Biointelligence

October 22, 2009

The Structural Genomics Knowledgebase

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 5:05 am
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Biology has become an increasingly data-rich subject. Many of the emerging fields of large-scale data-rich biology are designated by adding the suffix ‘-omics’ onto previously used terms. The importance to the life-science community as a whole of such large-scale approaches is reflected in the huge number of citations to many of the key papers in these fields; the human and mouse genome papers being the most obvious examples.

Well, in true sense, “Omics” is a general term for a broad discipline of science and engineering for analyzing the interactions of biological information objects in various ‘omes’. The main focus is on:
1) mapping information objects such as genes, proteins, and ligand.
2) finding interaction relationships among the objects
3) engineering the networks and objects to understand and manipulate the regulatory mechanisms
4) integrating various omes and omics subfields.

Structural Genomics is one such stream where a proper study of cellular and genetic components is performed. The RCSB Protein Data Bank (PDB) offers online tools, summary reports and target information related to the worldwide structural genomics initiatives from its portal at http://sg.pdb.org.

There are currently three components to this site:
1) Structural Genomics Initiatives contains information and links on each structural genomics site, including progress reports, target lists, target status, targets in the PDB and level of sequence redundancy.
2) Targets provides combined target information, protocols and other data associated with protein structure determination
3) Structures offers an assessment of the progress of structural genomics based on the functional coverage of the human genome by PDB structures, structural genomics targets and homology models.

This is a free, comprehensive resource produced in a collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG) and is of a great help to the scinetific research community.

More about this can be read at: http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D302

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August 8, 2009

What is Kiosk Viewer ?

Filed under: Bioinformatics,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 2:00 am
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Want to study protein s and their structures ?? Want to have an insight of the chosen protein structure ?? Then Kiosk Viewer is the right tool for you.

The Molecules in Motion Kiosk Viewer is a full-screen animation program that displays structures from different angles and perspectives, and focuses on chemical components within the structure. The Kiosk Viewer can be launched for any structure from the “Other Viewers” menu on the structure summary page, in PDB.

Here is a screenshot of the summary page from where Kiosk can be accessed.

Access Molecules in Motion using Kiosk Viewer

The Kiosk program runs on Mac, Windows and some versions of Linux (i.e. CentOS 5) only, and requires the latest version of Java. The program automatically downloads coordinate files into a folder, which lets users run Kiosk on an offline computer.

Here is a screen shot for the same.

A screenshot of 1KYSK protein Molecule in Kiosk Viewer

To customize the list of structures displayed in Kiosk, right click on the Kiosk Viewer link and save the file with a new name (with the .jnlp extension), for example myFavorites.jnlp. Edit the PDB IDs listed in the file and save it. Double click to launch Kiosk Viewer; press the Esc key to exit Kiosk Viewer.

To access Kiosk Viewer, follow this link: http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090804