Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献_第2页

ddX: Polarizable continuum solvation from small molecules to proteins ddX：从小分子到蛋白质的可极化连续溶解

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-07-31 DOI: 10.1002/wcms.1726

Michele Nottoli, Michael F. Herbst, Aleksandr Mikhalev, Abhinav Jha, Filippo Lipparini, Benjamin Stamm

{"title":"ddX: Polarizable continuum solvation from small molecules to proteins","authors":"Michele Nottoli, Michael F. Herbst, Aleksandr Mikhalev, Abhinav Jha, Filippo Lipparini, Benjamin Stamm","doi":"10.1002/wcms.1726","DOIUrl":"10.1002/wcms.1726","url":null,"abstract":"Polarizable continuum solvation models are popular in both, quantum chemistry and in biophysics, though typically with different requirements for the numerical methods. However, the recent trend of multiscale modeling can be expected to blur field-specific differences. In this regard, numerical methods based on domain decomposition (dd) have been demonstrated to be sufficiently flexible to be applied all across these levels of theory while remaining systematically accurate and efficient. In this contribution, we present ddX, an open-source implementation of dd-methods for various solvation models, which features a uniform interface with classical as well as quantum descriptions of the solute, or any hybrid versions thereof. We explain the key concepts of the library design and its application program interface, and demonstrate the use of ddX for integrating into standard chemistry packages. Numerical tests illustrate the performance of ddX and its interfaces.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 4","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1726","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141868959","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

HEOM-QUICK2: A general-purpose simulator for fermionic many-body open quantum systems—An update HEOM-QUICK2：费米子多体开放量子系统的通用模拟器--更新版

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-07-31 DOI: 10.1002/wcms.1727

Daochi Zhang, Lyuzhou Ye, Jiaan Cao, Yao Wang, Rui-Xue Xu, Xiao Zheng, YiJing Yan

{"title":"HEOM-QUICK2: A general-purpose simulator for fermionic many-body open quantum systems—An update","authors":"Daochi Zhang, Lyuzhou Ye, Jiaan Cao, Yao Wang, Rui-Xue Xu, Xiao Zheng, YiJing Yan","doi":"10.1002/wcms.1727","DOIUrl":"10.1002/wcms.1727","url":null,"abstract":"Many-body open quantum systems (OQSs) have a profound impact on various subdisciplines of physics, chemistry, and biology. Thus, the development of a computer program capable of accurately, efficiently, and versatilely simulating many-body OQSs is highly desirable. In recent years, we have focused on the advancement of numerical algorithms based on the fermionic hierarchical equations of motion (HEOM) theory. Being in-principle exact, this approach allows for the precise characterization of many-body correlations, non-Markovian memory, and non-equilibrium thermodynamic conditions. These efforts now lead to the establishment of a new computer program, HEOM for QUantum Impurity with a Correlated Kernel, version 2 (HEOM-QUICK2), which, to the best of our knowledge, is currently the only general-purpose simulator for fermionic many-body OQSs. Compared with version 1, the HEOM-QUICK2 program features more efficient solvers for stationary states, more accurate treatment of non-Markovian memory, and improved numerical stability for long-time dissipative dynamics. Integrated with quantum chemistry software, HEOM-QUICK2 has become a valuable theoretical tool for the precise simulation of realistic many-body OQSs, particularly the single atomic or molecular junctions. Furthermore, the unprecedented precision achieved by HEOM-QUICK2 enables accurate simulation of low-energy spin excitations and coherent spin relaxation. The unique usefulness of HEOM-QUICK2 is demonstrated through several examples of strongly correlated quantum impurity systems under non-equilibrium conditions. Thus, the new HEOM-QUICK2 program offers a powerful and comprehensive tool for studying many-body OQSs with exotic quantum phenomena and exploring applications in various disciplines.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 4","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141868965","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: 0

From predicting to decision making: Reinforcement learning in biomedicine 从预测到决策：生物医学中的强化学习

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-07-04 DOI: 10.1002/wcms.1723

Xuhan Liu, Jun Zhang, Zhonghuai Hou, Yi Isaac Yang, Yi Qin Gao

{"title":"From predicting to decision making: Reinforcement learning in biomedicine","authors":"Xuhan Liu, Jun Zhang, Zhonghuai Hou, Yi Isaac Yang, Yi Qin Gao","doi":"10.1002/wcms.1723","DOIUrl":"https://doi.org/10.1002/wcms.1723","url":null,"abstract":"Reinforcement learning (RL) is one important branch of artificial intelligence (AI), which intuitively imitates the learning style of human beings. It is commonly derived from solving game playing problems and is extensively used for decision-making, control and optimization problems. It has been extensively applied for solving complicated problems with the property of Markov decision-making processes. With data accumulation and comprehensive analysis, researchers are not only satisfied with predicting the results for experimental systems but also hope to design or control them for the sake of obtaining the desired properties or functions. RL is potentially facilitated to solve a large number of complicated biological and chemical problems, because they could be decomposed into multi-step decision-making process. In practice, substantial progress has been made in the application of RL to the field of biomedicine. In this paper, we will first give a brief description about RL, including its definition, basic theory and different type of methods. Then we will review some detailed applications in various domains, for example, molecular design, reaction planning, molecular simulation and etc. In the end, we will summarize the essentialities of RL approaches to solve more diverse problems compared with other machine learning methods and also outlook the possible trends to overcome their limitations in the future.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 4","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141561159","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: 0

