Binding Free Energy (MMGBSA) Analysis Service

The binding free energy refers to the interaction between the ligand and the receptor. With the continuous deepening of drug-protein interaction theory research and the rapid development of computer-aided technology, free energy calculation methods are gradually improved. Covalent interactions and non-bonding interactions are two types of interactions between ligands and receptors. Non-bonding interaction {weak interaction and low energy} exists in most systems, and is mainly composed of three items: van der Waals interaction, electrostatic interaction and hydrogen bonding interaction. All of the above can be calculated using the force field method. The covalent interaction (strong interaction and high energy) only exists in very few systems.

Binding free energy calculation.Figure 1. Binding free energy calculation.

Our simulation services

Project name Hydrogen bond analysis service
Samples requirement
  • The initial structure of the PDB ID (if molecular dynamics simulation service is required)
  • Molecular dynamics simulation raw data
Timeline 3-5 days.
Deliverables We provide you with raw data and calculation result analysis service.
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Classifications

Calculating the binding free energy can evaluate the ligand-receptor affinity determined by experiments and serve as a reference for drug design. Many binding energy calculation methods have been developed. The following three categories are the most primarily used:

Categories Descriptions

Classic free energy calculation methods

Binding free energy calculation 1 Thermodynamic integral method and free energy perturbation method are both classic methods. Both have strict theoretical basis and are applicable to almost any system. However, sampling is time-consuming and the amount of calculation is labor intense, thus they can only be used in simple cases.

Method based on empirical equation

Binding free energy calculation 2 This method decomposes the combined free energy into several energy terms, and then uses statistical methods to refer to the training set to obtain the empirical formula. The advantage is that the sampling time is short and the amount of calculation is small.

Empirical free energy calculation methods

Binding free energy calculation 3 This category mainly includes linear interaction energy (LIE) method and the MM-PB/GBSA method. The unique advantage of this type of method is that it can calculate the free energy of binding between a ligand and a receptor.

Our molecular dynamics analysis service but not limited to:

Binding free energy calculation 4

CD ComputaBio provides a variety of molecular dynamics analysis services, such as binding free energy calculation, binding free energy decomposition, and hydrogen bond calculation. Our team of experts can provide accurate analysis services for the system you choose, so you don’t have to worry about technical issues. Free energy of binding refers to the interaction between the ligand and the receptor. With the continuous deepening of drug-protein interaction theory research and the rapid development of computer-aided technology, the calculation method of free energy has been gradually improved. The analysis of these interaction forces is very critical. If you have related analysis service requirements, please feel free to contact us.

* It should be noted that our service is only used for research, not for clinical use.

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