Due to the increasing size of the studied systems and the limitation of computational resources and computational time, it is undoubtedly impractical to simulate the whole system by quantum mechanical methods, but if the simulation is performed only by molecular mechanical methods, it does not give reliable geometric structures or energies, not to mention the chemical reactions that occur. This is why the QM/MM method, a hierarchical approach that combines the accuracy of quantum mechanics with the advantages of the speed of molecular mechanics in molecular simulations, is often used to study chemical processes in solution and protein systems.
Principle
QM/MM is the division of the whole system into two parts: the model and the environment. The smaller part is the critical chemical region, which needs to be calculated using accurate and expensive QM methods; the remaining environmental part can be simulated using less accurate, but more efficient MM methods (MM methods do not describe well the bonding processes that occur in reactions and systems with complex electronic states).
Sepcific QM/MM Service Approaches We Offer
At Creative Enzymes, we have devised a QM/MM simulation method to study the range of structural and energetic changes involved in the reaction process at the atomic and electronic levels. In addition, our well-established QM/MM simulations facilitate the study of reaction mechanisms. Our fast and high-quality services include.
We use QM/MM MD simulations to help gain insight into a range of key information on the structure, energy changes involved in enzyme reactions from the atomic and electronic levels.
We perform free energy (PMF) simulations based on QM/MM simulations, pKa calculations and statistical analysis to study the catalytic mechanism.
We can also apply QM/MM potential energy surfaces combined with Feynman path integral free energy perturbation theory (PI-FEP) to calculate equilibrium isotope effects (EIE) and isotope fractionation factors (IFF) in the solution system.
Our team can also use QM/MM multi-scale biomolecular dynamics simulations to study the changes in electronic structure during receptor-ligand binding. Important information about molecular recognition and binding specificity can be obtained, which allows further study of the mechanisms of molecular interaction recognition and binding.
Applications
Molecular Dynamics Simulations
Geometry Optimization.
Free Energy Computation
Free Energy Perturbation
Computational Spectroscopy
Service Process
Our Features
Creative Enzymes has a group of technical experts specializing in DNA modifying enzyme QM/MM service. Our extensive research and technical experience can help our customers solve their technical problems.
Creative Enzymes has a proven, advanced DNA modifying technology platform that is constantly being improved to ensure that we can provide accurate, sensitive, and rapid analytical results for our customers.
Deliverables
Results raw data
Data analysis
Results analysis
Summary of relevant parameters
Why Choose Us?
At Creative Enzymes, our goal is to offer innovative, flexible and scalable solutions that can meet the needs of our customers. We strive to meet this challenge as a global company that places a high priority on collaborative interactions, rapid delivery of solutions, and providing the highest level of quality. If you would like to know more about this service, please feel free to contact us.
