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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
https://www.encodeproject.org/
Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.
Proper citation: Encode (RRID:SCR_015482) 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://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
http://apps.cytoscape.org/apps/cytohubba
Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above.
Proper citation: cytoHubba (RRID:SCR_017677) Copy
https://github.com/santeripuranen/SuperDCA
Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.
Proper citation: SuperDCA (RRID:SCR_018175) Copy
http://www.cbs.dtu.dk/services/BepiPred/index.php
Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BepiPred-2.0 (RRID:SCR_018499) Copy
http://www.cbs.dtu.dk/services/DiscoTope/
Web server to predict discontinuous B cell epitopes from protein three dimensional structures.
Proper citation: DiscoTope (RRID:SCR_018530) Copy
https://www.ddg-pharmfac.net/AllerTOP/
Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin.
Proper citation: AllerTop (RRID:SCR_018496) Copy
https://prosa.services.came.sbg.ac.at/prosa.php
Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling.
Proper citation: ProSA-web (RRID:SCR_018540) Copy
https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
Web tool for conserved domains searching within protein or coding nucleotide sequence.
Proper citation: Conserved Domains Search (RRID:SCR_018729) Copy
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