Unlocking the Power of Glycan-related Molecular Simulation

Based on our professional AI-assisted Glycoinformatics Development and AI-assisted Glycan Drug Discovery services, CD BioGlyco analyzes the binding affinity (BA) between ligands and receptors at the atomic and electronic levels through molecular docking, quantum chemical methods, and molecular dynamics (MD) simulations. Our lab uses computers to simulate the structure and behavior of glycan-related molecules at the atomic level of molecular modeling, which in turn simulates the physicochemical properties of the entire system.

Initial atomic model

Based on big data and artificial intelligence, integrating molecular simulation techniques, CD BioGlyco provides specialized computational modeling services by nuclear magnetic resonance (NMR), crystallographic, or homology modeling data. Our lab provides analysis services of the forces acting on each system atom, with detailed analysis of the forces generated by the interaction of bonded and non-bonded atoms.

NMR data is a very useful data package, and many of the receptor and ligand conformations we sample through MD simulations can be used to predict NMR measurements. Moreover, we provide a direct comparison service between experimental and theoretical NMR data.

Molecular conformation sampling and screening

Clustering analysis: CD BioGlyco evaluates the different conformations that a glycan or glycoprotein may have by computer simulation. We use conformational searches, saturated ring conformational searches, etc. to traverse as many of the dominant conformations of the ligand as possible to serve as a library of conformations for docking, thus improving docking accuracy.

Dominant conformation recognition: Each ligand has a variety of binding conformations. Our lab offers a specialized structural pattern screening service by combining free energy scoring, molecular stress energy, and professional judgment.

Site identification

Identifying cryptic and allosteric binding sites: In addition to the well-defined binding pockets revealed by NMR and X-ray crystal structures, our researchers provide potential drug site identification services including cryptic binding sites and druggable allosteric sites.

Professional analysis

Publication

Applications

• Glycan-related molecular simulation can be used to predict the binding information and mode of action of polysaccharide macromolecules.
• Glycan-related molecular simulation can be used for direct prediction of small molecule binding energies.
• Glycan-related molecular simulation can be used for target screening for glycan-related diseases.
• Glycan-related molecular simulation plays an increasingly important role in the development of new drug therapies.

Advantages of Us

• Our researchers have a wealth of experience in the industry, through a simple description of the project quickly understand the situation, and depending on the needs of the client, quickly establish a set of feasible service programs.
• After all the calculations are completed, our professional project team provides a comprehensive analysis report for the client.

Frequently Asked Questions

• What is molecular simulation?
  • Combining physical mathematics and chemistry, molecular simulation is to use computers to simulate the structure and behavior of molecules with molecular models at the atomic level, and then simulate various physical and chemical properties of molecular systems.
  • Molecular simulation simulates not only the static structure of molecules but also the dynamic behavior such as the bending motion of molecular chains, intermolecular hydrogen bonding and disassembly behavior, molecular adsorption on surfaces, molecular diffusion, etc.
• What advantages does molecular simulation offer in drug discovery?
  • Exploring all possible conformations of glycoproteins with the help of molecular simulations is an effective means of reproducing thermodynamic properties and analyzing all binding pocket conformations relevant to drug design.
  • Simple approximations based on Newtonian physics to simulate atomic motion effectively reduce the computational difficulty of molecular simulations in drug discovery.
  • As a small drug molecule approaches its target, which is the receptor, the receptor is not static but a large molecule in constant motion. In particular, molecular recognition and binding are very dynamic processes. With molecular simulation, it is possible to identify multiple binding sites of different conformations and enhance traditional virtual screening.

CD BioGlyco has rich experience in AI-assisted glycan drug discovery services. Our staff have mature industry experience, effectively solving the doubts in molecular simulation. Please feel free to contact us.

• Glycan-related Target Identification and Validation Service
• Glycan-related Small-molecule Design and Optimization Service
• Glycan-related Biomarker Discovery Service
• Glycan-related Computational Pathology Service
• Candidate Glycan-related Drug Prioritization Service
• Glycan-related High-throughput Virtual Drug Screening Service
• Glycan-related Drug Transmembrane Osmosis Analysis Service
• Glycan-related Drug Property Prediction Service
• De Novo Glycan-related Drug Design Service
• Multiple Glycan Targeting-related Drug Design Service
• Glycan Structure-based Drug Design Service
• Glycan-related Synthesis Pathway Generation Service