In thermodynamics, Gibbs energy is a thermal potential that describes the thermal properties of a system. It can be used to determine if a process is spontaneous and to calculate how much non-volumetric work a thermal system is capable of performing. One of the most popular and practical physical quantities when using thermodynamics in the study of chemistry is the Gibbs energy. A crucial area of study in the realm of computer science is the calculation of free energy. The difference in free energy between the initial and final states determines how spontaneously all physical, chemical, and biological processes occur.
Alfa Chemistry can use molecular dynamics (MD) simulations to determine the thermodynamic Gibbs energy, and the results agree very well with experiments. The binding of medicines and target enzyme molecules in living organisms occurs in isothermal isobaric conditions in real-world research settings. To determine the direction and limits of the process under isothermal isobaric conditions, it is natural to use the Gibbs free energy reduction principle to determine whether the drug molecule and the target enzyme molecule bind and the binding strength from the change of Gibbs free energy. This physics-based strategy is anticipated to considerably speed up the drug development and optimization process in the near future.
Free Energy Calculation Methods
Alfa Chemistry performs free energy calculations using a method based on MD simulations, which are able to fully sample the conformational changes of the system and can handle systems as large as proteins using explicit solvent models. The dimensions of free energy calculations can be classified according to evaluation algorithms, sampling methods, etc. Here the main categories are as follows.
Methods 1: Classical free energy calculation methods
These methods include Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). They are more rigorous in principle, and the calculation results are more accurate, but they require long time of data acquisition and have strict limitations on the calculation system. Moreover, these methods can only calculate the relative binding free energy between two ligands, so their application in drug design has been greatly limited in the past. However, thanks to the rapid development of computer performance in recent years, these methods have become the mainstream methods for the study of free energy in drug design due to their high accuracy the calculation.
Method 2: Master equation-based methods
This type of method assumes that the combined free energy comes from the contribution of different energy terms and that there is no cross interaction between these energy terms. These energy terms are calculated separately and summed to obtain the total energy. These methods only need to sample the pre-binding and post-binding conformations of the system without sampling the transition state, so the computational effort is greatly reduced compared to FEP and TI. The most representative of these methods is the MM/PBSA method.
Method 3: Free energy calculation methods based on empirical equations
This type of method teaches a little higher level than the first type of methods, and does not require molecular dynamics simulations to obtain the free energy of each state of the acquired system, but uses statistical methods to obtain the empirical equations for free energy calculation for the existing free energy data of the training set.
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