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http://crbs.ucsd.edu/

CRBS is a UCSD organized research unit (ORU) that exists to provide human resources, high technology equipment, and administrative services to researchers engaged in fundamental research on cell structure and function relationships in central nervous system processes, cardiovascular networking, and muscular contraction through multiple scales and modalities. CRBS scientists investigate these processes through invention, refinement, and deployment of sophisticated technologies, especially: - High-powered electron microscopes that reveal three-dimensional cell structures - State-of-the-art X-ray crystallography and magnetic resonance analysis that provide detail on protein structures at high-resolution - Laser-scanning and confocal light microscopes that reveal molecules tagged with fluorescent markers as they traffic within cells and pass transfer signals within and between cells - High performance computing and grid-based integration of distributed data CRBS facilitates an interdisciplinary infrastructure in which people from biology, medicine, chemistry, and physics can work with those from computer science and information technologies in collaborative research. Researchers share interests in the study of complex biological systems at many scales, from the structures of enzymes, proteins, and the body's chemical communications network at atomic and molecular levels, to an organism's physiology, strength, and support at cellular and tissue levels. The CRBS infrastructure integrates resources for high-performance computing, visualization, and database technologies, and the grid-integration of large amounts of archival storage data. The California Institute for Telecommunications and Information Technology (Cal-IT2) and the San Diego Supercomputer Center (SDSC) are collaborators in simulating the activity of biological systems, analyzing the results, and organizing the growing storehouse of biological information. CRBS is an entity evolving as research evolves. It forges interactions with biotechnology and biocomputing companies for technology transfer. Interaction, collaboration, and multiscale research produce new perspectives, reveal fruitful research topics, lead to the development of new technologies and drugs, and train a new generation of researchers in biological systems. Sponsors: CRBS is supported by the University of California at San Diego.

Proper citation: Center for Research in Biological Systems (RRID:SCR_002666) Copy   

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http://www.cs.ualberta.ca/~bioinfo/PA/GOSUB/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 30, 2015. Refer to Proteome Analyst 3.0. Subcellular Localization and GO General Molecular Function predictions for many model organism proteomes using Protein Analyst, with a very high coverage rate. When users blast their proteins against the database of results, they will not only be shown blast homologs from the model organisms, but also the Subcellular Localization and GO General Molecular Function predictions as well.

Proper citation: Proteome Analyst PA-GOSUB (RRID:SCR_008234) Copy   

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http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/

Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible

Proper citation: STRAP (RRID:SCR_005675) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/blast2/index.html

It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes.

Proper citation: Washington University Basic Local Alignment Search Tool (RRID:SCR_008285) Copy   

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http://www.uwstructuralgenomics.org/

It is a specialized research center supported by the Protein Structure Initiative (PSI) of the National Institute of General Medical Sciences (NIGMS), one of the National Institutes of Health (NIH). PSI is a federal, university, and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of PSI is to solve 10,000 protein structures in 10 years and to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. CESG is located within the Department of Biochemistry at the University of Wisconsin-Madison (Madison, WI) and the Department of Biochemistry at the Medical College of Wisconsin (Milwaukee, WI). CESG develops new methods and technologies to address unique eukaryotic bottlenecks and disseminates its methodologies and experimental results to the scientific community worldwide through: :- Cell-Free Protein Production Workshops :- Plasmids at PSI Materials Repository :- Posters Presented at Scientific Meetings :- Publications in PubMed / PubMed Central :- Sesame (LIMS) Available for Researchers :- Solved Structures in the Protein Data Bank :- Technology Dissemination Reports They have welcomed requests by researchers to solve eukaryotic protein structures, particularly medically relevant proteins, through our Online Structure Request System for Researchers. They have solved many community-nominated targets and deposited information about these targets in public databases and published on our investigations and findings. Sponsors: CESG is supported by NIH / NIGMS Protein Structure Initiative grant numbers U54 GM074901 and P50 GM064598.

Proper citation: CESG (RRID:SCR_008451) Copy   

•   Source: SciCrunch Registry

http://restraintsgrid.bmrb.wisc.edu/NRG/MRGridServlet

Original NMR (nuclear magnetic resonance) data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED) respectively as described in the references. There are 9,672,968 parsed constraints in 7159 entries. (Mar. 2013)

Proper citation: NMR Restraints Grid (RRID:SCR_006127) Copy   

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http://www.umd.be/BRCA1/

The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau.

Proper citation: UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) Copy   

•   Source: SciCrunch Registry

http://isaac.bioapps.biozentrum.uni-wuerzburg.de/isaac/modules/genome/species.xhtml

Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups.

