AI Article Synopsis
- Molecular dynamics (MD) simulations are effective for studying protein functions at an atomic level and are increasingly being used for RNA research.
- Implementing MD simulations for RNA in solution presents specific challenges that practitioners need to understand for proper usage.
- The chapter covers the basics of MD simulations, details the unique aspects of RNA simulations, discusses the technique's pros and cons, and gives examples of how it helps in understanding small RNA behavior.
Article Abstract
Molecular dynamics simulations have proved extremely useful in investigating the functioning of proteins with atomic-scale resolution. Many applications to the study of RNA also exist, and their number increases by the day. However, implementing MD simulations for RNA molecules in solution faces challenges that the MD practitioner must be aware of for the appropriate use of this tool. In this chapter, we present the fundamentals of MD simulations, in general, and the peculiarities of RNA simulations, in particular. We discuss the strengths and limitations of the technique and provide examples of its application to elucidate small RNA's performance.
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| http://dx.doi.org/10.1007/978-1-0716-3565-0_12 | DOI Listing |
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