Proteomics
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[edit] Categories which link here
[edit] Proteomics - Quick Links
[edit] Related subcategories
- 2D PAGE & MS
- Proteomics databases
- Proteomics research groups
- Proteomics education
- Proteomics institutes
- Proteomics companies
- Plant proteomics
- Proteomics protocols
- Proteomics glossaries
- Proteomics conferences, workshops and meetings
- Proteomics publications
- Proteomics directories
- Proteomics software
- Protein arrays
- Proteomics community
[edit] Proteomics - Web Resources
UniqueProt Creating representative protein sequence sets. UniqueProt is a practical and easy to use web service designed to create representative, unbiased data sets of protein sequences. The largest possible representative sets are found through a simple greedy algorithm using the HSSP-value to establish sequence similarity. UniqueProt is not a real clustering program in the sense that the representatives are not at the centres of well-defined clusters since the definition of such clusters is problem-specific. Overall, UniqueProt is a reasonable fast solution for bias in data sets. Web service for browsers or command line version for Linux also available.
ExPASy Proteomics server. Provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment.
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Bioverse
An object-oriented framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds, using computation to understand relationships between sequence, structure, and function of biomolecules.
Functional, structural and contextual annotation of proteins and proteomes. 
CluSTr Automatic classification of SWISS-PROT TrEMBL proteins. The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Analysis has been carried out for different levels of protein similarity, yielding a hierarchical organisation of clusters. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam, ProDom and SMART. Links to the InterPro graphical interface allow users to see at a glance whether proteins from the cluster share particular functional sites. CluSTr also provides cross-references to HSSP and PDB.
The Global Proteome Machine Organization Set up so that those doing proteomics with tandem MS could use their data to analyze proteomes. The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.
Rice Proteome Database Administrated by National Institute of Agrobiological Sciences. It provides links to rice proteomics protocols, 2D-PAGE gels database, references and other useful links. The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified proteins showing tissue and subcellular localization, corresponding to 4180 separate protein entries in the database. The Rice Proteome Database contains the calculated properties of each protein such as molecular weight, isoelectric point and expression experimentally determined properties such as amino acid sequences obtained using protein sequencers and mass spectrometry and the results of database searches such as sequence homologies. The database is searchable by keyword, accession number, protein name, isoelectric point, molecular weight and amino acid sequence, or by selection of a spot on one of the 2D-PAGE reference maps. Cross-references are provided to tools for proteomics and to other 2D-PAGE databases, which in turn provide many links to other molecular databases.
i-Tracker: For quantitative proteomics using iTRAQ i-Tracker extracts the quantitative data from iTRAQ experiments in a format easily linked to peptide identifications.
Human 2-D databases for Proteome Analyses
The 2-D PAGE databases contain data on proteins identified on various reference images. Also, you can search by protein name, keywords, Mr and pI or organelle or cellular component.
The Arabidopsis Mitochondrial Proteome Project
This link gives a comprehensive investigation of mitochondrial functions in plants. The proteome of mitochondria are characterized by high resolution 2D gel electrophoresis and mass spectrometry.
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The Proteome Society, California Founded in 1997, It is an early leader in uniting those interested in the field of Proteomics. Its model is to provide an open forum leading to collaboration among its members.
Swiss Proteomics Society
Dedicated to promote research and education in the science of Proteomics in Switzerland as well as in other countries.
Plant Energy Biology | ARC Centre of Excellence
Provides links to the databases developed at van Wijk Lab: Plastid Differentiation, Biogenesis and Adaptation; from Proteome to Function.
E-Protein: Home
Mission Statement: To provide a fully automated distributed pipeline for large-scale structural and functional annotation of all major proteomes via the use of cutting edge computer GRID technologies.
HUPO Proteomics Standards Initiative
HUPO Proteomics Standards Initiative. Mission Statement The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification.
Also see Proteomics Journal Watch
