Structure-based Virtual Screening (SBVS)
Structure-based virtual screening (SBVS) helps in understanding the molecular basis of diseases to a certain extent and offers significant advantages over traditional drug discovery methods. CD ComputaBio's structure-based virtual screening services can rapidly identify promising drug candidates, providing scientific solutions for pharmaceutical companies and research institutions.
Introduction to Structure-based Virtual Screening
Structure-based virtual screening utilizes the three-dimensional structural information of target proteins or other biological molecules to predict and screen potential drug candidate compounds. This method employs computer-aided simulations to identify and optimize small molecule compounds that can effectively bind to and modulate the function of known biological target structures.
Fig. 1 Framework of structure-based virtual screening. (Wu K, et al.; 2024)
Our Services
CD ComputaBio offers professional structure-based virtual screening services, leveraging advanced algorithms and technologies to identify potential drug molecules from three-dimensional structural data, including experimental data, homology modeling, and molecular dynamics simulations.
The General Scheme of SBVS Strategy
01 Protein Preparation
Determining amino acid protonation states, optimizing hydrogen bonds, managing charges and missing structures, addressing spatial conflicts, and evaluating water molecule retention at binding sites.
02 Binding Site Identification
Analyzing protein surface pocket shapes and chemical properties, identifying and validating potential drug binding sites through simulation to support subsequent screening.
03 Compound Database Preparation
Collecting compound data and filtering out unsuitable molecules to form a high-quality compound library for virtual screening. Additionally, designing compound libraries based on target characteristics to create personalized compound libraries.
04 Molecular Docking
Evaluating different ligand docking poses using the scoring function through the docking program, predicting the affinity between ligands and targets, and subsequently ranking the compounds.
05 Binding Free Energy Rescoring
To check the reliability of virtual screening results, further analysis of binding free energy through molecular dynamics simulations allows for rescoring, aiding in the identification of potential lead compounds.
Fig.2 CD ComputaBio structure-based virtual screening protocol.
Our Compound Screening Libraries
Structure-based virtual screening utilizes molecular docking calculations between compounds and drug targets to rapidly identify drug-like active compounds from tens of thousands to millions of molecules, significantly reducing the number of compounds needed for experimental screening. CD ComputaBio has extensive database resources, providing strong support for offering professional molecular docking-based or structure-based virtual screening services.
- Synthesizable Compound Library
- Bioactive Compound Library
- Lead-like Diversity Library
- Natural Product Compound Library
CD ComputaBio is dedicated to providing structure-based virtual screening services to support your research and innovation goals. If you are interested in our services, please feel free to contact us at any time. Our professional team is committed to serving you wholeheartedly, offering robust support for your drug development projects.
Reference:
- Wu, K.; et al. Structure-Based Virtual Screening for Methyltransferase Inhibitors of SARS-CoV-2 nsp14 and nsp16. Molecules. 2024, 29(10): 2312.
* For Research Use Only.
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