Protein aggregation is associated with many human diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD) and type 2 diabetes (T2D). Understanding the molecular mechanism of protein aggregation is essential for the development of therapy. Molecular dynamics (MD) simulation has proven to be a powerful tool for studying protein aggregation. However, it is difficult for conventional MD simulation to sample the entire conformation space of a complex protein system within an acceptable simulation time because it is easy to fall into a local minimum energy state. Many enhanced sampling methods have been developed. Among them, the replica exchange molecular dynamics (REMD) method has been particularly attractive. By combining MD simulation with Monte Carlo algorithm, the REMD method can easily overcome the high energy barrier and can fully sample the conformational space of proteins.
Figure 1. Replica exchange molecular dynamics (REMD).
|Project name||Replica Exchange Molecular Dynamics (REMD) services|
|Samples requirement||The initial structure of PDB ID, etc.|
|Timeline||Depends on the time you need to simulate.|
|Deliverables||We provide you with raw data and calculation result analysis service.|
|Step2||According to the number of available processors and the temperature range to be sampled.|
|Step3||After obtaining the temperature distribution, equilibrate the system separately at N temperatures (use a separate .mdp file for each temperature).|
|Step4||Run a short-term REMD simulation to obtain an estimate of the exchange probability (about 100 ps can get a good estimate).|
|Step5||Choose an initial conformation at each temperature depending on the reason for running REMD.|
CD ComputaBio offers a corresponding replica exchange molecular dynamics (REMD) services. Our molecular dynamics simulations provide accurate approximations of real molecular behaviors, and have proven to be very useful in understanding the biochemical basis of physiological events at different stages of drug development, even in different fields such as materials science. Our team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. We can also analyze these results for you. The CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals.