Steered Molecular Dynamics (SMD) Service
CD ComputaBio offers a comprehensive range of steered molecular dynamics (SMD) services designed to meet the specific research needs of our clients. Our team of experienced scientists and computational experts combines their expertise to deliver high-quality simulation results that provide deep insights into complex molecular systems.
Introduction to Steered Molecular Dynamics (SMD)
Steered molecular dynamics (SMD) induces unbinding of ligands and conformational changes in biomolecules on time scales accessible to molecular dynamics simulations. Time-dependent external forces are applied to a system, and the responses of the system are analyzed.
Fig 1. Steered Molecular Dynamics (SMD) simulations and machine learning algorithms were used to identify the physiochemical features that predict TCR-pMHC bond lifetime. (Rollins Z A, et al., 2022)
Applications of SMD
Carbon Nanotubes
SMD simulations can be used to study the mechanical properties of carbon nanotubes, such as their tensile strength and elasticity. By applying a controlled force to the nanotube, researchers can observe how the nanotube deforms and breaks, providing valuable insights into its mechanical behavior.
Protein Folding and Unfolding
SMD can be used to study the folding and unfolding pathways of proteins, providing insights into the underlying mechanisms and energy barriers involved. This information is crucial for understanding protein function and designing drugs that target specific protein conformations.
Our Services
CD ComputaBio boasts a proven track record of successful SMD projects across diverse domains, including drug discovery, protein engineering, and biomolecular design. CD ComputaBio offers cutting-edge SMD services designed to assist researchers in their researches of molecular mechanisms, interactions, and dynamics.
Customized SMD Simulations
- System Selection - Identifying the macromolecules or polymers of interest and defining the specific interactions to be studied.
- Force Application - Determining the nature and direction of forces to be applied during the simulations based on hypotheses or experimental observations.
Execution of SMD Simulations
- System Preparation - Setting up the molecular dynamics system, which includes solvation, ion placement, and energy minimization.
- SMD Configuration - Applying appropriate parameters for SMD simulations, including forces, constraints, and simulation protocols.
Molecular Types of SMD
Polymers
Carbon nanotubes
Proteins
Our Advantages
- Innovative Solutions
We stay at the forefront of computational chemistry and molecular dynamics research, incorporating the latest advancements in our services. This allows us to offer innovative solutions and stay ahead of the competition.
- Client-Centric Approach
We prioritize our clients' needs and satisfaction. Our personalized approach and excellent customer service make us a preferred choice for many pharmaceutical research organizations, biotech companies, and academic institutions.
Steered Molecular Dynamics is a powerful tool for investigating the intricate dynamics of molecular systems. CD ComputaBio is fully equipped to support your research endeavors with comprehensive SMD services. Our commitment to quality, advanced technology, and collaborative approach empowers you to achieve your research objectives and unlock discoveries. If you are interested in our services or have any other questions, please feel free to contact us.
Reference:
- Rollins Z A, Huang J, Tagkopoulos I, et al. A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics[J]. Computational and Structural Biotechnology Journal, 2022, 20: 3473-3481.
* For Research Use Only.
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