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Protein Molecular Dynamics Simulation


Proteins play a key role in practically every aspect of life and are the primary functional actors in living things. One of the key methods used in protein study is molecular dynamics (MD) simulations. Transitions between macromolecules' conformational states are crucial to numerous biological functions. Because they can deal with individual macromolecules at the atomic level of detail, MD simulations offer a practical alternative to experimental techniques for the investigation of conformational changes.

Protein Molecular Dynamics Simulation

The finite time span of simulation techniques is their primary flaw. Alfa Chemistry has developed Targeted Molecular Dynamics (TMD), which calculates the reaction path between two conformations of a molecule by continuously reducing the distance to the target conformation with the aid of constraints. The majority of large-scale conformational changes must be accelerated to be observed on the time scale of computationally feasible molecular dynamics simulations. It has been used to forecast the reaction pathways for protein conformational changes.

Our Services

Alfa Chemistry studies the molecular dynamics of protein systems using cutting-edge digital techniques. In conjunction with a shared atomic description of the protein, the CHARMM force field is used. Since executing numerous unfolding simulations using explicit water molecules can be computationally costly, solvents are taken into account through an implicit model. A mean-field description of the solvent is also provided by the implicit model, which eliminates the issues brought on by the relaxation of explicit water molecules around the protein. This is crucial for TMD and unfolding at high temperatures since the explicit solvent exhibits a considerable increase in friction and conformational changes are strongly accelerated. A solvent accessible surface (SAS) based model makes an attempt to simulate the solvation effect. Previous studies have shown that SAS models can be used for MD simulations of different proteins to avoid the main difficulties that arise in vacuum simulations.

Project NameProtein Molecular Dynamics Simulation Service
DeliverablesWe provide all raw data and analysis services to our customers.
Samples RequirementThe initial structure of the protein, PDB ID, etc.
Timeline DecideAccording to customers' needs
PricePlease contact us for an inquiry

The general workflow of our service includes the following steps:

  • Choose a model system to replace the missing pieces and ascertain the protonation state.
  • By resolving the Newtonian equations of motion, you may reduce the system's energy and bring it to equilibrium while ensuring that its attributes don't change over time.
  • After reaching equilibrium, a manufacturing run is carried out for a suitable amount of time to produce the trajectory, which is then examined to achieve the desired attributes.

The RMSD of protein sections during the TMD simulations.Fig 1. The RMSD of protein sections during the TMD simulations. (Khammari A, et al. 2020)

Our Advantages

  • The researchers all come from renowned universities or research centers and have extensive backgrounds in the simulation of protein molecular dynamics.
  • On a wide range of linked themes, we have either worked on our own or offered support to our clients. Numerous findings from the calculations and tests have been published in a number of major SCI publications in the field of life sciences.

Alfa Chemistry is dedicated to offering our clients high-end, premium technical services and has the extensive practical experience and core technologies in protein MD simulation. At various phases of drug development, this service has proven to be highly helpful in understanding the biochemical basis of physiological events by providing an accurate simulation of the behavior of genuine protein molecules. Please get in touch with us.


  • Khammari A, et al. (2020). "The Hot Sites of α-Synuclein in Amyloid Fibril Formation." Scientific Reports. 10(1): 12175.

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