The advent of distributed computing, new technologies such as copy-exchange MD, new methods (such as based on stochastic difference equations), and physics-based simplified models of proteins now make it possible to study protein folding pathways from fully unfolded structures. Molecular dynamics (MD) has become an invaluable tool for studying protein folding in silico. With years of experience, we provide customized folding and molecular simulation service to precisely meet customer requirements.

Introduction of Folding and Molecular Simulation

The problem of protein folding (that is, understanding how native proteins fold reliably into unique three-dimensional structures) remains one of the major challenges of protein engineering biology. To this end, a lot of theoretical and experimental research work has been invested. The researchers combined computer simulations with theoretical methods to solve this problem, molecular dynamics (MD) simulations being one of the most commonly used computational methods. MD is the most realistic simulation technique available, allowing the monitoring of all detailed interactions between protein and solvent atoms over time. Furthermore, MD can also be easily used to elucidate kinetic pathways that can probe folding and limited refolding events. MD plays an important role in discovering the relationship between protein structure and function.

Fig 1. The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations. (Wang M, et al., 2016)

Services

MD simulations can achieve spatial and temporal resolution beyond the capabilities of experimental methods, but are hampered in their ability to acquire biological time-scale data, as the fastest folded proteins are 10 µs-ms. But more than 40 years of MD simulations have paved the way for atomic molecular dynamics studies of protein folding and unfolding. As a leading service provider of protein engineering, Creative BioMart has successfully established a powerful platform for studying protein folding with molecular dynamics simulations to gain a more comprehensive understanding and assessment of protein folding/unfolding reactions. We can detect protein folds up to 100 amino acids in size.

Based on our deep understanding of protein structure and continuous exploration and progress in computer simulation, our scientists have successfully developed a variety of approaches to simulating folding with MD simulation. Verified by powerful physical force field-based MD simulation and quantitative experiments combined, we'll help you elucidate the nature of protein folding and accelerate your scientific research. Our advanced technologies include the following:

• Tightly coupled molecular dynamics (TCMD).
• Replica exchange molecular dynamics (REMD).
• High temperature unfolding.
• Coarse grained and minimalist models.
• Energy landscape theory.
• Path sampling.
• Markov state models.

Applications of Molecular Dynamics

• MD analysis of pathways provides insight into the energetics and details of allosteric transitions.
• Using simulation to improve virtual screening or docking processes, driving drug design.
• MD has been widely used for ab initio protein structure prediction, aiming to simulate protein folding ab initio.

Creative BioMart is committed to using molecular dynamics simulations to efficiently simulate conformational changes or ligand binding to evaluate molecular structure for computational studies of protein folding, and accelerate research in molecular biology for global customers. We will work with you to develop the most appropriate strategy and provide the most meaningful data for your research for accelerating the research of life sciences. If you are interested in our services, please do not hesitate to contact us for more information.

References

1. Hospital A, Goñi J R, Orozco M, et al.. (2015) Molecular dynamics simulations: advances and applications[J]. Advances and applications in bioinformatics and chemistry: AABC. 8: 37.
2. Wang M, Hu J, Zhang Z. (2016) The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations[J]. International journal of molecular sciences. 17(5): 612.

• Detection of Errors in Protein Models
• Molecular Docking Service
• Protein Conformational Isomerism Detection and Analysis Service
• Protein Crystallization Service
• Protein Model Ranking and Analysis Service