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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.
Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins.
Proper citation: NZYTech (RRID:SCR_016772) Copy
Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization.
Proper citation: Collaborative Computing Project for NMR (RRID:SCR_016983) Copy
http://www.biomexsolutions.co.uk/morda
Software package for molecular replacement protein structure solution using X-ray data. Includes database and set of programs for structure solution. Automatic molecular replacement pipeline.
Proper citation: MoRDa (RRID:SCR_017278) Copy
https://ous-research.no/bioinformatics/
Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services.
Proper citation: Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) Copy
https://omictools.com/rnacompete-tool
Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RNAcompete (RRID:SCR_015900) Copy
http://apps.cytoscape.org/apps/cluepedia
Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments.
Proper citation: CluePedia Cytoscape plugin (RRID:SCR_015784) Copy
http://disulfind.dsi.unifi.it/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.
Proper citation: DISULFIND (RRID:SCR_016072) Copy
http://molevol.cmima.csic.es/castresana/Gblocks_server.html
Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Gblocks (RRID:SCR_015945) Copy
http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN
Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
Proper citation: DOMALIGN (RRID:SCR_016085) Copy
https://github.com/osallou/cassiopee-c
Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.
Proper citation: Cassiopee (RRID:SCR_016056) Copy
http://bioplex.hms.harvard.edu/
Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection.
Proper citation: BioPlex (RRID:SCR_016144) Copy
Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium.
Proper citation: mentha (RRID:SCR_016148) Copy
Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.
Proper citation: Garlic (RRID:SCR_016118) Copy
https://www.rapidnovor.com/antibody-sequencing-service/
Service for monoclonal antibody protein sequencing. It derives the sequences directly from the protein using mass spectrometry and without the need to access the cell line.
Proper citation: REmAb (RRID:SCR_016239) Copy
https://github.com/ihmwg/IHM-dictionary
Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures.
Proper citation: IHM-dictionary (RRID:SCR_016186) Copy
Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations.
Proper citation: PDB-Dev (RRID:SCR_016185) Copy
https://github.com/Sung-Huan/ANNOgesic
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Proper citation: ANNOgesic (RRID:SCR_016326) Copy
Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.
Proper citation: CajaDB (RRID:SCR_016506) Copy
https://www.genome.jp/tools/dinies/
Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.
Proper citation: DINIES (RRID:SCR_016505) Copy
http://www.compbio.dundee.ac.uk/jpred/
Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.
Proper citation: Jpred (RRID:SCR_016504) Copy
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