Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献_第10页

Brownian dynamics simulations of biomolecular diffusional association processes 生物分子扩散结合过程的布朗动力学模拟

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-14 DOI: 10.1002/wcms.1649

Abraham Mu?iz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade

{"title":"Brownian dynamics simulations of biomolecular diffusional association processes","authors":"Abraham Mu?iz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade","doi":"10.1002/wcms.1649","DOIUrl":"https://doi.org/10.1002/wcms.1649","url":null,"abstract":"Brownian dynamics (BD) is a computational method to simulate molecular diffusion processes. Although the BD method has been developed over several decades and is well established, new methodological developments are improving its accuracy, widening its scope, and increasing its application. In biological applications, BD is used to investigate the diffusive behavior of molecules subject to forces due to intermolecular interactions or interactions with material surfaces. BD can be used to compute rate constants for diffusional association, generate structures of encounter complexes for molecular binding partners, and examine the transport properties of geometrically complex molecules. Often, a series of simulations is performed, for example, for different protein mutants or environmental conditions, so that the effects of the changes on diffusional properties can be estimated. While biomolecules are commonly described at atomic resolution and internal molecular motions are typically neglected, coarse-graining and the treatment of conformational flexibility are increasingly employed. Software packages for BD simulations of biomolecules are growing in capabilities, with several new packages providing novel features that expand the range of questions that can be addressed. These advances, when used in concert with experiment or other simulation methods, such as molecular dynamics, open new opportunities for application to biochemical and biological systems. Here, we review some of the latest developments in the theory, methods, software, and applications of BD simulations to study biomolecular diffusional association processes and provide a perspective on their future use and application to outstanding challenges in biology, bioengineering, and biomedicine.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1649","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5849808","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: 1

Recent advances in quantum fragmentation approaches to complex molecular and condensed-phase systems 复杂分子和凝聚相体系的量子碎片化研究进展

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-13 DOI: 10.1002/wcms.1650

Jinfeng Liu, Xiao He

{"title":"Recent advances in quantum fragmentation approaches to complex molecular and condensed-phase systems","authors":"Jinfeng Liu, Xiao He","doi":"10.1002/wcms.1650","DOIUrl":"https://doi.org/10.1002/wcms.1650","url":null,"abstract":"Quantum mechanical (QM) calculations are critical in quantitatively understanding the relationship between the structure and physicochemical properties of various chemical systems. However, the sharply increasing computational cost with the system size has severely hindered applying direct QM calculations on large-sized systems. Hence, linear-scaling and/or fragmentation QM methods have been proposed to overcome this difficulty. In this review, we focus on the recent development and applications of the electrostatically embedded generalized molecular fractionation with the conjugate caps (EE-GMFCC) method in probing various properties of complex large molecules and condensed-phase systems. The EE-GMFCC method is now capable of describing the localized excited states of biomolecules and molecular crystals with a chromophore. The EE-GMF method is also combined with anharmonic vibrational calculations for accurate simulation of the infrared spectrum of the magic number H+(H2O)21 cluster at the coupled cluster level. With an adaptive fragmentation scheme, the EE-GMF-based ab initio molecular dynamics is able to directly simulate chemical reactions occurred in atmospheric molecular clusters. Furthermore, by combining the EE-GMF(CC) method and deep machine learning techniques, neural network potentials can be efficiently constructed for accurate simulations of complex systems with the accuracy of high-level wave function methods. The EE-GMF(CC) method is expected to become a practical tool for quantitative description of complex large molecules and condensed-phase systems with high-level ab initio theories or ab initio quality potentials.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6219897","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}

引用次数: 5

The subsystem quantum chemistry program Serenity 子系统量子化学项目宁静号

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-07 DOI: 10.1002/wcms.1647

Niklas Niemeyer, Patrick Eschenbach, Moritz Bensberg, Johannes T?lle, Lars Hellmann, Lukas Lampe, Anja Massolle, Anton Rikus, David Schnieders, Jan P. Unsleber, Johannes Neugebauer

