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http://www.viprbrc.org/brc/home.do?decorator=vipr

Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.

Proper citation: Virus Pathogen Resource (ViPR) (RRID:SCR_012983) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://www.kegg.jp/

Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

Proper citation: KEGG (RRID:SCR_012773) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/

A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.

Proper citation: IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) Copy   

•   Source: SciCrunch Registry

http://PlasmoDB.org

Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.

Proper citation: PlasmoDB (RRID:SCR_013331) Copy   

•   Source: SciCrunch Registry

http://umber.sbs.man.ac.uk/dbbrowser/bioie/

BioIE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literature. Based on manual definition of templates and rules, it aims at precise sentence extraction rather than wide recall. After uploading source text or retrieving abstracts from MEDLINE, users can extract sentences based on predefined or user-defined template categories. BioIE also provides a brief insight into the syntactic and semantic context of the source-text by looking at word, N-gram and MeSH-term distributions. Important Applications of BioIE are in, for example, annotation of microarray data and of protein databases.

Proper citation: BioIE: Extracting Informative Sentences From the Biomedical Literature (RRID:SCR_013464) Copy   

•   Source: SciCrunch Registry

http://msstats.org/

A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations.

Proper citation: MSstats (RRID:SCR_014353) Copy   

•   Source: SciCrunch Registry

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

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.

Proper citation: I-TASSER (RRID:SCR_014627) Copy   

•   Source: SciCrunch Registry

http://www.zucic.org/garlic/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://mentha.uniroma2.it/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bioinf.bio.uth.gr/nat-ncs2

Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins.

Proper citation: NAT/NCS2 Hound (RRID:SCR_016473) Copy   

•   Source: SciCrunch Registry

http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf

Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution.

Proper citation: Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) Copy   

•   Source: SciCrunch Registry

https://imaps.genialis.com/iclip

Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions.

Proper citation: iMaps (RRID:SCR_016705) Copy   

•   Source: SciCrunch Registry