Drug Development Services
Ligand binding mode prediction
Understanding the ligand-binding mode is essential for elucidating drug action mechanisms and guiding the optimization of lead compounds. However, acquiring complex structures via experimental approaches such as X-ray crystallography or nuclear magnetic resonance is not only challenging but also expensive. Consequently, computational simulation docking has emerged as a pivotal research approach for predicting the three-dimensional intermolecular interactions. This technology aids researchers by computationally predicting and clarifying the binding modes between proteins and ligands, thereby delivering crucial insights for drug development. The industry predominantly employs the following methods for predicting protein-ligand binding modes:
- Molecular Docking based on conformational search and scoring functions: This involves sampling numerous potential conformations and positions of the ligand within the protein’s binding pocket. Scoring functions, generally rooted in physical interactions or empirical potential functions—with some based on artificial intelligence models like convolutional neural networks—rank these conformations to select the optimal binding conformation.
- Molecular Docking based on deep learning models: A variety of innovative methods that utilize deep learning models, such as Diffusion Models, have recently been developed. These models can directly produce the ligand’s binding conformation in the protein’s binding pocket without needing a conformational search, effectively complementing traditional docking methods, particularly when the binding pocket is undefined.
Service Offerings
- Performs protein structure modeling, binding pocket assessment, and active compound and complex structure research tailored to customer needs.
- Uses multiple docking methods to generate algorithm-recommended binding modes.
- Conducts thorough analysis of protein information and structure-activity relationships to determine the best binding modes.
Why ComMedX
- Extensive Technical Expertise: Our team has years of experience in computational chemistry, with substantial practical knowledge.
- Professional Workflow: Integrates domain expertise with computational data for more accurate predictions.
- Customized Services: Designs research projects specifically to meet customer requirements, ensuring optimal solutions for their business objectives.
Business Inquiry
For more information, please send a message to contact@commedx.com
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