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Targeting System


Understanding the biological processes of cell signaling and metabolic control requires an understanding of the structural characteristics of biological systems and the energetics of conformational changes. The energetic details of the conformational change process, in addition to the structural details of conformational changes in biological systems, are of great interest.

Molecular dynamics (MD) simulations have proven to be a valuable tool for studying the dynamic behavior of stable macromolecules at finite temperatures. The majority of conformational transformations, however, either happen by chance in simulations or at extraordinarily high temperatures outside the normal range of experimental settings. Targeted molecular dynamics (TMD) is a method for inducing conformational changes in known target structures at room temperature by applying time-dependent, purely geometric constraints. Alfa Chemistry offers specialized targeted molecular dynamics simulations to meet different customer needs.

Targeting System

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In TMD, steering forces direct a portion of the simulation's atoms toward the eventual "target" structure. The RMS separation between the current coordinates and the desired structure is computed at each time step. The force on each atom is given by the potential gradient.

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Since RMS grows linearly from the beginning RMSD of the first TMD step to the final RMSD of the last TMD step, it is the instantaneous best-fit RMSD distance between the current and goal locations. The TMDFile's beta column can be used to assign integer values to partition the atoms into non-overlapping bound domains. Each domain's forces on the atoms will be calculated separately from the other domains. The set of atoms utilized to fit the goal structure inside each domain may not be the same as the set that is biased toward the target structure.

Targeted molecular dynamics (TMD) simulated denaturation of native thiocyanate.Fig 1. Targeted molecular dynamics (TMD) simulated denaturation of native thiocyanate. (Karplus M, et al. 2005)

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One of the key methods used in protein research is MD simulation. MD simulations provide a practical alternative to experimental techniques for studying protein conformational changes. Alfa Chemistry has developed the TMD service, which calculates the reaction paths between two conformations of a molecule by continuously reducing the distance from the target conformation with the help of constraints.

Membrane phospholipids are complex molecules. They play important functional roles in biology. MD simulations are an important tool for understanding phospholipid membranes. Alfa Chemistry provides customers with state-of-the-art MD simulations of phospholipid membranes. Advances in computing power have made it possible to replace simple models with more complex ones.

MD simulations are a vital technique in the study of nucleic acids (DNA/RNA). MD provides detailed structural and kinetic insights. Alfa Chemistry provides its clients with best-in-class DNA/RNA MD simulation services.

Lipids, monosaccharides, second messengers, other natural products and metabolites, drugs and other exotic compounds are examples of small molecules. Alfa Chemistry provides world-class small molecule MD simulation services to its clients. For drug discovery applications, MD simulations have been widely used.


  • Understanding metamorphosis.
  • Molecular docking and drug design.
  • Refinement of structure prediction.

Our Advantages

  • Molecular dynamics simulation saves a lot of labor costs.
  • High computational accuracy; short computational cycle time.
  • Requires far less money than biological or chemical experiments.

Alfa Chemistry provides fast and high-quality TMD simulation services to global customers at competitive prices. This computing service is a customized innovative scientific research service. We need to evaluate each project before we can determine the corresponding analysis plan and price. If you are interested in our services, please contact us for more details.


  • Karplus M, et al. (2005). "Protein Structural Transitions and Their Functional Role." Philos Trans A Math Phys Eng Sci. 363(1827): 331-55.

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