On the emergence of machine-learning methods in bottom-up coarse-graining

IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Current opinion in structural biology Pub Date : 2025-02-01 DOI:10.1016/j.sbi.2024.102972
Patrick G. Sahrmann, Gregory A. Voth
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Abstract

Machine-learning methods have gained significant attention in the computational chemistry community as a viable approach to molecular modeling and analysis. Recent successes in utilizing neural networks to learn atomistic force-fields which ‘coarse-grain’ electronic structure have inspired similar applications to the thermodynamic coarse-graining of chemical and biological systems. In this review, we discuss the current viability and challenges in using machine-learning methods to represent coarse-grained force-fields, as well as the utility of machine-learning in various aspects of coarse-grained modeling.

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论自下而上粗粒度学习中机器学习方法的出现。
机器学习方法作为一种可行的分子建模和分析方法,在计算化学界得到了极大的关注。最近在利用神经网络学习“粗粒”电子结构的原子力场方面的成功,激发了类似于化学和生物系统的热力学粗粒化的应用。在这篇综述中,我们讨论了当前使用机器学习方法来表示粗粒度力场的可行性和挑战,以及机器学习在粗粒度建模的各个方面的应用。
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来源期刊
Current opinion in structural biology
Current opinion in structural biology 生物-生化与分子生物学
CiteScore
12.20
自引率
2.90%
发文量
179
审稿时长
6-12 weeks
期刊介绍: Current Opinion in Structural Biology (COSB) aims to stimulate scientifically grounded, interdisciplinary, multi-scale debate and exchange of ideas. It contains polished, concise and timely reviews and opinions, with particular emphasis on those articles published in the past two years. In addition to describing recent trends, the authors are encouraged to give their subjective opinion of the topics discussed. In COSB, we help the reader by providing in a systematic manner: 1. The views of experts on current advances in their field in a clear and readable form. 2. Evaluations of the most interesting papers, annotated by experts, from the great wealth of original publications. [...] The subject of Structural Biology is divided into twelve themed sections, each of which is reviewed once a year. Each issue contains two sections, and the amount of space devoted to each section is related to its importance. -Folding and Binding- Nucleic acids and their protein complexes- Macromolecular Machines- Theory and Simulation- Sequences and Topology- New constructs and expression of proteins- Membranes- Engineering and Design- Carbohydrate-protein interactions and glycosylation- Biophysical and molecular biological methods- Multi-protein assemblies in signalling- Catalysis and Regulation
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