Steered Molecular Dynamics Service

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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. CD ComputaBio 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

Overall solutions

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. CD ComputaBio provides you with two types of steered dynamics simulations:

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Constant force simulation
In the constant force SMD simulation, force is directly applied to one or more atoms, and its expansion or displacement is monitored throughout the dynamic process.
Constant speed simulation
In the constant speed SMD simulation, the harmonic potential of the movement (spring) is used to induce movement along the reaction coordinate. The free end of the spring (represented by the virtual atom) moves at a constant speed, while the protein atom attached to the other end of the spring is subjected to the turning force.

Algorithm

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.

Process of umbrella sampling simulation

Removing Water Molecules
Constant Velocity Pulling
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Fixed and SMD Atoms
Configuration File
Running the First SMD Simulation

Constant Force Pulling

The SMD Atom
Configuration File
Running the Second SMD Simulation

Analysis of Results

Force Analysis for Constant Velocity Pulling
Distance Analysis for Constant Force Pulling

AI-based approaches

Generally speaking, calculation methods based on the molecular dynamics framework can model the transition trajectory in detail, but the calculation cost is also high.
We propose the Steered molecular dynamics method based on artificial intelligence, which connects two given structures of proteins by sampling conformational paths.
This method focuses on small and medium-sized proteins and effectively simulates structural deformation by using molecular fragment replacement technology. In particular, this method grows a tree in a conformational space with the starting structure as the root, turning the tree to a target area defined around the target structure.
We investigate various deviation schemes on the progress coordinate to strike a balance between the coverage of the conformational space and the progress of achieving the goal.

Our services

Project name	Steered molecular dynamics (SMD) service
Advantages	Manipulating molecular dynamics. Interactive molecular dynamics. Visualization program for displaying, animating and analyzing biomolecular systems.
Services	CD ComputaBio 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.
Price	Inquiry

Significance of SMD

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.

Why choose us?

CD ComputaBio can offer leading technology, experienced and pioneering professional R & D team can meet your multiple system computing needs.
High efficiency, fast response, flexible research direction, low price, short cycle and high quality.
Dedicated/focused resources to help accelerate your timelines.
If you have any questions about our Steered molecular dynamics (SMD) service, please contact us.

Reference:

Hu S , Zhao X , Zhang L . Computational Study for the Unbinding Routes of β-N-Acetyl-d-Hexosaminidase Inhibitor: Insight from Steered Molecular Dynamics Simulations. International Journal of Molecular Sciences, 2019, 20(6), 1516