Recent advancements and challenges in orbital-free density functional theory 无轨道密度泛函理论的最新进展与挑战

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-06-12 DOI: 10.1002/wcms.1724

Qiang Xu, Cheng Ma, Wenhui Mi, Yanchao Wang, Yanming Ma

{"title":"Recent advancements and challenges in orbital-free density functional theory","authors":"Qiang Xu, Cheng Ma, Wenhui Mi, Yanchao Wang, Yanming Ma","doi":"10.1002/wcms.1724","DOIUrl":"https://doi.org/10.1002/wcms.1724","url":null,"abstract":"Orbital-free density functional theory (OFDFT) stands out as a many-body electronic structure approach with a low computational cost that scales linearly with system size, making it well suitable for large-scale simulations. The past decades have witnessed impressive progress in OFDFT, which opens a new avenue to capture the complexity of realistic systems (e.g., solids, liquids, and warm dense matters) and provide a complete description of some complicated physical phenomena under realistic conditions (e.g., dislocation mobility, ductile processes, and vacancy diffusion). In this review, we first present a concise summary of the major methodological advances in OFDFT, placing particular emphasis on kinetic energy density functional and the schemes to evaluate the electron–ion interaction energy. We then give a brief overview of the current status of OFDFT developments in finite-temperature and time-dependent regimes, as well as our developed OFDFT-based software package, named by ATLAS. Finally, we highlight perspectives for further development in this fascinating field, including the major outstanding issues to be solved and forthcoming opportunities to explore large-scale materials.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1724","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141315446","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

Modern machine-learning for binding affinity estimation of protein–ligand complexes: Progress, opportunities, and challenges 用于估算蛋白质配体结合亲和力的现代机器学习：进展、机遇与挑战

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-06-11 DOI: 10.1002/wcms.1716

Tobias Harren, Torben Gutermuth, Christoph Grebner, Gerhard Hessler, Matthias Rarey

{"title":"Modern machine-learning for binding affinity estimation of protein–ligand complexes: Progress, opportunities, and challenges","authors":"Tobias Harren, Torben Gutermuth, Christoph Grebner, Gerhard Hessler, Matthias Rarey","doi":"10.1002/wcms.1716","DOIUrl":"https://doi.org/10.1002/wcms.1716","url":null,"abstract":"Structure-based drug design is a widely applied approach in the discovery of new lead compounds for known therapeutic targets. In most structure-based drug design applications, the docking procedure is considered the crucial step. Here, a potential ligand is fitted into the binding site, and a scoring function assesses its binding capability. With the rise of modern machine-learning in drug discovery, novel scoring functions using machine-learning techniques achieved significant performance gains in virtual screening and ligand optimization tasks on retrospective data. However, real-world applications of these methods are still limited. Missing success stories in prospective applications are one reason for this. Additionally, the fast-evolving nature of the field makes it challenging to assess the advantages of each individual method. This review will highlight recent strides toward improved real world applicability of machine-learning based scoring, enabling a better understanding of the potential benefits and pitfalls of these functions on a project. Furthermore, a systematic way of classifying machine-learning based scoring that facilitates comparisons will be presented.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1716","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141304251","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

The computational molecular technology for complex reaction systems: The Red Moon approach 复杂反应系统的计算分子技术：红月方法

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-05-16 DOI: 10.1002/wcms.1714

Masataka Nagaoka

{"title":"The computational molecular technology for complex reaction systems: The Red Moon approach","authors":"Masataka Nagaoka","doi":"10.1002/wcms.1714","DOIUrl":"https://doi.org/10.1002/wcms.1714","url":null,"abstract":"For dealing with complex reaction (CR) systems that show typical chemical phenomena in molecular aggregation states, the Red Moon (RM) approach is introduced based on a new efficient and systematic RM methodology. First, the theoretical background with my motivation to develop the RM approach is presented from the recent necessity to perform ‘atomistic’ molecular simulation of large-scale and long-term phenomena of (i) complex chemical reactions, (ii) stereospecificity, and (iii) aggregation structures. The RM methodology uses both the molecular dynamics (MD) method for molecular motions (translation, rotation, and vibration of molecules) that frequently occur on a short-time scale and the Monte Carlo (MC) method for rare events such as chemical reactions that hardly do on that time scale. Then, under the transition rate using both the potential energy difference before and after a rare event trial and its chemical kinetic probability, it is tested and judged by the MC method whether the trial is possible (Metropolis method). Next, typical applications of the RM approach are reviewed in two main research fields, (i) polymerization and (ii) storage battery (rechargeable battery or secondary cell), with various examples of our successful studies. Finally, we conclude that the RM approach using the RM methodology should become an efficient new-generation approach as one promising computational molecular strategy (CMT). We believe it will play an essential role in surveying, at the multilevel resolution, various specificities of CR systems in molecular aggregation states.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1714","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140952708","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

