Vangaveti Sweta, Ranganathan Srivathsan V, Chen Alan A
The RNA Institute, University at Albany State University of New York, Albany, NY, USA.
Department of Chemistry, University at Albany State University of New York, Albany, NY, USA.
Wiley Interdiscip Rev RNA. 2017 Mar;8(2). doi: 10.1002/wrna.1396. Epub 2016 Oct 4.
Molecular simulations have become an essential tool for biochemical research. When they work properly, they are able to provide invaluable interpretations of experimental results and ultimately provide novel, experimentally testable predictions. Unfortunately, not all simulation models are created equal, and with inaccurate models it becomes unclear what is a bona fide prediction versus a simulation artifact. RNA models are still in their infancy compared to the many robust protein models that are widely in use, and for that reason the number of RNA force field revisions in recent years has been rapidly increasing. As there is no universally accepted 'best' RNA force field at the current time, RNA simulators must decide which one is most suited to their purposes, cognizant of its essential assumptions and their inherent strengths and weaknesses. Hopefully, armed with a better understanding of what goes inside the simulation 'black box,' RNA biochemists can devise novel experiments and provide crucial thermodynamic and structural data that will guide the development and testing of improved RNA models. WIREs RNA 2017, 8:e1396. doi: 10.1002/wrna.1396 For further resources related to this article, please visit the WIREs website.
分子模拟已成为生化研究的重要工具。当模拟正常运行时，它们能够对实验结果提供极有价值的解释，并最终给出新的、可通过实验检验的预测。不幸的是，并非所有模拟模型都是一样的，对于不准确的模型，就难以区分什么是真正的预测，什么是模拟假象。与广泛使用的众多成熟的蛋白质模型相比，RNA模型仍处于起步阶段，因此近年来RNA力场修正的数量一直在迅速增加。由于目前尚无普遍认可的“最佳”RNA力场，RNA模拟者必须根据其基本假设及其固有的优缺点，决定哪种力场最适合其目的。希望通过更好地理解模拟“黑匣子”内部的情况，RNA生物化学家能够设计出新的实验，并提供关键的热力学和结构数据，以指导改进RNA模型的开发和测试。WIREs RNA 2017, 8:e1396. doi: 10.1002/wrna.1396 有关本文的更多资源，请访问WIREs网站。
