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Antibody Physicochemical Properties Analysis Service


Fig 1. The Antibody Physicochemical Properties Analysis Service.

The antibody physicochemical properties analysis service from CD ComputaBio is a vital resource for researchers in the antibody development field. Understanding the physicochemical properties of antibodies is essential for effective applications in therapeutics, diagnostics, and fundamental research. Our service utilizes computational techniques to deliver detailed and precise analyses. This approach facilitates enhanced antibody design, optimization, and quality control, ultimately supporting advancements in biomedical applications and improving outcomes in various research endeavors.

Antibody Physicochemical Properties Analysis Service

Secondary and Tertiary Structure Determination

Using homology modeling and ab initio prediction methods, we can determine the secondary and tertiary structures of antibodies. This provides valuable information about the folding patterns, domain arrangements, and overall conformation of the antibody. Knowledge of the structure is fundamental for understanding properties such as antigen - binding regions, flexibility, and stability.

Aggregation Prediction

Aggregation of antibodies can affect their activity and safety. Using molecular dynamics simulations and energy - based calculations, we predict the propensity of antibodies to aggregate. This helps in identifying regions in the antibody that are prone to self - association and allows for the design of strategies to prevent aggregation, such as amino acid substitutions or formulation changes.

Thermal Stability Prediction

We use computational methods to predict the thermal stability of antibodies. This involves calculating the melting temperature (Tm) and other thermodynamic parameters related to the unfolding of the antibody. By analyzing the energetics of the antibody structure, we can identify regions that contribute to stability and predict the effects of mutations or environmental changes on stability.

Hydrophobicity Mapping

We create hydrophobicity maps of antibodies, which show the distribution of hydrophobic and hydrophilic regions on the antibody surface. This is important for understanding how antibodies interact with membranes, other proteins, and the solvent. Hydrophobic regions can be involved in binding to hydrophobic patches on antigens or in interactions with lipid bilayers.

Approaches of Antibody Physicochemical Properties Analysis Service

Sample Submission
Clients provide us with the antibody sample or its amino acid sequence. If only the sequence is available, we start with sequence - based analysis.
Structure Modeling
If the three - dimensional structure of the antibody is not known, we build a model using homology modeling or ab initio methods.
Model Validation
We validate our computational models by comparing them with available experimental data, if any.
Report Generation
The report is delivered to the client in a timely manner. We also offer to have a discussion with the client to explain the results.

Our Algorithm

At the core of our services lie our cutting-edge algorithms, meticulously developed and continuously optimized by our team of computational biologists and bioinformaticians.

Property Relationship (QSPR) Algorithm

The QSPR algorithm is used to establish relationships between the chemical structure of antibodies (represented by their amino acid sequences or structural features) and their physicochemical properties.

Function - Driven Property Analysis

We also consider the intended function of the antibody when analyzing its physicochemical properties. If the antibody is designed for a specific therapeutic or diagnostic application, we focus on the properties that are most relevant to that function.

Advantages

Iterative Optimization

We can use the results from experimental verification to further optimize our computational models. This iterative process improves the accuracy of our analysis over time and ensures that our service provides the most reliable results.

Flexible Solutions

We are flexible in our approach and can adapt to different types of antibodies, including monoclonal, polyclonal, and antibody fragments. We also take into account the client's time and budget constraints when designing the service.

Tailored to Client Needs

We offer a customized service that is tailored to the specific needs of each client. Whether the client is interested in a specific property analysis, such as solubility, or a comprehensive analysis of all physicochemical properties, we can design a service package accordingly.

The antibody physicochemical properties analysis aervice by CD ComputaBio provides a comprehensive and reliable solution for analyzing the physicochemical properties of antibodies. Our service, based on CADD techniques and supported by a multidisciplinary expert team, advanced computational resources, an integrated computational - experimental approach, and customized service offerings, enables accurate property analysis. This is crucial for the development, optimization, and quality control of antibodies in various applications, including therapeutics and diagnostics.

FAQ

How are antibody molecular weight and size determined computationally?

Computationally, the molecular weight of an antibody can be estimated based on its amino acid sequence. Each amino acid has a known average molecular weight, and by summing up the molecular weights of all the amino acids in the antibody, a rough estimate can be obtained. For a more accurate determination, especially considering post - translational modifications, computational models can be used in combination with experimental data. Regarding size, molecular dynamics simulations can provide information about the spatial dimensions of an antibody in different conformations. The root - mean - square deviation (RMSD) of atomic positions during a simulation can give an indication of the size and flexibility of the antibody.

What about the analysis of antibody charge and isoelectric point?

The charge of an antibody can be analyzed computationally by considering the pKa values of the ionizable amino acid side chains. There are software tools that can calculate the net charge of an antibody at a given pH based on the amino acid composition. The isoelectric point (pI), which is the pH at which the antibody has a net zero charge, can also be calculated in a similar way. Additionally, electrostatic potential maps can be generated using computational methods to visualize the charge distribution on the surface of the antibody.

How is antibody hydrophobicity analyzed?

Antibody hydrophobicity can be analyzed through computational methods in multiple ways. One approach is to calculate the hydrophobicity index for each amino acid in the antibody sequence and then sum them up or analyze them on a per - domain or per - region basis. Another method is to use molecular dynamics simulations to study the exposure of hydrophobic residues to the solvent. If hydrophobic residues are more exposed, it can indicate a higher hydrophobicity. Additionally, hydrophobicity can be visualized using computational tools that map hydrophobic regions on the 3D structure of the antibody. This analysis is important because hydrophobic interactions can affect antibody folding, stability, and binding.

What role does computational modeling play in understanding antibody conformational stability?

Computational modeling, especially molecular dynamics simulations, plays a significant role in understanding antibody conformational stability. MD simulations can be run for extended periods to observe how an antibody's structure fluctuates over time. By calculating the potential energy of the antibody system during the simulation, it is possible to identify stable and unstable conformations. The root - mean - square fluctuation (RMSF) of atomic positions can be used to measure the flexibility of different parts of the antibody, with higher RMSF values indicating more flexibility and potentially lower conformational stability.
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