{"title":"The subsystem quantum chemistry program Serenity","authors":"Niklas Niemeyer, Patrick Eschenbach, Moritz Bensberg, Johannes T?lle, Lars Hellmann, Lukas Lampe, Anja Massolle, Anton Rikus, David Schnieders, Jan P. Unsleber, Johannes Neugebauer","doi":"10.1002/wcms.1647","DOIUrl":"https://doi.org/10.1002/wcms.1647","url":null,"abstract":"SERENITY [J Comput Chem. 2018;39:788–798] is an open-source quantum chemistry software that provides an extensive development platform focused on quantum-mechanical multilevel and embedding approaches. In this study, we give an overview over the developments done in Serenity since its original publication in 2018. This includes efficient electronic-structure methods for ground states such as multilevel domain-based local pair natural orbital coupled cluster and Møller–Plesset perturbation theory as well as the multistate frozen-density embedding quasi-diabatization method. For the description of excited states, SERENITY features various subsystem-based methods such as embedding variants of coupled time-dependent density-functional theory, approximate second-order coupled cluster theory and the second-order algebraic diagrammatic construction technique as well as GW/Bethe–Salpeter equation approaches. SERENITY's modular structure allows combining these methods with density-functional theory (DFT)-based embedding through various practical realizations and variants of subsystem DFT including frozen-density embedding, potential-reconstruction techniques and projection-based embedding.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1647","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6111307","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: 7

Growing Spicy ONIOMs: Extending and generalizing concepts of ONIOM and many body expansions 种植辣洋葱:扩展和概括洋葱和许多身体扩展的概念

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-11-22 DOI: 10.1002/wcms.1644

Phillip Seeber, Sebastian Seidenath, Johannes Steinmetzer, Stefanie Gr?fe

引用次数: 2

Integrating model simulation tools and cryo-electron microscopy 整合模型模拟工具和低温电子显微镜

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-11-21 DOI: 10.1002/wcms.1642

Joseph George Beton, Tristan Cragnolini, Manaz Kaleel, Thomas Mulvaney, Aaron Sweeney, Maya Topf

{"title":"Integrating model simulation tools and cryo-electron microscopy","authors":"Joseph George Beton, Tristan Cragnolini, Manaz Kaleel, Thomas Mulvaney, Aaron Sweeney, Maya Topf","doi":"10.1002/wcms.1642","DOIUrl":"https://doi.org/10.1002/wcms.1642","url":null,"abstract":"The power of computer simulations, including machine-learning, has become an inseparable part of scientific analysis of biological data. This has significantly impacted the field of cryogenic electron microscopy (cryo-EM), which has grown dramatically since the “resolution-revolution.” Many maps are now solved at 3–4 Å or better resolution, although a significant proportion of maps deposited in the Electron Microscopy Data Bank are still at lower resolution, where the positions of atoms cannot be determined unambiguously. Additionally, cryo-EM maps are often characterized by a varying local resolution, partly due to conformational heterogeneity of the imaged molecule. To address such problems, many computational methods have been developed for cryo-EM map reconstruction and atomistic model building. Here, we review the development in algorithms and tools for building models in cryo-EM maps at different resolutions. We describe methods for model building, including rigid and flexible fitting of known models, model validation, small-molecule fitting, and model visualization. We provide examples of how these methods have been used to elucidate the structure and function of dynamic macromolecular machines.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1642","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5765770","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: 5

Cover Image, Volume 12, Issue 6 封面图片，第12卷，第6期

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-11-21 DOI: 10.1002/wcms.1648

Xin He, Baihua Wu, Youhao Shang, Bingqi Li, Xiangsong Cheng, Jian Liu

引用次数: 0

Atomistic neural network representations for chemical dynamics simulations of molecular, condensed phase, and interfacial systems: Efficiency, representability, and generalization 分子、凝聚相和界面系统化学动力学模拟的原子神经网络表征:效率、可表征性和泛化

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-11-16 DOI: 10.1002/wcms.1645

