Steered Molecular Dynamics Service

At CD ComputaBio, we offer cutting-edge Steered Molecular Dynamics (SMD) services that cater to the specific needs of our clients in the biotechnology, pharmaceutical, and materials science industries. Our expertise in computational biology and molecular dynamics simulations enables us to provide tailored solutions that drive innovation and accelerate research and development processes. Through our SMD service, we empower researchers to gain deeper insights into molecular interactions, protein folding, and ligand binding mechanisms, ultimately facilitating the design of novel therapeutics and materials.

Overview of Steered Molecular Dynamics

Steered Molecular Dynamics is a powerful computational technique that allows researchers to study the response of biomolecular systems to external forces. By applying controlled pulling forces to specific atoms or groups within a molecular system, SMD simulations can elucidate key mechanical properties, such as binding affinities, mechanical stability, and unfolding pathways.

Our Services

Data analysis steered molecular dynamics service

Force Analysis and Data Interpretation

Our experienced scientists leverage sophisticated data analysis techniques to extract meaningful insights from simulation data, enabling clients to understand the underlying mechanical principles governing molecular interactions.

System modeling

Pathway Analysis and Kinetics Modeling

Our expertise in pathway analysis and kinetics modeling allows us to predict reaction mechanisms, characterize energy landscapes, and explore the dynamics of molecular systems under mechanical stress.

Binding free energy plot

Binding Free Energy Calculations

We offer advanced binding free energy calculations using SMD simulations to estimate the strength of protein-ligand interactions and predict binding affinities with high accuracy.

DNA-protein system simulation

One-stop SMD Solution

Whether investigating protein unfolding mechanisms, studying DNA-protein complexes, or probing the mechanical properties of biomaterials, we deliver comprehensive SMD solutions that address unique scientific challenges.

Our Force Field Selection

At CD ComputaBio, we carefully select force fields that best capture the dynamics and energetics of biomolecular systems, considering factors such as:

Protein Type and Structure

Ligand Properties

Solvent Environment

Sample Requirements

To initiate an SMD service project with CD ComputaBio, clients are encouraged to provide the following information:

Target System - Details of the biomolecular system of interest, including protein structures, ligands, nucleic acids, or macromolecular complexes.
Specific Research Goals: Clear objectives and research questions that define the scope of the SMD study and guide simulation setup and analysis.
Simulation Parameters: Parameters such as simulation length, timestep, temperature, and solvent conditions required for accurate SMD simulations.
Data Analysis Requirements: Preferences for data visualization, force profiles, energy landscapes, unbinding pathways, and other output formats essential for interpreting simulation results.

Our Advantages

Quality Assurance

Quality control and validation are integral parts of our service offerings. We ensure the accuracy and reliability of our SMD simulations through rigorous testing, benchmarking against experimental data, and continuous refinement of our methodologies.

Collaboration and Support

We believe in fostering collaborative relationships with our clients to achieve mutual success. Our team provides ongoing support, consultation, and guidance throughout the project lifecycle, ensuring that your research objectives are met and exceeded.

If you are seeking to unlock the mysteries of molecular interactions, understand complex biological systems, or accelerate drug discovery efforts, CD ComputaBio is your trusted partner in computational biology and molecular dynamics simulations. Contact us today to learn more about our Steered Molecular Dynamics services and how we can support your research goals with tailored solutions and expert guidance.

Reference:

Yang R, Wu S, Wang S, et al. Refinement of SARS-CoV-2 envelope protein structure in a native-like environment by molecular dynamics simulations[J]. Frontiers in molecular biosciences, 2022, 9: 1027223.

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