Protein structure modeling is a group of computational method used to describe the three-dimensional structure of a protein or protein complex. CD ComputaBio offers a wide range of protein structure modeling services to address the lack of protein crystal structures during drug discovery. Our structure modeling services cover a wide range of protein types.

Introduction to Protein Structure Modeling

Protein structure modeling is a crucial method in modern molecular biology, aiming to predict the 3D structure of proteins based on their amino acid sequences. Template-based protein modeling methods include threading modeling and comparative modeling. This protein structure modeling method relies on detectable similarity between a large portion of the modeled sequence and at least one known structure. Proteins from the same family are more conserved in their amino acid sequence. Therefore, if similarities between two proteins in the same family can be detected at the sequence level, it is often possible to assume that the structures are similar and model accordingly.

Fig 1. Protein complex structure prediction and evaluation pipeline. (Chen X, et al., 2024)

Computational Tools for Protein Structure Modeling

Our Services

CD ComputaBio uses computational modeling to predict 3D structure of proteins. We have extensive experience in modeling various proteins. The generated structures are evaluated and can be used for a variety of purposes, such as predicting ligand binding sites. Our services are listed below but are not limited to:

Methods of Protein Structure Modeling

Process of Protein Structure Modeling

1. 1Sequence Identification - to search for proteins with known 3D structures that are related to the target sequence
2. 2Sequence Alignment - to pick those structures that will be used as templates and align their sequences with the target sequence
3. 3Model Building - to build the model for the target sequence given its alignment with the template structures
4. 4Model Refinement - to evaluate the model, using a variety of criteria.

What You'll Receive

Integration with Downstream Studies

Accurate protein structure modeling is not the final goal—it is the foundation for a wide range of downstream computational and drug discovery applications. At CD ComputaBio, we ensure that every modeled structure is analysis-ready, validated, and seamlessly integrated into advanced computational workflows, enabling you to accelerate your research from structure to function and from target to therapeutic candidate.

🔬 Structure-Based Molecular Docking

Our high-quality protein models are optimized for protein–ligand and protein–protein docking studies, ensuring reliable interaction predictions.

👉 Value to you: Improve hit identification accuracy and reduce false positives in early-stage drug discovery.

⚙️ Molecular Dynamics (MD) Simulation

To go beyond static structures, we provide molecular dynamics simulations to evaluate protein stability and conformational flexibility under physiological conditions.

👉 Value to you: Gain deeper insights into structural dynamics and validate docking results with time-resolved data.

💻 Virtual Screening & Hit Discovery

We integrate modeled structures into virtual screening pipelines to identify potential lead compounds efficiently.

👉 Value to you: Rapidly identify promising candidates while significantly reducing experimental screening costs.

🎯 Binding Site Identification

Understanding where and how molecules interact with your protein is critical. We provide comprehensive binding site analysis based on structural and physicochemical properties.

👉 Value to you: Enable rational drug design, target validation, and mechanism-of-action studies.

Why Work with Us Instead of Using Free Docking Tools?

Published Data

Case 1. Development of Anti-PD-L1 Antibodies Based on AlphaFold2 Structure Prediction

This research demonstrates a concrete application of advanced protein structure modeling in antibody engineering. The investigators utilized AlphaFold2 to predict the complex structure of Programmed Death-Ligand 1 (PD-L1) and its receptor, PD-1, allowing for a detailed analysis of the critical interaction interface. Based on this high-resolution predictive model, the team performed the rational design of a known antibody, modifying its structure to more effectively block the PD-1/PD-L1 signaling pathway.

Fig 2. Structure prediction.²

Frequently Asked Questions

CD ComputaBio focuses on protein structure modeling services, using a variety of modeling methods and rich knowledge to provide protein structure modeling solutions. If you are interested in our services or have any questions, please feel free to contact us.

References:

1. Chen X, Liu J, Park N, et al. A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models[J]. Biomolecules, 2024, 14(5): 574.
2. Du K, Huang H. Development of anti-PD-L1 antibody based on structure prediction of AlphaFold2[J]. Frontiers in Immunology, 2023, 14: 1275999.

• Membrane Protein Modeling Service
• Receptor Protein Modeling Services
• Viral Protein Modeling Service
• Nucleic Acid Binding Protein Modeling Service
• Glycoprotein Modeling Service
• Bioactive Peptide Modeling Services