Yaolong Zhang, Qidong Lin, Bin Jiang

{"title":"Atomistic neural network representations for chemical dynamics simulations of molecular, condensed phase, and interfacial systems: Efficiency, representability, and generalization","authors":"Yaolong Zhang, Qidong Lin, Bin Jiang","doi":"10.1002/wcms.1645","DOIUrl":"https://doi.org/10.1002/wcms.1645","url":null,"abstract":"Machine learning techniques have been widely applied in many fields of chemistry, physics, biology, and materials science. One of the most fruitful applications is machine learning of the complicated multidimensional function of potential energy or related electronic properties from discrete quantum chemical data. In particular, substantial efforts have been dedicated to developing various atomistic neural network (AtNN) representations, which refer to a family of methods expressing the targeted physical quantity as a sum of atomic components represented by atomic NNs. This class of approaches not only fully preserves the physical symmetry of the system but also scales linearly with respect to the size of a system, enabling accurate and efficient chemical dynamics and spectroscopic simulations in complicated systems and even a number of variably sized systems across the phases. In this review, we discuss different strategies in developing highly efficient and representable AtNN potentials, and in generalizing these scalar AtNN models to learn vectorial and tensorial quantities with the correct rotational equivariance. We also review active learning algorithms to generate practical AtNN models and present selected examples of AtNN applications in gas-surface systems to demonstrate their capabilities of accurately representing both molecular systems and condensed phase systems. We conclude this review by pointing out remaining challenges for the further development of more reliable, transferable, and scalable AtNN representations in more application scenarios.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5663359","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}

引用次数: 10

Computational protein design with data-driven approaches: Recent developments and perspectives 用数据驱动的方法计算蛋白质设计:最近的发展和观点

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-11-15 DOI: 10.1002/wcms.1646

Haiyan Liu, Quan Chen

引用次数: 3

Establishing the catalytic and regulatory mechanism of RNA-based machineries 建立基于rna的机制的催化调控机制

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-10-21 DOI: 10.1002/wcms.1643

Jure Bori?ek, Jana Aupi?, Alessandra Magistrato

{"title":"Establishing the catalytic and regulatory mechanism of RNA-based machineries","authors":"Jure Bori?ek, Jana Aupi?, Alessandra Magistrato","doi":"10.1002/wcms.1643","DOIUrl":"https://doi.org/10.1002/wcms.1643","url":null,"abstract":"Ribonucleoprotein (RNP)-machineries are comprised of intricate networks of long noncoding RNAs and proteins that allow them to actively participate in transcription, RNA processing, and translation. RNP-machineries thus play vital roles in gene expression and regulation. Recent advances in cryo-EM techniques provided a wealth of near-atomic-level resolution structures setting the basis for understanding how these fascinating multiscale complexes exert their diverse roles. However, these structures represent only isolated snapshots of the plastic and highly dynamic RNP-machineries and are thus insufficient to comprehensively assess their multifaceted mechanisms. In this review, we discuss the role and merit of all-atom simulations in disentangling the mechanism of eukaryotic RNA-based machineries responsible for RNA processing. We showcase how all-atom simulations can capture their large-scale functional movements, trace the signaling pathways that are at the root of their massive conformational remodeling, explain recognition mechanisms of specific RNA sequences, and, lastly, unravel the chemical mechanisms underlying the formation of functional RNA strands. Finally, we review the methodological pitfalls and outline future challenges in modeling key functional aspects of these large molecular engines with all-atom simulations. In addition to providing insights into the most basic processes that govern all forms of life, in-depth mechanistic comprehension of RNP-machineries offers a foundation for developing innovative therapeutic strategies against the variety of human diseases linked to deregulated RNA metabolism.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5796578","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}

引用次数: 5

Recent advances in computational studies on voltage-gated sodium channels: Drug design and mechanism studies 电压门控钠通道的计算研究进展:药物设计和机制研究

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-10-20 DOI: 10.1002/wcms.1641

Gaoang Wang, Lei Xu, Haiyi Chen, Yifei Liu, Peichen Pan, Tingjun Hou

引用次数: 1