web application for differential expression and pathway analysis of RNA-Seq data.
Proper citation: iDEP: Integrated Differential Expression and Pathway analysis (RRID:SCR_027373) Copy
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.
Proper citation: COACH (RRID:SCR_027684) Copy
https://github.com/cytoscape/RCy3
Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R.
Proper citation: RCy3 (RRID:SCR_027668) Copy
https://weghornlab.org/software.html
Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer.
Proper citation: CBaSE (RRID:SCR_027765) Copy
https://github.com/vanallenlab/comut
Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.
Proper citation: CoMUT (RRID:SCR_027745) Copy
https://github.com/SalasLab/HiTIMED
Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens.
Proper citation: HiTIMED (RRID:SCR_028180) Copy
Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package.
Proper citation: PyContact (RRID:SCR_025066) Copy
Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.
Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy
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