Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) has been found to perform well in determining the effect of mutations on the association process and identifying hot spots in protein-protein complexes.
Figure 1. Binding free energy decomposition analysis services.
|Project name||Binding free energy decomposition analysis services|
|Deliverables||We provide you with raw data and calculation result analysis service.|
Classical free energy calculation methods
|The calculated alanine scan (CAS, where the absolute Gbind of the wild-type system is calculated, and several of its mutant residues have been replaced by alanine) is a classic free energy calculation method. It modifies the MD simulation from the wild-type system and introduces the alanine mutation in the extracted frame. The difference between Gbind between the wild-type system and the mutant can be directly compared with the results of the experimental alanine scan (AS).|
Method based on empirical equation
|Combined with free energy decomposition (BFED), this process aims to calculate the contribution of each atom or group of atoms (usually side chains) to Gbind. Like CAS, BFED also determines the energy based on the contribution of interaction and solvation energy, entropy the nature of the change. The MM–GBSA variant is attractive to BFED, not only because it is much faster than MM–PBSA, but also because the paired nature of the GB equation allows Gelec; Gsolv to decompose into atomic contributions in a direct way.|
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.