Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献_第5页

Correction to “The versatility of the Cholesky decomposition in electronic structure theory” 对 "乔利斯基分解在电子结构理论中的多功能性 "的更正

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-02-17 DOI: 10.1002/wcms.1707

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A brief history of amyloid aggregation simulations 淀粉样蛋白聚集模拟简史

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-02-15 DOI: 10.1002/wcms.1703

Hebah Fatafta, Mohammed Khaled, Batuhan Kav, Olujide O. Olubiyi, Birgit Strodel

{"title":"A brief history of amyloid aggregation simulations","authors":"Hebah Fatafta, Mohammed Khaled, Batuhan Kav, Olujide O. Olubiyi, Birgit Strodel","doi":"10.1002/wcms.1703","DOIUrl":"https://doi.org/10.1002/wcms.1703","url":null,"abstract":"Amyloid proteins are characterized by their tendency to aggregate into amyloid fibrils, which are often associated with devastating diseases. Aggregation pathways typically involve unfolding or misfolding of monomeric proteins and formation of transient oligomers and protofibrils before the final aggregation product is formed. The conformational dynamics and polymorphic and volatile nature of these aggregation intermediates make their characterization by experimental techniques alone insufficient and also require computational approaches. Over the past 25 years, the size of simulated amyloid aggregation systems and the length of these simulations have increased significantly. These advances are discussed here. The review includes simulation approaches that model the aggregating peptides or proteins at both the all-atom and coarse-grained levels, use molecular dynamics simulations or Monte Carlo sampling to simulate the conformational changes, and present results for various amyloid peptides and proteins ranging from Lys-Phe-Phe-Glu (KFFE) as the smallest system to <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>Aβ</mi>\u0000 </mrow>\u0000 <annotation>$$ mathrm{A}upbeta $$</annotation>\u0000 </semantics></math> as an intermediate-sized peptide to α-synuclein. The presentation of the history of amyloid aggregation simulations concludes with a discussion of where the future of these simulations may lie.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1703","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139744921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design 揭开钾通道秘密的计算方法：结构、机理和药物设计

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-02-15 DOI: 10.1002/wcms.1704

Lingling Wang, Qianqian Zhang, Henry H. Y. Tong, Xiaojun Yao, Huanxiang Liu, Guohui Li

{"title":"Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design","authors":"Lingling Wang, Qianqian Zhang, Henry H. Y. Tong, Xiaojun Yao, Huanxiang Liu, Guohui Li","doi":"10.1002/wcms.1704","DOIUrl":"https://doi.org/10.1002/wcms.1704","url":null,"abstract":"Potassium (K+) channels play vital roles in various physiological functions, including regulating K+ flow in cell membranes, impacting nervous system signal transduction, neuronal firing, muscle contraction, neurotransmitters, and enzyme secretion. Their activation and switch-off are directly linked to diseases like arrhythmias, atrial fibrillation, and pain etc. Although the experimental methods play important roles in the studying the structure and function of K+ channels, they are still some limitations to enclose the dynamic molecular processes and the corresponding mechanisms of conformational changes during ion transport, permeation, and gating control. Relatively, computational methods have obvious advantages in studying such problems compared with experimental methods. Recently, more and more three-dimensional structures of K+ channels have been disclosed based on experimental methods and in silico prediction methods, which provide a good chance to study the molecular mechanism of conformational changes related to the functional regulations of K+ channels. Based on these structural details, molecular dynamics simulations together with related methods such as enhanced sampling and free energy calculations, have been widely used to reveal the conformational dynamics, ion conductance, ion channel gating, and ligand binding mechanisms. Additionally, the accessibility of structures also provides a large space for structure-based drug design. This review mainly addresses the recent progress of computational methods in the structure, mechanism, and drug design of K+ channels. After summarizing the progress in these fields, we also give our opinion on the future direction in the area of K+ channel research combined with the cutting edge of computational methods.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139744922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Two-dimensional hypercoordinate chemistry: Challenges and prospects 二维超配位化学：挑战与前景

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-30 DOI: 10.1002/wcms.1699

Bingyi Song, Li-Ming Yang

{"title":"Two-dimensional hypercoordinate chemistry: Challenges and prospects","authors":"Bingyi Song, Li-Ming Yang","doi":"10.1002/wcms.1699","DOIUrl":"https://doi.org/10.1002/wcms.1699","url":null,"abstract":"Planar hypercoordinate compounds are fascinating but challenging to be realized. The difficulty in stabilizing and fabricating such compounds prevent us from in-deep understanding these compounds and exploring potential applications. Molecular-level insights on underlying mechanism for the formation of viable hypercoordinate compounds is the key towards the development of this field. This review aims to summarize recent advances in this direction. Regular polygons ALCN (A and L are central and ligand atoms, CN is coordination number) are generally applicable models used to derive the unified mathematical relations between the radii of constitute atoms and the angles of regular polygons as exemplified by two typical examples Gr14LCN and TMBCN (Gr14 is Group 14 element, TM is transition metal, B is boron). Effective schemes and some useful rule of thumb are proposed towards the architecture of 2D hypercoordinate crystals ALx (x is composition ratio). A set of design flow chart and several effective design strategies and principles are suggested for 2D-HyperMaters. Potential diverse applications of 2D-HyperMaters are discussed and summarized. Grand blueprint for planar hypercoordinate chemistry is drew. Finally, future prospects of 2D-HyperChem is outlooked.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139655510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Subsystem density-functional theory (update) 子系统密度函数理论（更新）

