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[转载]热点专题 | 蛋白质与核酸结构功能的建模与模拟
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为了展现国内外在"蛋白质与核酸结构功能的建模与模拟"研究领域的代表性成果，"Chinese Physics B"(CPB)编辑部邀请谭志杰和肖奕两位老师作为客座编辑，组织了" Modeling and simulations for the structures and functions of proteins and nucleic acids "专题，敬请关注！
编者按
|谭志杰 教授 武汉大学
|肖 奕 教授 华中科技大学
蛋白质和核糖核酸（RNA）是非常基本和重要的生物大分子。其中蛋白质是生命的物质基础，是生命活动的主要执行者；而RNA除了能储存和传递生物遗传信息以及编码蛋白质外，近年来发现了大量的非编码RNA，它们被称为生物中的“暗物质”，执行着催化和基因调控等诸多功能。蛋白质和RNA的功能与其结构紧密相关，蛋白质一般是由20种氨基酸缩合而成的链状大分子，RNA则由4种核苷酸缩合而成，蛋白质和RNA的序列和以及由此形成的空间结构的多样性，决定了其多样的生物功能。
近年来，关于蛋白质和RNA结构及其与功能关系的研究取得了很大进展。这得益于Anfinsen热力学原理的提出、实验测量数据的大量积累和高性能计算的快速发展，关于蛋白质、RNA及其复合体结构的建模与模拟，以及对其结构与功能关系的理解也取得了巨大的进步，包括各类分子力场和分子动力学模拟软件的发展、各类蛋白质和RNA结构折叠模型和结构预测方法的发展以及上述理论和计算方法对相关系统的广泛应用等等。人工智能的机器学习和深度学习也极大地推动了此领域的进步，如在传统的基于物理和生物信息学的方法中引入深度学习技术显著提升了结构预测精度，基于人工智能的AlphaFold2对单体蛋白质结构的预测超越了传统的方法。在此蓬勃发展的领域，中国科学家也做出了很多相当出色的工作。
为了反映此领域的发展，Chinese Physics B组织了此专辑。围绕蛋白质和RNA结构与功能的建模及模拟，本专题发表了来自相关领域一些活跃的研究小组的8篇综述和6篇原创研究，涉及了本领域内的多个方面。包括与蛋白质相关的研究和综述：蛋白质-蛋白质对接的预测、细菌群体感应动力学的建模、蛋白质中平均力势计算的分子动力学、蛋白质折叠核与去折叠动力学、朊蛋白变体在朊转换中机制的分子动力学、免疫应答蛋白构象的动力学、多体蛋白质-蛋白质相互作用预测综述、蛋白质折叠孤子模型综述、分子动力学中慢动力学模式分析方法综述等；还有与RNA相关的研究和综述：基于直接耦合分析的RNA二级结构预测、RNA二级结构折叠动力学综述、RNA三级接触作用预测综述、基于机器学习的RNA三级结构预测综述以及RNA三级结构评估中统计势的综述等。希望本专题能够对蛋白质和RNA相关国内外研究同行有所帮助和启示，并促进该领域的合作交流与发展。
REVIEWS
Statistical potentials for 3D structure evaluation: From proteins to RNAs
Ya-Lan Tan(谭雅岚), Chen-Jie Feng(封晨洁), Xunxun Wang(王勋勋), Wenbing Zhang(张文炳), and Zhi-Jie Tan(谭志杰)
Chin. Phys. B, 2021, 30 (2): 028705
Quantitative modeling of bacterial quorum sensing dynamics in time and space
Xiang Li(李翔), Hong Qi(祁宏), Xiao-Cui Zhang(张晓翠), Fei Xu(徐飞), Zhi-Yong Yin(尹智勇), Shi-Yang Huang(黄世阳), Zhao-Shou Wang(王兆守), and Jian-Wei Shuai(帅建伟)
Chin. Phys. B, 2020, 29 (10): 108702
The theory of helix-based RNA folding kinetics and its application
Sha Gong(龚沙), Taigang Liu(刘太刚), Yanli Wang(王晏莉), Wenbing Zhang(张文炳)
Chin. Phys. B, 2020, 29 (10): 108703
Computational prediction of RNA tertiary structures using machine learning methods
Bin Huang(黄斌), Yuanyang Du(杜渊洋), Shuai Zhang(张帅), Wenfei Li(李文飞), Jun Wang(王骏), Jian Zhang(张建)
Chin. Phys. B, 2020, 29 (10): 108704
Application of topological soliton in modeling protein folding: Recent progress and perspective
Xu-Biao Peng(彭绪彪), Jiao-Jiao Liu(刘娇娇), Jin Dai(戴劲), Antti J Niemi, Jian-Feng He(何建锋)
Chin. Phys. B, 2020, 29 (10): 108705
Find slow dynamic modes via analyzing molecular dynamics simulation trajectories
Chuanbiao Zhang(张传彪), Xin Zhou(周昕)
Chin. Phys. B, 2020, 29 (10): 108706
Review of multimer protein–protein interaction complex topology and structure prediction
Daiwen Sun(孙黛雯), Shijie Liu(刘世婕), Xinqi Gong(龚新奇)
Chin. Phys. B, 2020, 29 (10): 108707
