Cui Qiang, Pal Tanmoy, Xie Luke
Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.
Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.
J Phys Chem B. 2021 Jan 28;125(3):689-702. doi: 10.1021/acs.jpcb.0c09898. Epub 2021 Jan 6.
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
量子力学/分子力学（QM/MM）模拟已成为许多化学和生物化学研究中不可或缺的工具。鉴于其取得的巨大成功，包括获得2013年诺贝尔化学奖的认可，QM/MM方法是否仍存在“亟待解决的挑战”，尤其是对于生物分子系统而言？在这篇简短的观点文章中，我们讨论了几个我们认为会极大影响QM/MM模拟对许多（即便不是全部）生物分子的稳健性和定量适用性的问题。我们通过本研究小组及该领域其他研究小组近期研究中的观察结果和相关进展来突出这些问题。尽管篇幅有限，但我们希望这些讨论能引起广泛关注，并激发更多有助于推动该领域朝着有意义的方向发展的新进展。
