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Aug 2 11

VLifeMDS 4.0 arrived

by Yogesh Wagh

vlifemds logoVLifeMDS 3.5 licensed users, here is a good news for you. Now you can avail the free upgrade to VLifeMDS 4.0, this is valid for all users who have licensed VLifeMDS 3.5 after December, 31 2010.

Here is what you get in VLifeMDS 4.0

Enhanced Graphics
• Improved channel and cavity surfaces
• Fast Connoly surface generation
• Intuitive Ramachandran plot
Advanced Homology Modeling
• Auto Homology modeling
• Support for new sequence database from RCSB
• Intuitive modification and model building
• Multi template Homology modeling
Advancement in GRIP Docking
• Ligand wise systematic output
• Improved performance with speed
LeadGrow – Virtual library generation
• Applicability domain check
• GRIP docking based screening
• kNN-MFA based screening
Advanced LeadGrow – Multi template combinatorial library generation
VLife QSARPlus
• Applicability domain check
• Contour visualization with PLS MFA
• Multiple response QSAR modeling
AutoQSAR workflow for multiple model building
SCOPE: Score based method for lead optimization
Structure based pharmacophore generation
GLib: Combinatorial library generation using GQSAR model
GQSAR model based activity optimization with GUI
Multicore enabled
Scripting
• Python Integration
• Script console
• Command line support on Linux

 

Yogesh Wagh

I am science and technology savvy, I love my role of taking ideas and concepts to reality with commercial means. I am currently spearheading the complex businesses like Drug Discovery computational and experimental technology. Do not hesitate to contact me if you would like to partner with VLife for innovating and developing the technology for science.

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Aug 2 11

Need of technology for effective drug repurposing

by Sudhir Kulkarni

drug repositioning

Drug re-purposing is a well known route used by pharmaceutical companies to bring new product(s) in the market by using existing information of the known product. The benefits of drug re-purposing are: lesser requirements for non-clinical studies, faster reach to market, effective re-use of existing information, etc.

There are several ways in which indications for re-purposed products are identified. The most well known path is to find out other indications or disease pathways in which original target make impact. This type of drug re-purposing is known as ‘line extension’ and several examples of this kind exist. The most challenging drug re-purposing is to identify new target(s) for existing drug which is known to make significant impact on disease pathways.  There are several experimental approaches reported to identify novel targets of existing drugs, such as high throughput screening, cell based assays to screen test molecule against know protein targets and many more. However, these approaches are not comprehensive enough to ensure that all potential targets have been screened and researcher has not missed any opportunity. Computational technologies provide such comprehensive screening of therapeutic targets.

For computational technologies to provide reliable and comprehensive results and thereby offer new product development opportunities, one requires well thought out information base as well as seamless technology that does not require manual intervention. The information base for such computational technology will consist of comprehensive listing therapeutic targets involved in various diseases. Further, this will require information about structure of these therapeutic targets either from X-ray, NMR or via molecular modeling. The information base would also require knowledge of existing ligands with activities for these therapeutic targets. These ligands can be docked in to respective targets to validate the docking procedure as well as to understand interactions of residues with ligands. This information creates base for further high-throughput docking of drugs in various therapeutic targets. One also requires database of approved drugs with corresponding low energy conformers. Once all above information is collected, the high throughput docking of drugs in various therapeutic targets is preformed and activities of drugs which bind to targets are predicted. The success of such docking largely depends upon how accurately pose of drug in target is determined and how accurately it is ranked with respect to existing ligands for the target. Further, such docking will require automated technology to submit computational tasks, organize it and classify useful results from others. After compiling results of targets where drug has demonstrated putative binding, a list of most promising targets for the drug can be obtained.

Thus, computational technology can provide excellent first level screening (hypothesis) before doing detailed experimental validation of hypothesis. Have a look at this case study on one of the pharmaceutical company we worked with.

Sudhir Kulkarni

I am theoretical and computational chemist. Working as Vice-President, Discovery at VLife Sciences Technologies Pvt. Ltd. I am closely associated with technology devevelopment for computer aided drug discovery and drug repurposing. My areas of interest are computational method development, diabetic complications and cancer. In addition, I have interest in organometallic chemistry, qunatum chemistry and weak molecular interactions.

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Feb 8 11

Hello world!

by Yogesh Wagh

How often we come up with an idea which can be taken forward for some serious innovation? Many of us just shelve those thoughts as we have our own priorities, why not have a forum to discuss about these simple and complex ideas.

We invite the scientific innovators who believe in handshake of computational and experimental science. If you have something to write about or contribute, especially in the area of computational chemistry, molecular modeling, medicinal chemistry or protein sciences:  just send me an email to yogeshw@vlifesciences.com . We would love to have you as our guest author on VLife blog for science and technology. Let everyone hear about the good science and technology.

 

 

Yogesh Wagh

I am science and technology savvy, I love my role of taking ideas and concepts to reality with commercial means. I am currently spearheading the complex businesses like Drug Discovery computational and experimental technology. Do not hesitate to contact me if you would like to partner with VLife for innovating and developing the technology for science.

More Posts - Website - Twitter