Methods and applications of RNA contact prediction
Huiwen Wang(王慧雯), Yunjie Zhao(赵蕴杰)
Chin. Phys. B, 2020, 29 (10): 108708
ARTICLES
Folding nucleus and unfolding dynamics of protein 2GB1
Xuefeng Wei(韦学锋) and Yanting Wang(王延颋)
Chin. Phys. B, 2021, 30 (2): 028703
Protein-protein docking with interface residue restraints
Hao Li(李豪) and Sheng-You Huang(黄胜友)
Chin. Phys. B, 2021, 30 (1): 018703
Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation
Xiaofeng Zhang(张晓峰), Zilong Guo(郭子龙), Ping Yu(余平), Qiushi Li(李秋实), Xin Zhou(周昕), Hu Chen(陈虎)
Chin. Phys. B, 2020, 29 (7): 078701
Improving RNA secondary structure prediction using direct coupling analysis
Xiaoling He(何小玲), Jun Wang(王军), Jian Wang(王剑), Yi Xiao(肖奕)
Chin. Phys. B, 2020, 29 (7): 078702
Twisting mode of supercoil leucine-rich domain mediates peptide sensing in FLS2–flg22–BAK1 complex
Zhi-Chao Liu(刘志超), Qin Liu(刘琴), Chan-You Chen(陈禅友), Chen Zeng(曾辰), Peng Ran(冉鹏), Yun-Jie Zhao(赵蕴杰), Lei Pan(潘磊)
Chin. Phys. B, 2020, 29 (10): 108709
Structural and dynamical mechanisms of a naturally occurring variant of the human prion protein in preventing prion conversion
Yiming Tang(唐一鸣), Yifei Yao(姚逸飞), Guanghong Wei(韦广红)
SPECIAL TOPIC —Twistronics
SPECIAL TOPIC — Machine learning in condensed matter physics
SPECIAL TOPIC — Phononics and phonon engineering
SPECIAL TOPIC — Water at molecular level
SPECIAL TOPIC — Optical field manipulation
SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids
SPECIAL TOPIC —Terahertz physics
SPECIAL TOPIC — Ultracold atom and its application in precision measurement
SPECIAL TOPIC — Topological 2D materials
SPECIAL TOPIC — Active matters physics
SPECIAL TOPIC — Advanced calculation & characterization of energy storage materials & devices at multiple scale
TOPICAL REVIEW — Advanced calculation & characterization of energy storage materials & devices at multiple scale
SPECIAL TOPIC — A celebration of the 100th birthday of Kun Huang
TOPICAL REVIEW — A celebration of the 100th birthday of Kun Huang
SPECIAL TOPIC — Strong-field atomic and molecular physics
TOPICAL REVIEW — Strong-field atomic and molecular physics
TOPICAL REVIEW — Topological semimetals
SPECIAL TOPIC — Topological semimetals
SPECIAL TOPIC — Photodetector: Materials, physics, and applications
TOPICAL REVIEW — Photodetector: Materials, physics, and applications
TOPICAL REVIEW — Fundamental research under high magnetic fields
Virtual Special Topic — High temperature superconductivity
Virtual Special Topic — Magnetism and Magnetic Materials
官网：http://cpb.iphy.ac.cn https://iopscience.iop.org/journal/1674-1056
https://blog.sciencenet.cn/blog-3377544-1272272.html
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