Membrane Protein Molecular Dynamics Simulation Service

Molecular dynamics is a computer simulation method for analyzing membrane proteins and systems. All atomic and coarse-grained simulations can be used to explore membrane protein interactions with specific lipids in detail, predicting lipid-binding sites that are highly consistent with available structural data. On the basis of successful protein-lipid interaction simulations, large-scale simulations revealed protein crowding and aggregation, resulting in slow and abnormal diffusion kinetics within the true cell membrane model. The current method allows near-atomic resolution simulation of small membrane organelles and enveloped viruses, thereby revealing key aspects of their structural and functionally important dynamics.

Membrane protein molecular dynamics.Figure 1. Membrane protein molecular dynamics.

Membrane protein molecular dynamics simulation service

Membrane proteins play a key role in cell biology. About 20% of genes encode membrane proteins, which constitute the main drug target category. Significant progress has been made in the structural biology of membrane proteins. More than 2500 structures have been generated in PDB, which is equivalent to more than 700 different membrane protein types. Simulations using molecular dynamics has become an important complement to the experimental structure and biophysical techniques for studying membrane proteins and their interaction with lipids. CD ComputaBio uses molecular dynamics to simulate single membrane proteins and more complex membrane systems.

Our simulation services

Project name Membrane proteins molecular dynamics simulation service
Samples requirement The initial structure of the membrane proteins, PDB ID, etc.
Timeline Depends on the time you need to simulate.
Deliverables We provide you with raw data and calculation result analysis service.
Price Inquiry

The Software We Use:

  • GROMACS (http://www.gromacs.org/Downloads): A suite of programs for molecular dynamics simulations.
  • Modeller (http://salilab.org/modeller/download_installation.html): A program for homology modeling. Note that it requires registration, but it is free for academic use.
  • DSSP (ftp://ftp.cmbi.ru.nl/pub/software/dssp/): A program for determining secondary structure of proteins. The program is available as a prebuilt binary for Windows as well as for Linux.
  • Martinize.py (http://md.chem.rug.nl/cgmartini/index. php/downloads/tools/204-martinize): A program for generating coarse-grained structures and topologies from atomistic structure files of proteins and nucleic acids.

Membrane protein molecular dynamics simulation service

Membrane Protein System Setup

  • Coarse-graining of the system and adding a lipid bilayer, water, and ions.
  • Bilayer and water equilibration.
  • Backmapping to all-atom representation.

Simulation Analysis

  • Simulation quality assurance.
  • Protein structure and quality assurance.
  • Lipid bilayer around the protein.

Membrane protein molecular dynamics simulation service 1

Features

  • Calculation of free energy (combination, solvation, interaction).
  • Manipulating molecular dynamics.
  • Interactive molecular dynamics.
  • Visualization program for displaying, animating and analyzing biomolecular systems.

Our advantage

  • Molecular dynamics simulation saves a lot of labor costs.
  • Short calculation period and fast speed.
  • The funds required are far less than biological or chemical experiments.
  • High calculation accuracy.

Our molecular dynamics simulation service but not limited to:

As one of the world's leading computational biology companies, CD ComputaBio can offer you with professional member molecular dynamics simulations to customers. With years of experience in the field of bioinformatics, we are willing to provide customers with the best molecular dynamic simulation services!

* For Research Use Only.

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