Targeted Molecular Dynamics (TMD) Simulation


Targeted Molecular Dynamics (TMD) Simulation

Understanding changes in molecular structures under various conditions is crucial for pharmaceutical research and drug discovery. Targeted Molecular Dynamics (TMD) Simulation is a well-established method in the biomolecular simulation sphere. Here at CD ComputaBio, our TMD simulation services help visualize the molecular transition pathways; these transitions are often inferred from the dynamic motions that occur between functional states of macromolecules. These services, therefore, facilitate the comprehension of essential processes such as conformational changes and large-scale movements in biomolecular systems.

Our Service


Transition Pathway Determination

Our TMD simulation services help identify the transition pathways between two conformations. It provides a clearer understanding of the conformational changes of the molecule.


Energy Barrier Determination

With TMD, we can calculate the energy involved in conformational changes, thus predicting and determining the barriers to these transitions.


Analysis Services

Other than transition and energy barrier determination, we also provide insightful analyses of the simulation results that allow for a more comprehensive and substantial interpretation of the obtained data.


Target-Specific Simulations

We tailor our simulations to target specific regions of interest within biomolecular complexes, enabling us to explore the conformational changes and dynamic behaviors.


Validation and Verification

Before delivering results to our clients, we rigorously validate and verify our TMD Simulation data against experimental benchmarks and known structural information.

Algorithms in Targeted Molecular Dynamics

Machine Learning Integration

Machine Learning Integration

Machine learning plays a crucial role in our algorithm, enabling predictive modeling of molecular interactions, binding affinity, and structural dynamics. By leveraging machine learning models trained on vast datasets of molecular properties, our algorithm offers predictive insights that guide decision-making in drug design and optimization.

Enhanced Sampling Methods

Enhanced Sampling Methods

We have incorporated advanced enhanced sampling methods, such as metadynamics and accelerated molecular dynamics, into our algorithm to overcome energy barriers and simulate rare events with high efficiency. These techniques enable the exploration of complex biological processes in unprecedented detail.

Adaptive Sampling

Adaptive Sampling

Our algorithm employs adaptive sampling techniques to efficiently explore the conformational space of biomolecular systems. By dynamically adjusting sampling strategies based on simulation progress and system complexity, we optimize computational resources and accelerate the discovery of relevant structural insights.

Sample Requirements

To initiate a TMD simulation project with CD ComputaBio, we require the following sample information:

Protein Sequence

Molecular structures (e.g., proteins, ligands, nucleic acids)

Parameters Information

Initial coordinates and velocities
Force field parameters

System Information

Simulation length and conditions

Our team will work closely with you to ensure that the sample requirements are met and that the simulation setup aligns with your research objectives.

Results Delivery

Upon completion of the TMD simulation, you can expect the following deliverables from CD ComputaBio:

RMSF Calculation

RMSF Calculation

RMSD Calculation

RMSD Calculation

Conformational changes analysis

Conformational changes analysis

Structural assessments

Structural assessments

Our Advantages

Expertise and Experience

Our team of computational biologists, chemists, and data scientists brings a wealth of experience in drug discovery and computer-aided design. With a track record of successfully delivering innovative solutions to our clients, we are committed to excellence in every project we undertake.

Customized Solutions

At CD ComputaBio, we understand that each research project is unique. That's why we offer personalized solutions that are tailored to meet the specific requirements and objectives of our clients. Whether you need to explore protein-ligand interactions, or optimize drug candidates, we have the expertise to help you achieve your goals.

Cutting-Edge Technology

We stay at the forefront of technological advancements in computational drug design to ensure that our clients have access to the most advanced tools and methodologies available. By leveraging state-of-the-art software and algorithms, we deliver results that are both scientifically rigorous and practically applicable.

At CD ComputaBio, our aim is to provide you with trustworthy, precise, and affordable TMD simulation services, aiding you in your drug discovery and research strategy. Contact us today to learn more about how our services can enhance your research and propel your drug discovery efforts forward.

* For Research Use Only.
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