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https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html
Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.
Proper citation: BLASTClust (RRID:SCR_016641) Copy
https://www.ncbi.nlm.nih.gov/orffinder
Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.
Proper citation: Open Reading Frame Finder (RRID:SCR_016643) Copy
Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC).
Proper citation: Illuminating the Druggable Genome (RRID:SCR_016924) Copy
Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins.
Proper citation: NZYTech (RRID:SCR_016772) Copy
http://cctop.enzim.ttk.mta.hu/
Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.
Proper citation: CCTOP (RRID:SCR_016963) 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
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
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://bioinfo3d.cs.tau.ac.il/PatchDock/
Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles.
Proper citation: PatchDock (RRID:SCR_017589) Copy
Bioanalyzer system is automated electrophoresis tool that provides an analytical evaluation of various samples types in many workflows, including next generation sequencing NGS, gene expression, biopharmaceutical, and gene editing research. Digital data is provided in timely manner and delivers assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for accurate result, and data may be exported in many different formats.
Proper citation: Agilent: 2100 Bioanalyzer Instrument (RRID:SCR_018043) 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
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
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
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