National level Workshop in Chemoinformatics

26th- 27th Feb 2011

Workshop groups will study problems with hands-on examples using computational chemistry methods and discuss issues highlighted by examples and Case Studies presented by instructors. A Case Study set with a focus on chemical database creation and filtering drug like compounds will be used to link all workshop activities throughout the workshop.

• Hands on training on commercial softwares of Drug discovery
• Application of Chemoinformatics in drug discovery
• Interaction and guidance from eminent scientist from NCL
• Training from industry experts from Chemoinformatics domain.
• Analyzing chemical fingerprint
• Generating Knowledge from structure and different chemical databases
• Using various chemical structure drawing and visualization tools
• Digitizing your chemical Data.
• Storing molecules in wide array of format
• Awards for top 3 groups

For any queries contact:

RASA Life Science Informatics
301, 3rd Floor, Dhanashree Apartment,
Opposite Chittaranjan Vatika, Model Colony,
Shivaji Nagar, Pune - 411016.
Tel: 02065600408, 02025665752 or email us at workshop@rasalsi.com

For downloading workshop broacher please visit www.rasalsi.com

Drug Target For The Most Potent Botulinum Neurotoxin Determined

Brookhaven Lab researchers Subramanyam Swaminathan, Desigan Kumaran and Richa Rawat.

"We have found a highly efficient inhibitor of botulinum neurotoxin type A - the most potent of seven neurotoxins produced by the bacterium Clostridium botulinum. This finding can lead to a very effective drug to stop the devastating effects of the toxin," said Dr. Subramanyam Swaminathan,

Botulinum neurotoxin -- responsible for the deadly food poisoning disease botulism and for the beneficial effects of smoothing out facial wrinkles - can also be used as a dreaded biological weapon. When ingested or inhaled, less than a billionth of an ounce can cause muscle paralysis and eventual death. Although experimental vaccines administered prior to exposure can inhibit the destructive action of this neurotoxin - the most deadly protein known to humans -- no effective pharmacological treatment exists. Scientists have now taken the first step toward designing an effective antidote to the most potent form of botulinum neurotoxin.

Do you want to know more?

A centralized database of Indian Drug Commission approved drugs

Indian Drug Database
An attempt is made to collect/design the Indian approved drugs and the experimentally determined and computed three-dimensional (3D)-structures and their functional annotations are deposited...
Do you want to know more?

Protein data bank archives 50,000th molecule structure

Research archive doubles in size since 2004

NEW BRUNSWICK, N.J. The Protein Data Bank (PDB) based at Rutgers, The State University of New Jersey, and the University of California-San Diego (UCSD) this month reached a significant milestone in its 37-year history. The 50,000th molecule structure was released into its archive, joining other structures vital to pharmacology, bioinformatics and education.

With its origins in a handwritten petition circulated at a scientific meeting, the PDB is the single worldwide repository for the three-dimensional structures of large molecules and nucleic acids। This freely available online library allows biological researchers and students to study, store and share molecular information on a global scale.

Officially founded in 1971 with seven structures at Brookhaven National Laboratory, the archive is managed by a consortium called the worldwide Protein Data Bank (wwPDB).

Today, the PDB archive receives approximately 25 new experimentally determined structures from scientists each day and more than 5 million files are downloaded from the PDB archive every month. Users include structural biologists, computational biologists, biochemists, and molecular biologists in academia, government and industry as well as educators and students.
Notable examples include recent structures of the adrenergic receptor, which will revolutionize the discovery of drugs to fight heart disease, allergies and numerous other diseases, and the structures of many enzymes from HIV, which have been pivotal in the design of new therapies to fight AIDS.

Advances in science and technology have helped the archive grow by leaps and bounds in the last 10 years, said Helen M। Berman, director of the RCSB PDB and Rutgers Board of Governors professor of chemistry and chemical biology, noting that the size of the PDB has doubled in just the last three and a half years.

We are estimating that the PDB will not only double but triple to 150,000 structures by 2014, said Philip E. Bourne, associate director of the RCSB PDB and professor of pharmacology at the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences.

for details visit:

Protein data bank archives 50,000th molecule structure

Click here for more information

Click here for more information

CAS numbers are not public domain, are they?

"Work created before the existence of copyright and patent laws also form part of the public domain. The Bible and the inventions of Archimedes are in the public domain. However, copyright may exist in translations or new formulations of this work." [Wikipedia]

As posted by Tony is the Chemical Abstract Service (CAS) discouraging using their CAS services for assigning correct CAS numbers to structures for any third party database. Wikipedia is a source of structures, which is public domain due to its GNU FDL. Still, this does not imply that any translation of structures, e.g. CAS numbers, are in the public domain, too. Honestly, this raises a serious problem for curating CAS numbers on Wikipedia and this raises indeed the question, if they should not be dropped from Wikipedia, and any other information source, at all? Is it not better having no information, than having wrong information?

A CAS number is for me only one certain translation of a chemical structure. In this case, the only source and creator for CAS numbers is the American Chemical Society. CAS claims that their services can not be used for curating other data sources. Does this also mean that people can not use CAS numbers from publications?

"The public domain can also be defined in contrast to trademarks. Names, logos, and other identifying marks used in commerce can be restricted as proprietary trademarks for a single business to use. Trademarks can be maintained indefinitely, but they can also lapse through disuse, negligence, or widespread misuse, and enter the public domain. It is possible, however, for a lapsed trademark to become proprietary again, leaving the public domain." [Wikipedia]

And does this also mean that scientists are basically not allowed publishing CAS numbers and structures in scientific publications? How can CAS numbers then be used at all, if we can not store this information?

Many questions, and who will answer them? And, if they got answered what is the way forward for getting curated structures within the public domain? I would say (again, this time in nicer words): 'get organized scientists worldwide!' If CAS can do it, we can do it? It may take longer to get the party started, but if we do not start it will never happen.
"An ideal collaborative resource would be designed for large-scale data mining, contain curated historical data, and have data standards and deposition tools that could constantly bring in data from the published literature. ... In other words, the party might take longer to get started than hoped for, but it should be worth the wait." [M. Baker, DOI 10.1038/nrd2148]

Source: CAS numbers are not public domain, are they?