Steered Molecular Dynamics (SMD), as a branch of molecular dynamics, can be used to simulate macromolecular biological systems and is mainly used to study the dynamic process of ligand binding/dissociation in molecular complexes. Receptor-ligand dissociation is of great significance in the study of receptor-ligand interaction and molecular recognition. The study of the dissociation process can generate important information about the structure-function relationship and binding pathways of the receptor-ligand complex. Steered molecular dynamics allows you to explore biological processes on timescales accessible to molecular dynamics simulations. Protheragen has extensive experience in the field of stretched molecular dynamics. Our researchers can quickly understand the situation of the project through a simple description, and quickly formulate a feasible research plan according to the needs of customers
Conventional de novo drug design is time consuming, laborious, and resource intensive. In recent years, emerging in silico approaches have been proven to be critical to accelerate the process of bringing drugs to market. Molecular dynamics (MD) simulations of single molecule and molecular complexes have been commonly applied to achieve accurate binding modes and binding energies of drug-receptor interactions. A derivative of MD, namely, steered molecular dynamics (SMD), has been demonstrated as a promising tool for rational drug design. Protheragen provides you with two types of steered dynamics simulations:
The basic idea behind any SMD simulation is to apply an external force to one or more atoms (we call SMD atoms). In addition, you can keep another set of atoms fixed and study the behavior of the protein under various conditions. In the following simulation, one ubiquitin atom will be fixed and another atom will be pulled to stretch and unfold ubiquitin. Before running the actual simulation, the system will be prepared and the required files will be created.
|Project name||Steered molecular dynamics (SMD) service|
|Services||Protheragen can provide umbrella sampling simulation of various systems|
|Cycle||Depends on the time you need to simulate and the time required for the system to reach equilibrium.|
|Product delivery mode||The simulation results provide you with the raw data and analysis results of mbrella sampling simulation.|
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. SMD has already provided important qualitative insights into biologically relevant problems, as demonstrated here for applications ranging from identification of ligand binding pathways to explanation of elastic properties of proteins.
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