Bioinformatics data plays vital role: Kalam

Thiruvananthapuram, Sep 21:

Stressing that the convergence of Bioscience and Information Technology into Bioinformatics has given thrust to genomics-based drug discovery and development, President A P J Abdul Kalam said there was a growing need for new informatics tools to help manage the influx of data from genomics and turn that data into tomorrow's drugs.

''Bioinformatics data plays a vital role and is emerging as a business model for the medical and pharmaceutical sector. It has a major role in key areas such as gene prediction, data mining, protein structure modeling and prediction, protein folding and stability, macromolecular assembly and modeling of complex biological systems,'' he said during an Interaction with Siddha and Ayurvedic medical college students at the Santhigiri Ashram at Pothencode on the outskirts of the city.

Mr Kalam said the need of the hour was to network the existing facilities and expertise with commitment and conviction to augment and facilitate the pace of research and development in the field of Indian traditional medicine. ''Our country is rich in human resources, particularly of scientists, doctors, technologists and engineers. The basic infrastructure is available for advanced research.'' he added.

The President said that there were tremendous opportunities for technologists to work for the objective of ''Integrated Health For All'' in a mission mode approach.

Researchers Simulate Complete Structure of Virus -- On A Computer

In their quest to study life, biologists apply engineering knowledge somewhat differently: They "reverse engineer" life forms, test fly them in the computer, and see if they work in silico the way they do in vivo. This technique previously had been employed for small pieces of living cells, such as proteins, but not for an entire life form until now.

The accomplishment, performed by computational biologists at the University of Illinois at Urbana-Champaign and crystallographers at the University of California at Irvine, is detailed in the March issue of the journal Structure.

Deeper understanding of the mechanistic properties of viruses, the researchers say, could not only contribute to improvements in public health, but also in the creation of artificial nanomachines made of capsids -- a small protein shell that contains a viral building plan, a genome, in the form of DNA or RNA.

For their first attempt to reverse engineer a life form in a computer program, computational biologists selected the satellite tobacco mosaic virus because of its simplicity and small size.
The satellite virus they chose is a spherical RNA sub-viral agent that is so small and simple that it can only proliferate in a cell already hijacked by a helper virus -- in this case the tobacco mosaic virus that is a serious threat to tomato plants.

A computer program was used to reverse engineer the dynamics of all atoms making up the virus and a small drop of salt water surrounding it. The virus and water contain more than a million atoms altogether.

The necessary calculation was done at Illinois on one of the world's largest and fastest computers operated by the National Center for Supercomputing Applications. The computer simulations provided an unprecedented view into the dynamics of the virus.

The computer simulations were carried out in Schulten's Theoretical and Biophysics Group's lab at the Beckman Institute for Avanced Science and Technology.

Phasing Out Theoretical Model Depositions to the PDB Archive

Effective October 15, 2006, PDB depositions will be restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules. This policy was recommended and endorsed by a working group comprised of structural and computational biologists and endorsed by the wwPDB advisory committee. Thus, theoretical model depositions (such as models determined purely in silico using, for example, homology or ab initio methods) will no longer be accepted.

Theoretical models that have been previously released or that will be released from now until October 15, 2006 will continue to be publicly available via the existing models archive at ftp://ftp.rcsb. org/pub/pdb/ data/structures/ models/current/.

A summary of the implementation plan for the phasing out of theoretical models is available in HTML and PDF formats. A paper describing the outcome of the Workshop on Archiving Structural Models of Biological Macromolecules will be available in the August 16 issue of Structure1.

Questions about this transition should be sent to info@wwpdb.org.