Contact Area Analysis Services
Computer-aided drug design has changed the landscape of pharmaceutical research, enabling scientists to accelerate the drug development process through computational methods. At CD ComputaBio, our scientists provide a wide range of contact area analysis services to support your drug development and scientific research projects. By utilizing optimized algorithms and advanced computational tools, we are able to accurately calculate contact surface area and buried surface area, identifying key amino acid residues or functional groups that affect binding affinity and selectivity.
Introduction to Contact Area Analysis
Contact area refers to the surface area of two molecules, such as ligands and receptors, that are in direct contact with each other when they interact. Specifically, it measures the surface area occupied by atoms or groups within a certain distance between two molecules when forming a complex. These areas are the main places for physical and chemical interactions between molecules, such as hydrogen bonds, hydrophobic interactions, electrostatic interactions, etc.
Fig.1 Example of interatomic and inter-residue contacts. (Olechnovič K, et al.; 2020)
Contact area analysis is a process that uses certain algorithms to clarify the degree of interaction between two molecules. It plays an important role in understanding the molecular recognition process and predicting the binding sites between proteins and ligands. It is essential for the discovery and design of new drugs and their respective targets. This analysis helps to understand the nature and strength of molecular binding, identify amino acid residues or functional groups that play a key role in the interaction process, and thus deeply understand the interaction mechanism between molecules.
Applications of Contact Area Analysis
- 1Binding Strength Assessment
The tightness of the binding between the two can be assessed by calculating the contact surface area between the ligand and the receptor. The larger the contact area, the stronger the interaction between the molecules.
- 2Identification of Key Interaction Sites
Analysis of the contact area can determine which amino acid residues or functional groups play a major role in binding, which helps guide the structural optimization of the ligand and improve the binding affinity.
- 3Assisted Drug Design and Optimization
Comparing the contact area and interaction pattern of different ligands with the same receptor can screen candidate compounds with better efficacy and selectivity to accelerate drug development.
Our Services
CD ComputaBio uses advanced computational methods and professional software tools to provide you with high-quality contact area analysis services. We not only provide clear 3D models and visualization images that intuitively display the contact area and interaction details but also comprehensive analysis reports, including data results, chart displays, and professional interpretations, to support your research and decision-making.
Our scientists are skilled in identifying and quantifying the contact areas between different molecules and provide detailed maps of molecular interfaces, including but not limited to:
Protein Complex Contact Area Analysis
We study protein-protein interaction interfaces to evaluate binding modes and interface contact areas.
Nucleic Acids Complex Contact Area Analysis
We analyze the binding areas and contact areas of nucleic acids with proteins or small molecules. We also study DNA-DNA, RNA-RNA, or DNA-RNA interactions.
Protein-Ligand Contact Area Analysis
We evaluate the contact area of small molecules with biomacromolecules binding sites and examine the interaction strengths, contributing residues, and surface areas involved at the interface.
Enzyme-Substrate Contact Area Analysis
We evaluate the interaction between enzymes and substrates and analyze the contact area of key active sites.
Glycoproteins Contact Area Analysis
We study the interaction between carbohydrates and proteins and evaluate the effect of glycosylation on molecular function.
Polysaccharide-Receptor Contact Area Analysis
We accurately calculate the contact area between polysaccharides and receptors and quantitatively evaluate the interaction strength.
Tools for Contact Area Analysis
Molecular Docking Analysis
By employing MD simulations, CD ComputaBio can elucidate the transient interactions between drugs and their targets, providing valuable insights into the stability and dynamics of binding complexes.
Pharmacophore Modeling
CD ComputaBio employs state-of-the-art modeling methods to construct pharmacophore models based on contact area analysis, facilitating the rational design of potent and selective drug molecules.
Visual Analysis
Our scientists use professional molecular visualization software to transform complex contact area data into intuitive and vivid three-dimensional structure diagrams, helping you gain a deeper understanding of the interaction mechanism between molecules.
- PyMOL
- UCSF Chimera/ChimeraX
- PISA
- LigPlot+
- Discovery Studio
- VoroMQA
CD ComputaBio's contact area analysis service provides detailed information regarding protein-drug interactions. Depending on your project's needs, we can customize the analysis to provide the most valuable insights for your drug design and modification process. Please feel free to contact us for more details on our services!
References:
- Hockenberry AJ, et al. Evolutionary couplings detect side-chain interactions. PeerJ. 2019;7:e7280.
- Olechnovič K, et al. Contact Area-Based Structural Analysis of Proteins and Their Complexes Using CAD-Score. Methods Mol Biol. 2020;2112:75-90.
* For Research Use Only.
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