Molecular Docking Service
Understanding the interactions between molecules is important, CD ComputaBio's molecular docking service is designed to provide clients with comprehensive solutions for researchers, aiming to explore these molecular interactions at a detailed level. CD ComputaBio combines cutting-edge computational techniques with in-depth domain knowledge to offer valuable insights into how molecules bind and interact with each other.
Introduction to Molecular Docking
Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. By using algorithms, the method explores different orientations and conformations of the ligand around the receptor's binding site. The best-scoring pose is considered as the most likely binding mode of the ligand to the receptor.
Figure 1. Process of Molecular Docking. (Doss C G P, et al., 2024)
Principles of Molecular Docking
The core of molecular docking lies in simulating the spatial arrangement of a ligand within the binding site of a receptor to predict its most stable binding conformation. This process involves both geometric and energetic matching, aiming to identify the lowest-energy binding mode that achieves optimal interaction between the ligand and receptor. Docking algorithms typically consist of two main steps: sampling all possible conformations of the ligand within the receptor's binding site and ranking these conformations using a scoring function.
Molecular Docking in Drug Discovery
Molecular docking is a computational technique that predicts the binding affinity of ligands to receptor proteins. Although it has potential uses in nutraceutical research, it has developed into a formidable tool for drug development. Bioactive substances called nutraceuticals are present in food sources and can be used in the management of diseases. Finding their molecular targets can help in the creation of disease-specific new therapies. This computational approach accelerates the drug discovery process, offering valuable insights for pharmaceutical research.
Key Concepts in Molecular Docking
| Concepts |
Descriptions |
| Binding Pose |
The 3D orientation of the ligand within the receptor's binding site. |
| Binding Affinity |
The strength of interaction, often estimated using scoring functions. |
| Search Algorithm |
Explores possible ligand conformations and orientations (e.g., genetic algorithms, Monte Carlo simulations). |
| Scoring Function |
Evaluates and ranks docking poses based on binding energy (e.g., force field-based, empirical, or knowledge-based scoring). |
Popular Molecular Docking Software
| AutoDock Vina |
Fast, open-source docking tool with gradient optimization.
High speed, good accuracy, supports flexible docking. |
| AutoDock 4 |
Earlier version of AutoDock with Lamarckian GA.
Handles flexible residues, good for research. |
| GOLD |
Uses genetic algorithm for flexible docking.
High accuracy, good for protein-ligand & protein-protein docking. |
| Glide (Schrödinger) |
High-precision docking with hierarchical filters.
Excellent for drug discovery, induced fit docking. |
Key Areas of Molecular Docking
Understanding Protein-Ligand Interactions
Molecular docking provides insights into the molecular basis of protein-ligand interactions. By predicting the binding mode and affinity, researchers can understand how a ligand binds to a protein and the key residues involved in the interaction.
Structural Validation
Docking can be used to validate the experimental structure of a protein-ligand complex. By comparing the predicted binding mode with the experimental structure, researchers can assess the accuracy of the docking method and gain insights into the structure-function relationship of the complex.
Drug Repurposing
Molecular docking can be used to repurpose existing drugs for new indications. By screening a library of drugs against a target protein, researchers can identify drugs that bind to the target and have the potential to be used for a new disease or condition.
Our Services
The molecular docking service from CD ComputaBio offers a comprehensive solution for researchers in drug discovery, molecular biology, and related fields. With in-depth understanding of molecular docking, advanced software, and an experienced team, we can assist you at every stage of your molecular docking research.
By Molecular Types
By Docking Methods
By Workflow
Protein and Ligand Preparation: Acquire 3D structures of the protein (via X-ray/NMR or homology modeling) and ligand. Preprocess the protein by removing water, adding hydrogens, and fixing missing atoms. Convert the ligand format, add hydrogens, optimize geometry, and compute charges for docking.
Docking Algorithm Selection: For the grid-based method, pre-compute the interaction energy; the molecular mechanics method uses the force field to calculate the interaction energy and optimize the conformation.
Docking Simulation: Place the ligand randomly or systematically at the binding site. Conduct conformational searches through algorithms such as simulated annealing.
Post-processing and Analysis: Rank the docking conformations according to the scores, select the conformations with high scores, visually inspect and analyze the interactions to determine their rationality.
CD ComputaBio offers a corresponding molecular docking service. Our molecular docking provides accurate approximations of real molecular behaviors, and have proven to be very useful in understanding the biochemical basis of physiological events at different stages of drug development, even in different fields such as materials science. Our team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. If you are interested in our services or have any questions, please feel free to contact us.
Reference:
- Doss C G P, Chakraborty C, Narayan V, et al. Computational approaches and resources in single amino acid substitutions analysis toward clinical research. Advances in protein chemistry and structural biology, 2024, 94: 365-423.
* For Research Use Only.
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