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-30 DOI: 10.1002/wcms.1700

Christoph R. Jacob, Johannes Neugebauer

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Complexity of life sciences in quantum and AI era 量子和人工智能时代生命科学的复杂性

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-17 DOI: 10.1002/wcms.1701

Alexey Pyrkov, Alex Aliper, Dmitry Bezrukov, Dmitriy Podolskiy, Feng Ren, Alex Zhavoronkov

{"title":"Complexity of life sciences in quantum and AI era","authors":"Alexey Pyrkov, Alex Aliper, Dmitry Bezrukov, Dmitriy Podolskiy, Feng Ren, Alex Zhavoronkov","doi":"10.1002/wcms.1701","DOIUrl":"https://doi.org/10.1002/wcms.1701","url":null,"abstract":"Having made significant advancements in understanding living organisms at various levels such as genes, cells, molecules, tissues, and pathways, the field of life sciences is now shifting towards integrating these components into the bigger picture to understand their collective behavior. Such a shift of perspective requires a general conceptual framework for understanding complexity in life sciences which is currently elusive, a transition being facilitated by large-scale data collection, unprecedented computational power, and new analytical tools. In recent years, life sciences have been revolutionized with AI methods, and quantum computing is touted to be the next most significant leap in technology. Here, we provide a theoretical framework to orient researchers around key concepts of how quantum computing can be integrated into the study of the hierarchical complexity of living organisms and discuss recent advances in quantum computing for life sciences.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1701","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139488608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Variational determination of the two-electron reduced density matrix: A tutorial review 双电子还原密度矩阵的变量测定：教程回顾

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-17 DOI: 10.1002/wcms.1702

A. Eugene DePrince III

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Cover Image, Volume 14, Issue 1 封面图片，第 14 卷第 1 期

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-11 DOI: 10.1002/wcms.1709

Sarah Löffelsender, Pierre Beaujean, Marc de Wergifosse

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Jellyfish: A modular code for wave function-based electron dynamics simulations and visualizations on traditional and quantum compute architectures 水母:基于波函数的电子动力学模拟和传统和量子计算架构可视化的模块化代码

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2023-11-27 DOI: 10.1002/wcms.1696

Fabian Langkabel, Pascal Krause, Annika Bande

{"title":"Jellyfish: A modular code for wave function-based electron dynamics simulations and visualizations on traditional and quantum compute architectures","authors":"Fabian Langkabel, Pascal Krause, Annika Bande","doi":"10.1002/wcms.1696","DOIUrl":"10.1002/wcms.1696","url":null,"abstract":"Ultrafast electron dynamics have made rapid progress in the last few years. With Jellyfish, we now introduce a program suite that enables to perform the entire workflow of an electron-dynamics simulation. The modular program architecture offers a flexible combination of different propagators, Hamiltonians, basis sets, and more. Jellyfish can be operated by a graphical user interface, which makes it easy to get started for nonspecialist users and gives experienced users a clear overview of the entire functionality. The temporal evolution of a wave function can currently be executed in the time-dependent configuration interaction method (TDCI) formalism, however, a plugin system facilitates the expansion to other methods and tools without requiring in-depth knowledge of the program. Currently developed plugins allow to include results from conventional electronic structure calculations as well as the usage and extension of quantum-compute algorithms for electron dynamics. We present the capabilities of Jellyfish on three examples to showcase the simulation and analysis of light-driven correlated electron dynamics. The implemented visualization of various densities enables an efficient and detailed analysis for the long-standing quest of the electron–hole pair formation.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1696","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138505210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chemical complexity challenge: Is multi-instance machine learning a solution? 化学复杂性挑战:多实例机器学习是解决方案吗?

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2023-11-27 DOI: 10.1002/wcms.1698

Dmitry Zankov, Timur Madzhidov, Alexandre Varnek, Pavel Polishchuk

{"title":"Chemical complexity challenge: Is multi-instance machine learning a solution?","authors":"Dmitry Zankov, Timur Madzhidov, Alexandre Varnek, Pavel Polishchuk","doi":"10.1002/wcms.1698","DOIUrl":"10.1002/wcms.1698","url":null,"abstract":"Molecules are complex dynamic objects that can exist in different molecular forms (conformations, tautomers, stereoisomers, protonation states, etc.) and often it is not known which molecular form is responsible for observed physicochemical and biological properties of a given molecule. This raises the problem of the selection of the correct molecular form for machine learning modeling of target properties. The same problem is common to biological molecules (RNA, DNA, proteins)—long sequences where only key segments, which often cannot be located precisely, are involved in biological functions. Multi-instance machine learning (MIL) is an efficient approach for solving problems where objects under study cannot be uniquely represented by a single instance, but rather by a set of multiple alternative instances. Multi-instance learning was formalized in 1997 and motivated by the problem of conformation selection in drug activity prediction tasks. Since then MIL has found a lot of applications in various domains, such as information retrieval, computer vision, signal processing, bankruptcy prediction, and so on. In the given review we describe the MIL framework and its applications to the tasks associated with ambiguity in the representation of small and biological molecules in chemoinformatics and bioinformatics. We have collected examples that demonstrate the advantages of MIL over the traditional single-instance learning (SIL) approach. Special attention was paid to the ability of MIL models to identify key instances responsible for a modeling property.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1698","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138505251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0