Force Field-based Docking Service
The interactions between small molecules and biological targets are complex and multifaceted. Understanding these interactions is crucial for the design of effective therapeutics. CD ComputaBio offer a comprehensive force field-based docking service designed to enhance the molecular docking process.
What is Force Field-based Docking?
Force field-based docking is a computational method in molecular docking. It uses a force field, which is a set of equations and parameters to calculate the energy of molecular systems. By minimizing the energy of the ligand-receptor complex, it predicts the most favorable binding modes and orientations of molecules. This helps in understanding molecular interactions in drug design and other fields.
Figure 1. Force Field-based Docking.( Nawrocki G, et al. 2022)
Advantages of Force Field-based Docking
- Force field-based docking is capable of accurately describe intermolecular interactions. It models at the atomic level in detail and can account for solvation effects, thus enabling the accurate prediction of ligand binding modes.
- Force Field-based Docking method is highly flexible, capable of handling various molecular systems and different protein structures. It has excellent scalability and is suitable for large-scale virtual screening as well as multi-target and multi-ligand research.
Our Service
Force Field-based Docking Service is an indispensable asset in drug discovery and related biological research, offering unparalleled insights and solutions. Our team of seasoned experts, with their profound knowledge and extensive experience in the field, ensures the delivery of precise and trustworthy outcomes.
Workflow of Force Field-based Docking
Molecular Structure Preparation
CD ComputaBio leverages an extensive library of protein structures sourced from both public databases and our proprietary in-house databases. We provide homology modeling services for proteins that without crystal structures.
Force Field-based Docking Simulation
The docking calculation is executed using the prepared small molecule ligand and target protein datasets. Our specialized software, grounded in force field principles, meticulously simulates the potential binding modes of the complex.
Post-Docking Analysis
The docking results are analyzed by us by ranking the ligand poses based on their binding energies or other scoring functions. Typically, the poses with the lowest energy are regarded as the most likely binding modes.
Further Refinement (Optional)
If required, we carry out additional refinement steps on the top-ranked docking poses. This may involve molecular dynamics simulations to account for the flexibility of the protein and ligand, or energy minimization.
Trajectory Analysis
- Stability Analysis Service: RMSD,RMSF Analysis Service
- Interaction Analysis: Hydrogen Bond Interaction Analysis Service, Hydrophobic Interaction Analysis Service
- Binding Free Energy Analysis Service
- Binding Mode Analysis Services
Force Fields Type We Provide
The Amber force field is a force field that is widely used in biomolecular simulations. It is highly effective in simulating biomolecules such as proteins, nucleic acids, carbohydrates, and lipids.
The CHARMM force field is also a powerful molecular mechanics force field. It features high accuracy and flexibility and is capable of performing precise simulations on various molecular systems.
The OPLS force field mainly focuses on the simulation of organic small molecules and biomolecules. Its parameterization process emphasizes the accuracy of simulating liquid systems, so it performs excellently in dealing with molecular interactions in solvent environments.
Applications of Force Field-based Docking
Force Field-based Docking service can be applied in numerous molecular arenas. Our Force Field-based Docking service is uniquely designed to handle a wide variety of molecular systems, including but not limited to:
Get Started Today!
CD ComputaBio's force field-based docking service is a comprehensive and powerful solution for molecular research and drug discovery. With its accurate predictions, customizability, and a range of included services, it offers valuable support to researchers and companies in various industries. For inquiries or to schedule a consultation, please contact us.
Reference:
- Nawrocki G, Leontyev I, Sakipov S, et al. Protein–Ligand Binding Free-Energy Calculations with ARROW─ A Purely First-Principles Parameterized Polarizable Force Field. Journal of Chemical Theory and Computation, 2022, 18(12): 7751-7763.
* For Research Use Only.
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