Binding Free Energy Analysis Service
Binding free energy analysis is a crucial method for evaluating the strength of interactions between a ligand and its target by calculating the binding free energy. This approach is widely utilized in drug discovery and optimization. CD ComputaBio offers professional binding free energy analysis services to assist clients in accurately predicting molecular binding affinities, thereby enhancing the efficiency of drug discovery and optimization.
Overview of Binding Free Energy
Binding free energy (ΔG) quantifies the thermodynamic stability of molecular interactions, such as ligand-receptor or protein-protein binding. It reflects the balance between favorable forces (e.g., hydrogen bonds, hydrophobic effects) and entropic costs of complex formation. Computationally, methods like molecular dynamics simulations, free energy perturbation (FEP), or MM/PBSA predict ΔG to assess binding affinity and specificity. In drug discovery, optimizing ΔG guides lead compound selection by enhancing target engagement while minimizing off-target effects.
Fig. 1 Binding free energies of ACE–peptides complexes obtained by MM/GBSA. (CHEN R, et al., 2021)
Common Binding Free Energy Calculation Methods
- Molecular Mechanics/Poisson-Boltzmann Surface Area Method (MM/PBSA)
Combines molecular mechanics, the Poisson-Boltzmann equation, and surface area models to calculate binding free energy from molecular dynamics trajectories.
- Molecular Mechanics/Generalized Born Surface Area Method (MM/GBSA)
Similar to MM/PBSA but uses the Generalized Born model for solvation free energy calculations.
- Free Energy Perturbation (FEP)
Determines free energy differences by gradually changing the molecular system's Hamiltonian, often used for ligand-target binding.
- Thermodynamic Integration (TI)
Computes free energy differences by integrating gradients along the pathway of Hamiltonian changes.
- Linear Interaction Energy (LIE)
Predicts binding free energy using electrostatic and van der Waals interactions from molecular dynamics simulations.
Our Services
Leveraging its advanced computational platform and specialized bioinformatics team, CD ComputaBio offers highly accurate binding free energy analysis services to enhance drug discovery and molecular interaction studies. This service integrates molecular dynamics simulations with free energy calculation methods, ensuring that clients receive reliable and reproducible data. This provides critical support for drug design and optimization.
Small Molecule-Targets Binding
Analysis
Employ MM-PBSA/GBSA and alchemical free energy perturbation (FEP) methods to quantify ligand-receptor binding free energy, guiding lead optimization for small molecules, peptides, or antibodies.
Nucleic Acid-Ligand Binding
Analysis
Characterize binding free energy of small molecules or proteins with DNA/RNA targets (e.g., G-quadruplexes, riboswitches) to support antiviral or gene therapy drug development.
Lipids and Membrane Systems Binding
Analysis
Binding free energy calculations on lipids and membrane systems help in understanding membrane dynamics, lipid-lipid and lipid-protein interactions, and the impact of compounds on membrane properties.
Antibody-Antigen Interaction Profiling
Analysis
Analyze key residues in CDR regions driving antibody-antigen binding, predict affinity changes upon mutations, and support humanization/affinity maturation campaigns.
Proteins-Ligand Binding
Analysis
Binding free energy analysis is used to study protein folding, stability, and conformational changes, as well as protein-protein and protein-ligand interactions.
Ions and Metal Complexes Binding
Analysis
Applying binging free energy analysis to ions and metal complexes provides insights into their binding sites, coordination chemistry, and role in enzymatic functions.
CD ComputaBio offers comprehensive binding free energy analysis services to help customers accurately evaluate drug-target interactions using our advanced technology platform and expert team. If you encounter any challenges during the analysis process, please don't hesitate to contact us for complete support.
Reference:
- CHEN R, MIAO Y, HAO X, et al. Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation [J]. Food science & nutrition, 2021, 9(6): 2943-53.
* For Research Use Only.
