Interactive Molecular Dynamics Simulation Service
Interactive molecular dynamics (MD) simulation is a computer simulation technique that allows one to use the laws of physics to predict how a system of interacting particles will behave over time. As an expert in computational biology, CD ComputaBio's professional molecular simulation and drug design team provides one-stop services from molecular docking, virtual screening to interactive MD simulation to customers around the world.
Introduction to Interactive Molecular Dynamics Simulation
Studying the dynamic development of biological systems and considering the flexibility of proteins is key to understanding biological processes and interactions between macromolecules. This is because many biological phenomena involving proteins are very dynamic processes, including transport, molecular recognition, enzyme catalysis, and allosteric regulation. Static models produced by traditional NMR, X-ray crystallography, and homology modeling provide valuable insights into macromolecular structures, while MD simulations can provide atomic-level information about protein conformational changes and binding thermodynamics under predetermined physiological conditions (e.g., temperature, pressure).
Fig. 1 Schematic representation of a classic molecular dynamics simulation (MD) process. (Puentes PR, et al.; 2020)
Interactive MD simulations are based on classical mechanics, quantum mechanics, and statistical mechanics, and use computers to numerically solve the equations of motion of molecular systems to simulate and study the structure and properties of molecular systems. This technology not only obtains the motion trajectory of atoms, but also observes various microscopic details during the atomic motion process, such as the structural dynamics, thermodynamic properties, and functional mechanisms of molecular systems. It is a powerful supplement to the time scales that can't be reached by existing experimental methods and theoretical calculations.
Our Services
Interactive MD simulation plays an extremely important role in computer-aided drug discovery (CADD). It can't only be used to identify hidden or allosteric binding sites in proteins and enhance the effectiveness of traditional virtual screening methods, but also directly predict the binding energy between small molecules and target proteins and provide quantitative evaluation.
CD ComputaBio uses the most advanced interactive MD simulations software tools to deeply study the molecular dynamics of different molecular systems and help customers predict the changes in different molecular systems over time. This allows you to deeply understand the molecular interaction mechanism, accelerate the drug development process, and explore events of biological and pharmaceutical importance.
By Molecule Type
By Analysis Type
Electrostatic Interaction Analysis
Salt-Bridge Analysis
Fig. 2 Flow chart for interactive molecular dynamics simulation. (CD ComputaBio)
Tools for Interactive Molecular Dynamics Simulation
GROMACS
GROMACS, one of the fastest and most popular analysis tools, is mainly used to simulate the dynamic behavior of biological macromolecules such as proteins, lipids, and nucleic acids. It supports the setup and analysis of complex simulations, which can be used to simulate a variety of biological processes such as protein folding, membrane dynamics, protein-ligand interactions, etc.
AMBER
AMBER is an integrated software package for molecular dynamics simulations, focusing on the simulation of proteins, nucleic acids, carbohydrates and small molecules. It provides accurate force field parameters such as AMBER ff14SB and GAFF. This simulation helps predict how molecules interact with each other and how they respond to various external factors such as temperature and pressure.
NAMD
NAMD is a force field commonly used in our molecular dynamics simulations for high-performance simulations of large biomolecular systems such as protein systems. This force field describes the interactions between atoms in a molecule and is used to predict the conformation (three-dimensional shape) and dynamics of the system. The software can be seamlessly combined with Visual Molecular Dynamics (VMD) software for easy visualization and analysis.
OpenMM
OpenMM is an open source library for molecular dynamics simulations, focusing on high-performance GPU-accelerated computing. The library is suitable for the study of various biomolecular systems. Its powerful functions make it an ideal tool for studying protein and nucleic acid molecular dynamics as well as large-scale molecular simulations.
Results Delivery
A report is used to present the analysis results, research achievements and possible interpretation scenarios of interactive molecular dynamics simulations, including:
- Molecular Conformation Analysis - Cluster analysis, dominant conformation identification.
- Interaction Analysis - Hydrogen bond network, salt bridge, contact area analysis.
- Binding Free Energy Calculation - MMPBSA, MMGBSA, FEP.
- Backbone Fluctuation Analysis - RMSD (root-mean-square-deviation) and RMSF (root-mean-square fluctuation).
- Hotspot Residue Analysis - Alanine-scanning, energy-decomposition.
- Conformational Transition Analysis - Principal component analysis (PCA), energy-landscape plotting.
Interactive MD simulation analysis is one of the essential steps in designing new drugs using computational methods. CD ComputaBio provides cutting-edge interactive MD simulation services to accelerate your research and development process. Our scientists have rich practical experience and core technologies in homology modeling and molecular docking research, providing you with efficient and high-quality technical services. Please don't hesitate to contact us, if you are interested in our services.
References:
- Puentes PR, et al. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics (Basel). 2020;9(12):854.
- Filipe HAL, et al. Molecular Dynamics Simulations: Advances and Applications. Molecules. 2022;27(7):2105.
- Nam KH. Molecular Dynamics—From Small Molecules to Macromolecules. International Journal of Molecular Sciences. 2021; 22(7):3761.
* For Research Use Only.
Related Services
