VLife ProModel for Homology Modeling and Protein Analysis

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ProModel: Homology modeling

Products > VLifeMDS > ProModel

ProModel is a complete package for modeling proteins, whose crystal structure is unknown based on the amino acid sequences of a close homologue. ProModel allows homology modeling from either a selected template or a user defined template. Users can perform an automated homology modeling simply by reading in the template file or can perform a knowledge based manual modeling by specific loop insertions or by changing specific amino acid residues. A local BLAST speeds up the process of modeling.

ProModel enables an exhaustive analysis of the target protein structure, active site and channels. The user can conveniently view, edit and superimpose proteins with ProModel. Facilities to distribute the secondary structure elements, distribute the Phi-Psi angles of residues in Ramachandran plot, identify and visualize cavities and channels make it a very useful product. ProModel is available for both Linux and Windows^® operating systems.

Key features

Automated homology modeling
An intuitive easy to user interface allows an automated homology modeling simply by reading in the template file obtained from a local BLAST.

Manual homology modeling
Modeling in manual mode allows mutation, excision, deletion and insertion of residues as also the insertion of a loop by selecting the start and end anchors. ProModel provides a choice to insert the loop based on the RMSD and similarity of the loop from among the results obtained by VLifeMDS from its database.

Rotamer library
The built-in rotamer library allows exploration of accessible amino acid side chain conformations.

Cavity identification
ProModel identifies all the cavities present in the protein and ranks them based on their size. Detailed information such as volume, surface area, residues in the neighborhood of cavity is calculated and presented. Mapping of electrostatic and hydrophobic properties over the cavity surface enable a complete analysis of the cavity.

Channel identification
ProModel can identify and visualize channels thus allowing identification of the regions that are exposed to the exterior. The channel surface can also be mapped using electrostatic potential and hydrophobicity.

Superimposition of modeled structure of the protein human estrogen receptor α on its crystal structure (1L2I).

Advantages of VLife products

Peer reviewed algorithms
Algorithms in VLifeMDS have wide acceptance in scientific community. These algorithms are either published or are patent pending. There are multiple case studies of research conducted with VLifeMDS.

Ease of plug-in / plug-out
Although an integrated platform, VLifeMDS has a modular architecture. Customers can buy the whole suite in one-go or buy incrementally as per the evolving needs of their research projects. Incremental module additions seamlessly integrate with rest of the modules to provide a consistent experience.

Ease of customization & integration
VLifeMDS is developed fully in-house with complete ownership of every line of code. This provides unprecedented flexibility to add-on/ customize the product to suit customer specifications as well as integrating it to customers' existing discovery workbench.

Case studies: Application of VLife products

	Application of enzymes to enhance drug action View
	Target Identification for existing nutraceutical molecule View
	Homology modeling using BioPredicta View