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Protein modeling and docking

A structure based design approach by definition is centered on the knowledge of the target protein structure. In absence of availability of such a structure a computationally generated model of the target based on a homologous protein is commonly used. Docking of the candidate small molecule into the correct active site of the target is a required step in determining the binding of the molecule to its target. Computationally predicted binding is often the only way of practically predicting the binding of the molecule with the target in-vitro or in-vivo.

VLife’s Protein Modeling and Docking service can assist in performing a complete structure base design project. Scope of these services could include optimizing the structure of the target protein, if available in public databases or developing a homology model of the target protein to replicate the target within very stringent levels of accuracy. This could be followed by an analysis of the protein or the model to identify active sites, mapping of the cavities and channels followed by docking of the small molecule into the correct cavity.

A choice of docking methods and techniques coupled with a variety of scoring functions enable our scientists to complete the design exercise in the most comprehensive manner. A specialized infrastructure combining the very best technologies for modeling, docking and visualization with a multi core parallel processing computational cluster enables our scientists to deliver this services in the most time efficient way.
Protein modeling and docking
Where VLife can help
Some other representative activities where our Knowledge Services can help you are:

  •  Fragment based molecule design
  •  Focused virtual library design
  •  Protein – protein interaction studies
  •  Compounds prioritization
  •  Pharmacophore guided molecule design
  •  Scaffold hopping
  •  Structure based search
  •  Data search and mining
  •  ‘What-if’ scenario analysis
Our expertise in computational discovery
Success with computation technology requires awareness of not only its strengths but also of the areas where it needs augmentation from other approaches. Being developers of computational technologies, we have proved our expertise by creating IP in 3 NCE classes and 7 new indication discoveries.
Wide diversity of experience
We cater to a variety of sectors and within them, a diversity of areas. e.g. in pharmaceuticals, we have successfully delivered discovery projects in oncology, anti-fungal, diabetes, CNS etc.
State-of-art technology portfolio
Clients benefit from the whole range of VLife's technologies having validated algorithms, published innovations and efficient workflows which are accessible to clients through VLife services.
In-house custom development skills
Generic technologies sometimes are inadequate or inefficient in complex research. For such needs, our in-house team has skills to develop custom technologies ensuring reliable research.
Case studies: VLife services
Homology modeling Homology modeling using BioPredicta View
Enzymes Application of enzymes to enhance drug action View
Target Identification Target Identification for existing nutraceutical molecule View
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