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In silico Protein Engineering

The fast and accurate prediction of optimized amino acid
sequences that can improve the functionalities of protein

Technology at Quantumzyme

QZyme WorkbenchTM

QZyme WorkbenchTM is a fully automated proprietary in silico protein engineering platform, evolved by integrating open-source computational chemistry and biology/bioinformatics tools in combination with customised algorithms and scripts.

QZyme WorkbenchTM is capable of tackling several important aspects of protein modelling and engineering including, but not limited to, structural refinement, ligand docking, conformational sampling, estimating substrate binding affinity, modelling catalytic reaction, identifying mutable hotspots, further hotspot optimization.

To mitigate these challenges Quantumzyme has developed an in silico protocol known as the QZyme WorkbenchTM that is capable of tackling several important aspects of protein modeling and engineering.

QZyme PilotTM

Initial hypothesis framing from key intelligence and information assimilation based on data, leads from a novel suggestion to an effective proposition

QZyme ModellerTM

Developing high confidence 3D model in the absence of accurate structural information by applying algorithms best suited for each case

QZyme CatMecTM

In-depth comparison study of the catalytic mechanism of the enzyme to lay the foundation for a robust enzyme development strategy

QZyme HotspotTM

Discovery of key functional residues engaged in substrate binding; transition-state stabilization; product release and estimating their mutability for enzyme engineering

QZyme DesignerTM

Creation of a focused library of variants with optimised functional hotspots and in depth study of hundreds of variants designed to elucidate desired activity

QZyme Pilot

Initial hypothesis framing from key intelligence and information assimilation based on data, leads from a novel suggestion to an effective proposition

QZyme Modeller

Developing high confidence 3D model in the absence of accurate structural information by applying algorithms best suited for each case

QZyme CatMec

In-depth comparison study of the catalytic mechanism of the enzyme to lay the foundation for a robust enzyme development strategy

QZyme Hotspot

Discovery of key functional residues engaged in substrate binding; transition-state stabilization; product release and estimating their mutability for enzyme engineering

QZyme Designer

Creation of a focused library of variants with optimised functional hotspots and in depth study of hundreds of variants designed to elucidate desired activity

Advanced techniques tailored for protein engineering

Structural refinement and modeling
Ligand docking
Conformational sampling
Estimating substrate affinity-1
Modelling catalytic mechanism-1
Identifying mutable hotspots
Hotspot optimization

Advanced techniques tailored for protein engineering

Home grown powerful framework for enzyme engineering
A complete toolkit to understand your enzyme from sequence to its activity
Tailor made enzyme
Based on your requirement, the enzyme is enhanced to its full potential
Enhanced sampling method
We use enhanced sampling methods such as Umbrella Sampling, Metadynamics along with quantum level calculations such as Semiempirical Quantum Mechanics and Quantum Mechanics/Molecular Mechanics calculation, to get in-depth knowledge of the enzyme for predicting the best variants
AI/ML-hybrid variant predictor
A recent yet powerful addition to our technology which helps to predict the enzyme activity and also facilitate selection of right parameter for analysis
Alchemical calculation
A statistical mechanics method that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations. The free energy difference is calculated from state A to state B, showing complete view of reaction
Quantitative structural activity relationship
4th dimensional view of high-resolution details of enzymatic reaction

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