Creative Enzymes use molecular dynamics simulations to predict changes in ligand and enzyme systems over time in order to explore important biological and pharmaceutical events. Specifically, experimentally determined structures can be refined, enzyme-ligand binding can be evaluated, and biocatalytic processes can be studied.MD simulation is particularly useful in computer-aided drug discovery. It can be used to identify hidden or xenobiotic binding sites, enhance traditional virtual screening methods, and directly predict the binding energy of small molecules.

Figure 1. Restriction Enzyme Molecular Dynamics Simulations.

Sepcific Restriction Enzyme Molecular Dynamics Simulations Approaches We Offer

Creative Enzymes offer a one-stop restraint enzyme molecular dynamics simulations service that can meet your research needs for restriction enzyme research.

Conventional molecular dynamics simulations

• Study of the interaction mechanisms of ligand-receptor complex systems: interaction patterns, induced fit effects, protein backbone motions.
• Predicting the binding free energy of active small molecules (and thus Ki, IC50) to elucidate the mechanism or to guide structural modification.
• Optimization of protein structures, e.g. structural optimization of structures obtained from homology modelling.

Other Advanced Methods

• Stretching molecular dynamics (SMD).
• Copy exchange molecular dynamics (REMD).
• Targeted molecular dynamics (TMD).
• Micro-motion elastic band (NEB) calculations.

QM/MM and QM/MM/MD

• The study of enzyme catalytic mechanisms, often including transition state courses.
• Proton transfer, charge migration reaction processes.
• Induced luminescence mechanism.

Analysis content

• Backbone fluctuations: RMSD, RMSF.
• Interactions: hydrogen bonding, salt bridges, angles, dihedral angles, hydration, interaction spectra.
• Binding free energy: MM/PB(GB)SA.
• Conformational sampling: clustering, PCA, simple normal mode analysis, secondary structure analysis, potential energy surface scanning, dominant conformation identification.
• Hot residues: alanine scanning, energy decomposition.

Workflow

• Structural preparation, including structural treatment of restriction enzymes and small molecules as well as coenzymes, solvent molecules, etc.
• Performing kinetic simulations, including energy optimization, heating, equilibrium phase and production phase.
• Analytical trajectories, including RMSD/RMSF, hydrogen bonding analysis, cluster analysis, PCA, and binding free energy calculations.

Service Process

Our Features

• We have accumulated many years of essence in the field of enzyme service, helping customers to speed up project development and improve the overall success rate of the project.
• At Creative Enzymes, simply let us know your specific project needs. We will suggest the best strategy for you.

Deliverables

• Related molecular dynamics simulation results raw data
• Molecular dynamics simulation report
• Data analysis
• Image and result analysis
• Results analysis
• Stability assessment report
• Summary of relevant simulation parameters

Why Choose Us?

Creative Enzymes is a company that provides professional and comprehensive restriction enzyme molecular dynamics simulations service services. We have years of experience to meet your specific project needs to add value to your research projects. Creative Enzymes can provide you with personalized solutions to help you thrive every step of the way around your interest in your workflow. If you would like to know more about this service, please feel free to contact us.