Proper citation: InterSpecies Analysing Application using Containers (RRID:SCR_006243) Copy   

•   Source: SciCrunch Registry

http://kronos.biol.uoa.gr/~mariak/dbDNA.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An annotated and searchable collection of protein sequences for the families of DNA-binding proteins. DnaProt maximizes family information retrieval and helps reveal the relationships within the various functional binding classes. This classification system, implemented in an web-based management resource, is available for online DNA-binding pattern search and specific DNA-binding record retrieval. The database contains 3238 full-length sequences (retrieved from the SWISS-PROT database, release 38) that include, at least, a DNA-binding domain. Sequence entries are organized into families defined by PROSITE patterns, PRINTS motifs and de novo excised signatures. Combining global similarities and functional motifs into a single classification scheme, DNA-binding proteins are classified into 33 unique classes, which helps to reveal comprehensive family relationships. To maximize family information retrieval, DnaProt contains a collection of multiple alignments for each DNA-binding family while the recognized motifs can be used as diagnostically functional fingerprints. All available structural class representatives have been referenced. The resource was developed as a Web-based management system for online free access of customized data sets. Entries are fully hyperlinked to facilitate easy retrieval of the original records from the source databases while functional and phylogenetic annotation will be applied to newly sequenced genomes.

Proper citation: DnaProt (RRID:SCR_006230) Copy   

•   Source: SciCrunch Registry

http://www.benchfly.com/

A video production and hosting resource designed to help scientists record and share lab protocols. The site also makes video protocols available.

Proper citation: BenchFly (RRID:SCR_006259) Copy   

•   Source: SciCrunch Registry

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

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy   

•   Source: SciCrunch Registry

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://ctdbase.org/

A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.

Proper citation: Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) Copy   

•   Source: SciCrunch Registry

http://www.pombase.org/

Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions.

Proper citation: PomBase (RRID:SCR_006586) Copy   

•   Source: SciCrunch Registry

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

Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.

Proper citation: InterPro (RRID:SCR_006695) Copy   

•   Source: SciCrunch Registry

http://aps.unmc.edu/AP/main.php

Database and data analysis system dedicated to glossary, nomenclature, classification, information search, prediction, design, and statistics of Antimicrobial peptides and beyond. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in the past several years. Peptides will be registered into this database if: # they are from natural sources (bacteria, protozoa, fungi, plants, and animals); # their antimicrobial activities are demonstrated (MIC

Proper citation: APD (RRID:SCR_006606) Copy   

•   Source: SciCrunch Registry

http://www.mechanobio.info/

Portal that deals with the process of mechanotransduction, providing in-depth, regularly updated reviews on the mechanics of cellular and molecular function. Each review is written by scientists and subsequently peer reviewed by experts in the field to ensure the content is accurate, reliable and up to date. Each review emphasizes the functional and mechanical aspects of a process, rather than the genetic aspects, with the aim of making this resource accessible to a wider audience. MBInfo is an ideal resource for scientists working in alternative fields, individuals working in industries where products are based on biological principles or students seeking a reliable introduction to a given cellular process. Each topic is written in a pyramid structure. The top of the pyramid is represented by an overview page, providing a basic description of a given function or process. These pages target a broad spectrum of readers and assume only a basic understanding of biology. Further down the pyramid, the reader will encounter the steps involved in the process described and functional modules that address specific mechanical aspects. These pages outline the protein complexes involved and the mechanisms by which they achieve the given process or function. These pages assume the readers have a more in-depth knowledge of scientific terms and principles. For every topic, a series of graphics and/or animations are available. These supplement the reviews, clarify information and guide the reader through complex processes pictorially. This makes MBInfo an ideal teaching resource, whether in the classroom or for clients trying to understand your product. All images and text are copyright protected and are for personal use only. Current Topics include: * Cellular Structures in Mechanosensing and Cell Motility * Methods in the Study of Mechanobiology * Nuclear Mechanotransduction Almost 100 stand alone Glossary Terms are now available. These include short definitions or summaries of proteins and processes that relate to broader topics discussed within the site. Browse an extensive range of figures, tables and videos in our resources section. New quizzes and other interactive content can also be found.

Proper citation: MBInfo (RRID:SCR_006768) Copy   

•   Source: SciCrunch Registry

http://cellfinder.de/

Database of mapped validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text. Operated under the Open Source/Access model, community and scientific networking applications will allow users to store and retrieve their data and to explore cells and their interactions on singular and complex resolution levels. The involvement of stem cell registries and banks will allow direct access to selected cells. The set up the stem cell data repository will involve three lines of action: * the acquisition of scientific data and contents * the standardized description of this data, its organization with the help of ontologies and technical implementation * the integration of existing sources/logistics and to ensure sustainable long-term operation

Proper citation: CellFinder (RRID:SCR_006598) Copy   

•   Source: SciCrunch Registry

http://bar.utoronto.ca/welcome.htm

Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available.

Proper citation: BAR (RRID:SCR_006748) Copy   

•   Source: SciCrunch Registry

http://www.peptideresource.com/

A guide to peptide-related research and products including custom peptide suppliers, peptide synthesis reagent suppliers that provide resins, coupling reagents, and protected amino acids as well as biologically active peptides and substrates, peptide synthesizers for solution or solid phase peptide synthesis, peptide sequence analysis services, software to calculate the chemical or biochemical properties of peptides, including the prediction of antigenicity or difficult-to-synthesize sequences. There is an additional section on Proteomics Tools for the identification of proteins from peptide sequences determined by mass spectrometry. The site also contains a set of links to educational materials about peptide related research topics.

Proper citation: Peptide Resource Page: Your Complete Guide to Peptide Research and Suppliers (RRID:SCR_006676) Copy   

•   Source: SciCrunch Registry