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2. Vlife BioPredicta™

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Scientific Software Services :: Chemistry :: Molecular Docking :: Vlife BioPredicta™

Vlife BioPredicta™ #404

BioPredicta™ is an advanced tool for all bio - molecule related activities such as homology modeling, protein analysis and studying protein - ligand interactions. It includes GRIPTM, a novel methodology for protein - peptide and protein - ligand docking. GRIP has demonstrated capabilities to deliver more accurate and fast docking results even for complex ligand chemistries.

Learn more about Vlife BioPredicta™ Suite

BioPredicta™ included Tools

BioPredicta™
Features

Vlife Engine™	Homology Modeling	Protein Analysis
	Protein Handling	Molecular Docking

From simple visualization to complex protein editing, BioPredicta facilitates all modeling activities like generation of homology model, model validation and analysis as well as molecular docking. BioPredicta enables analysis of protein cavities in terms of shape and electrostatic as well as hydrophobic properties, which provide critical clues for optimization of ligand design.

BioPredicta seamlessly interfaces with other VLife products like VLifeEngine™. This enables users to conveniently access supporting operations like molecule management, conformation analysis and geometry optimization.

BioPredicta module allows to perform all biomolecule related activities, such as homology modeling, protein analysis and to study protein - ligand interactions.

In order to study protein-ligand interactions, a protein structure of interest can be collected from database if 3D crystal structure is known or can be built using template based homology modeling facility.

The protein analysis facility of BioPredicta helps to check/repair geometry of protein structure and visualization of various protein cavities before undertaking any protein-ligand interaction study.

The molecular docking facility of BioPredicta helps in understanding of mode of binding of ligands to their receptors for successful design of more efficient drugs.

click on image to enlarge

MEP mapped on Channel of retinoic acid receptor beta

BioPredicta™ Salient Features

Homology Modeling

BLAST link to perform sequence alignment and editing

Manual mode for specific mutation, insertion, deletion and excision

RMSD and similarity score based loop insertion

Auto mode for automatic model building with user selected template and alignment

Rotamer library for side chain conformer exploration

Protein Analysis

Cavity and channel identification, property mapping, shape – size analysis

Cavity ranking based on hydrophobic surface area of residue within cavity

Protein cleaning, Ramchandran plot and local geometry analysis

Secondary structure assignment based on atomic coordinates

Docking

Stochastic: GA based for rapid flexible docking

Systematic: GRID based for exhaustive rigid docking

Manual: Interactive docking for precise analysis

Multiple scores: PLP, DockScore, Steric + Electrostatic, Electrostatic

Docking flexibility: Auto, manual and batch docking facility

Comprehensive visualizer for protein – ligand interaction

GRIP

GRIP is a rapid and accurate protein - ligand docking methodology, implemented innovatively in BioPredicta. GRIP has demonstrated superior results in terms of speed and accuracy in computational studies on variety of receptors and compound libraries.

Besides protein – ligand docking, GRIP is also useful for protein - peptide docking and interaction analysis. The GRIP scoring function is implemented in a novel way for fast but precise capturing of ligand – receptor interactions in the active site of proteins.

GRIP docking is available as rigid as well as flexible docking, where unique conformers of a set of ligands is taken as input.

Provides option for ligand guided as well as cavity guided docking

Available in manual, automated and batch mode

Takes into consideration hydrogen bonding, repulsions and dispersion interactions

Wide range of parameterizations available for better scanning of the placement space

Molecule Builder/ Analyzer

On-line 2D sketching utility

2D to 3D conversion

3D editor for various manipulations relating to chirality, charges, labeling etc.

Multiple force fields: UFF, MMFF, MMFF94, MMFF94-S etc.

Conformation Analysis

Systematic method of conformation generation for an exhaustive conformation search

Consideration of chirality of atoms and facility to explore all possible chiralities

Conformer generation of non - aromatic rings via ring flip algorithm

Generation of diverse conformers using torsion RMS to span maximum conformational space

Generation of conformers using different seed numbers of Monte - Carlo method to exhaustively span the conformational space

Advantages

Allows the biomolecule handling facilities. Starting from simple visualization as well as editing of protein, this module allows more complex modeling activities like generation of homology model of protein, model validation analysis and molecular docking studies.

Allows analysis of protein cavities in terms of shape and electrostatic as well as hydrophobic properties, which further will provide clues for optimization of ligand design.

Features

Homology Modeling
Homology modeling feature of BioPredicta allows execution of the BLAST program for the protein sequence to be modeled to get the template sequence for modeling. This allows selection of template protein for building homology model. This also enables both manual and automated homology modeling from the selected template.

Protein Analysis
The protein analysis feature of Biopredicta allows:

Performing protein local geometry check

Identification of residues crossing in protein model

Visualization of Ramachandran plot

Cavity identification

Channel identification

Ligand interaction visualizer

Molecular Docking
The Molecular Docking feature allows rapid identification of the binding mode of ligands to their receptors. This could be done using systematic methods (Grid) or stochastic method (genetic algorithm). Various scoring functions like PLP score, XCscore and Steric + Electrostatic are available for evaluation of the docked poses.

System Requirements

The following lists the supported operating systems and minimum hardware requirements:

Operating Systems	Windows® NT/2000/XP
Optional Operating system:	Windows Vista®
Recommended Hardware Minimum free hard disk space: 1 GB Minimum required memory: 1 GB (2 GB if operating with Windows Vista) Operating system version numbers are the suggested minimum versions.
Graphic Cards	The majority of graphic cards that support hardware-accelerated OpenGL.

Pricing

VLife BioPredicta™ Suite is available with Licensing Term of 1 Year or Licensing Term of 3 Years. The Pricing for the following License-Areas are available under request. Feel free to contact us for pricing. Industry and ‘for – profit’ Research Organizations (Commercial) Government, Semi-Government and private ‘not-for-profit’ Research Organizations Academic, Universities, Colleges, High School etc. This software is available with Volume or Site License Option with major discounts. Contact us for a price quote.

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Price: Contact for pricing

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