Ligand Compound Screening Service

1 Product Overview

This product offers strong specificity and flexibility. It performs molecular docking simulations based on the structural information of known target proteins to identify compounds that are highly compatible with receptor structures. Additionally, virtual screening allows for real-time adjustment of screening criteria and parameters to meet different screening requirements, providing exceptional flexibility and adaptability.

Not only does this product help identify potential high-affinity compounds, but it also provides insights into the binding modes between compounds and target proteins through molecular docking and modeling analysis. The analytical and predictive nature of this data enables researchers to further understand the Structure-Activity Relationship (SAR) of the identified compounds, offering valuable support for subsequent compound optimization and efficacy improvement.

2 Product Screening Workflow

2.1 Construction of Customized Compound Libraries and Receptor Protein Models

KeJingBio has reserved a database of over 10 million compounds, including molecular structures, physicochemical properties, and drug-likeness parameters. Researchers can select their desired compound libraries based on their research focus, narrowing the screening scope to identify high-quality, cost-effective compounds and reducing early research costs.

Upon confirmation of the protein name, species, and amino acid sequence, relevant protein information is collected. If the target protein lacks a complete 3D structure resolved by cryo-electron microscopy, technical experts will use AlphaFold 3 to accurately model the protein structure based on its sequence, evaluate the confidence of the model, and ensure its accuracy and reliability.

图1 科晶生物已储备化合物库大类

图2 科晶生物按照疾病化合物库分类

2.2 Preliminary Docking Screening

This product utilizes AutoDock Vina for molecular docking. Using default docking parameters, large-scale preliminary screening is conducted on all candidate compounds. The binding energies are ranked from lowest to highest, and the top 5% of compounds with the lowest binding energies proceed to the next stage, the "Precise Screening" phase.

2.3 Precise Docking Screening

Docking parameters are adjusted to enhance the thoroughness of the docking process, and the top 5% of compounds from the previous round are re-evaluated. The new binding energy scores are obtained, and the top 5% of compounds with the lowest binding energies proceed to the next stage, the "Ultra-Precise Screening" phase.

2.4 Ultra-Precise Docking Screening

In the final evaluation phase, docking parameters are maximized within computational capacity. The latest binding energy scores of all candidate compounds are ranked from lowest to highest. Researchers can use these results as a reference to select compounds for subsequent experimental validation.

2.5 Visualization of Binding Conformations (Optional)

Using DiffDock and NeuralPlexer, the binding conformations of target compounds and the receptor protein are analyzed in detail. The best binding modes are identified based on confidence scores, and interactions between compound groups and amino acid residues of the target protein are examined. This analysis guides subsequent compound modifications to improve activity and stability while reducing drug toxicity.

3 Deliverables