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http://www.ebi.ac.uk/pdbsum

Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.

Proper citation: PDBsum (RRID:SCR_006511) Copy   

•   Source: SciCrunch Registry

http://supfam.mbu.iisc.ernet.in/index.html

SUPFAM is a database that consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 3.0) of SUPFAM uses homologous families in Pfam (Version 23.0) and SCOP (Release 1.69) which are examples of sequence -alignment and structure classification databases respectively. The two steps involved in setting up of SUPFAM database are * Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information. * An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies. The SUPFAM database can be used in either the Browse mode or Search mode. In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed. In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SUPFAM (RRID:SCR_005304) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/depressiondatabase/

The Major Depressive Disorder Neuroimaging Database (MaND) contains information of 225 studies which have investigated brain structure (using MRI and CT scans) in patients with major depressive disorder compared to a control group. 143 studies and 63 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website.

Proper citation: Major depressive disorder neuroimaging database (RRID:SCR_005835) Copy   

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http://decipher.sanger.ac.uk/

Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes.

Proper citation: DECIPHER (RRID:SCR_006552) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/db/Search

Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Proper citation: Genes to Cognition Database (RRID:SCR_002735) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/goldman-srv/pandit

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.

Proper citation: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) Copy   

•   Source: SciCrunch Registry

http://old.genedb.org/genedb/glossina/

As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis.

Proper citation: GeneDB Gmorsitans (RRID:SCR_004310) Copy   

•   Source: SciCrunch Registry

http://merops.sanger.ac.uk/

An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

Proper citation: MEROPS (RRID:SCR_007777) Copy   

•   Source: SciCrunch Registry

http://www.mlst.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic moblity of their gene products. MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Brian Spratt. This site is hosted at Imperial College with funding from the Wellcome Trust. The location of the subsites for the individual species are shown on their respective front pages.

Proper citation: MLST (RRID:SCR_010245) Copy   

•   Source: SciCrunch Registry

https://opentrials.net/

Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally.

Proper citation: Open Trials (RRID:SCR_015570) Copy   

•   Source: SciCrunch Registry

http://mousebrain.org/

Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.

Proper citation: mousebrain.org (RRID:SCR_016999) Copy   

•   Source: SciCrunch Registry

http://geroprotectors.org

Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases.

Proper citation: GEROprotectors (RRID:SCR_016737) Copy   

•   Source: SciCrunch Registry

http://www.ukbiobank.ac.uk/

Biobank provides data collected at Assessment Center and via online questionnaires on participants aged 40-69 years recruited throughout United Kingdom and provides summary information to improve prevention, diagnosis and treatment of serious and life threatening illnesses.

Proper citation: UK Biobank (RRID:SCR_012815) Copy   

•   Source: SciCrunch Registry

https://github.com/kjolley/BIGSdb

Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level.

Proper citation: BIGSdb (RRID:SCR_023551) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://github.com/huwjenkins/fragon

Software tool for rapid high resolution structure determination from ideal protein fragments. Pipeline to determine crystal structures using molecular replacement with small fragments followed by density modification. It is available through CCP4.

Proper citation: fragon (RRID:SCR_019158) Copy   

•   Source: SciCrunch Registry

http://www.wcb.ed.ac.uk/research/facilities

Facility provides regular training sessions, tools, advice and data analysis services to Centre members.

Proper citation: University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility (RRID:SCR_017151) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry

https://github.com/alexlib/KymoButler-1

Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis.

Proper citation: KymoButler (RRID:SCR_021717) Copy   

•   Source: SciCrunch Registry

https://shiny.cnsgenomics.com/mRnd/

Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach.

Proper citation: mRnd (RRID:SCR_022156) Copy   

•   Source: SciCrunch Registry