Viral Protein Modeling Service

Viral proteins are encoded by the viral genome and include both structural and non-structural proteins. Structural and functional studies of viral proteins pave the way for understanding viral infection mechanisms and developing targeted drugs and vaccines. CD ComputaBio relies on the world's leading computational biology platform and integrates multi-dimensional technologies such as machine learning, deep learning, and molecular dynamics simulation to provide scientific research institutions and pharmaceutical companies with a full-process solution for high-precision viral protein modeling.

Introduction to Viral Protein Modeling

Viral protein modeling is important for understanding viral biology and developing antiviral therapies. It involves computational prediction of the three-dimensional (3D) structure and property analysis of viral proteins, which is crucial for understanding viral mechanisms, developing antiviral drugs, and designing vaccines. Viral protein modeling helps to quickly identify active sites and allosteric regulatory regions of key viral replication proteins (such as SARS-CoV-2 main protease and HIV reverse transcriptase), accelerating inhibitor design. Viral protein modeling helps to analysis of virus-host interaction mechanisms. For example, by modeling the binding interface between the spike protein and ACE2, researchers can effectively predict the immune escape potential of mutant strains, such as Omicron, and generate valuable insights for the development of broadly protective vaccines.

Fig 1. Viral protein family (VPF) function prediction using protein language models (PLMs) uncovers novel biology. (Flamholz Z N, et al., 2024)

Challenges and Advancements of Viral Protein Modeling

Low-Resolution Modeling

Using low-resolution modeling technology, the prediction coverage rate is still maintained at 75% at medium resolution (4-6Å), which greatly expands the range of available data.

Multi-target Cross-Interference Analysis

Apply the HOMOLOBIND algorithm to construct a virus-host interaction network, predict the selectivity differences of drugs for multi-protein targets, and avoid off-target effects.

Our Services

CD ComputaBio offers customized viral protein modeling services, from structure prediction to functional analysis. Leveraging integrated databases (PDB, viral protein, and proprietary) and AI-powered models, CD ComputaBio support accurate modeling of post-translational modifications such as glycosylation and phosphorylation, covering more than 90% of known viral protein families.

By Viral Proteins Types

DNA Virus Proteins Modeling	HPV Protein Modeling	Poxviridae Protein Modeling
	Parvovirus Protein Modeling	Mimivirus Protein Modeling
	Baculoviridae Protein Modeling	Archaeal Viruses Protein Modeling
	Polyomaviridae Protein Modeling	More
RNA Virus Proteins Modeling	Influenza A Virus Protein Modeling	Dengue Virus Protein Modeling
	HIV-1 Protein Modeling	Rabies Virus Protein Modeling
	HCV Protein Modeling	Respiratory Syncytial Virus Protein Modeling
	Lassa Virus Protein Modeling	Toscana Virus Protein Modeling
	Cardiovirus Protein Modeling	More
Prion Proteins Modeling	Human Prion Protein Modeling	Rat Prion Protein Modeling
Prion Proteins Modeling	More

By Modeling Types

Thermodynamics Analysis
Stability Analysis
More

Software for Viral Protein Modeling

GROMACS

High-performance molecular dynamics simulation software for conformational rearrangement of viral capsid proteins and simulation of membrane fusion processes (such as pH-dependent conformational changes of Ebola virus GP protein).

AutoDock Vina

It is used to screen inhibitors targeting viral proteins (such as anti-HIV integrase compound library screening).

HADDOCK

Flexible docking based on experimental constraints to analyze the interface interactions between viral proteins and host receptors (such as the binding interface between HPV L1 protein and neutralizing antibodies).

Cytoscape

Visualize the regulatory nodes of viral proteins in host signaling pathways (such as the interaction network between Epstein-Barr virus LMP1 protein and NF-κB pathway).

Our Advantages

Multi-algorithm Fusion Verification Platform: Synchronously run multiple modeling software and molecular dynamics simulations, and eliminate single algorithm bias through consensus mechanism.
System-Level Dynamic Behavior Analysis: Through ultra-large-scale molecular dynamics simulation and Markov state model (MSM), reveal the structure and function of viral proteins and capture transient binding interfaces that are difficult to observe in traditional experiments.
The World's Largest Viral Protein Database: Integrate PDB, viral protein library and self-built library, cover 2000+ high-precision models of virus strains, and support cross-species transfer learning

CD ComputaBio offers a comprehensive suite of services to model viral proteins with high accuracy. Our team of experts, state-of-the-art tools, and customized solutions ensure that we deliver high-quality results to our clients. By choosing CD ComputaBio, you can accelerate your drug discovery process, reduce costs, and improve the success rate of your projects. For inquiries or to discuss your specific project requirements, please contact us today.

Reference:

Flamholz Z N, Biller S J, Kelly L. Large language models improve annotation of prokaryotic viral proteins[J]. Nature microbiology, 2024, 9(2): 537-549.

* For Research Use Only.

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