Time-resolved photoelectron spectroscopy via trajectory surface hopping 通过轨迹表面跳变实现时间分辨光电子能谱学

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-05-09 DOI: 10.1002/wcms.1715

Pratip Chakraborty, Spiridoula Matsika

引用次数: 0

Design of molecularly imprinted polymers (MIP) using computational methods: A review of strategies and approaches 使用计算方法设计分子印迹聚合物 (MIP)：策略与方法综述

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-05-04 DOI: 10.1002/wcms.1713

Enayat Mohsenzadeh, Vilma Ratautaite, Ernestas Brazys, Simonas Ramanavicius, Sarunas Zukauskas, Deivis Plausinaitis, Arunas Ramanavicius

{"title":"Design of molecularly imprinted polymers (MIP) using computational methods: A review of strategies and approaches","authors":"Enayat Mohsenzadeh, Vilma Ratautaite, Ernestas Brazys, Simonas Ramanavicius, Sarunas Zukauskas, Deivis Plausinaitis, Arunas Ramanavicius","doi":"10.1002/wcms.1713","DOIUrl":"https://doi.org/10.1002/wcms.1713","url":null,"abstract":"This paper focuses on the computationally assisted design of molecularly imprinted polymers (MIP), emphasizing the selected strategies and chosen methods of approach. In summary, this paper provides an overview of the MIP fabrication procedure, focusing on key factors and challenges, where the fabrication of MIP includes a step-by-step process with extensive experimental procedures. This brings challenges in optimizing experimental conditions, such as the selection of monomer, cross-linker, and their relevant molar ratios to the template and solvent. Next, the principles of computational methods are elucidated to explore their potential applicability in solving the challenges. The computational approach can tackle the problems and optimize the MIP's design. Finally, the atomistic, quantum mechanical (QM), and combined methods in the recent research studies are overviewed with stress on strategies, analyses, and results. It is demonstrated that optimization of pre-polymerization mixture by employing simulations significantly reduces the trial-and-error experiments. Besides, higher selectivity and sensitivity of MIP are observed. The polymerization and resulting binding sites by computational methods are considered. Several models of binding sites are formed and analyzed to assess the affinities representing the sensitivity and selectivity of modeled cavities. Combined QM/atomistic methods showed more flexibility and versatility for realistic modeling with higher accuracy. This methodological advancement aligns with the principles of green chemistry, offering cost-effective and time-efficient solutions in MIP design.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140826122","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: 0

Enhanced sampling strategies for molecular simulation of DNA 增强 DNA 分子模拟的采样策略

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-04-05 DOI: 10.1002/wcms.1712

Bernadette Mohr, Thor van Heesch, Alberto Pérez de Alba Ortíz, Jocelyne Vreede

{"title":"Enhanced sampling strategies for molecular simulation of DNA","authors":"Bernadette Mohr, Thor van Heesch, Alberto Pérez de Alba Ortíz, Jocelyne Vreede","doi":"10.1002/wcms.1712","DOIUrl":"https://doi.org/10.1002/wcms.1712","url":null,"abstract":"Molecular dynamics (MD) simulations can provide detailed insights into complex molecular systems, such as DNA, at high resolution in space and time. Using current computer architectures, time scales of tens of microseconds are feasible with contemporary all-atom force fields. However, these timescales are insufficient to accurately characterize large conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale challenge. The first approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The path-metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi-dimensional CV space. The second strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are generally fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two-dimensional Müller–Brown potential. DNA applications are featured for two different processes: the Watson–Crick–Franklin to Hoogsteen transition in adenine–thymine base pairs and the binding of a DNA-binding protein domain to DNA.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 2","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1712","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140351641","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

Diffusion models in protein structure and docking 蛋白质结构和对接中的扩散模型

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-04-05 DOI: 10.1002/wcms.1711

Jason Yim, Hannes Stärk, Gabriele Corso, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola

{"title":"Diffusion models in protein structure and docking","authors":"Jason Yim, Hannes Stärk, Gabriele Corso, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola","doi":"10.1002/wcms.1711","DOIUrl":"https://doi.org/10.1002/wcms.1711","url":null,"abstract":"Generative AI is rapidly transforming the frontier of research in computational structural biology. Indeed, recent successes have substantially advanced protein design and drug discovery. One of the key methodologies underlying these advances is diffusion models (DM). Diffusion models originated in computer vision, rapidly taking over image generation and offering superior quality and performance. These models were subsequently extended and modified for uses in other areas including computational structural biology. DMs are well equipped to model high dimensional, geometric data while exploiting key strengths of deep learning. In structural biology, for example, they have achieved state-of-the-art results on protein 3D structure generation and small molecule docking. This review covers the basics of diffusion models, associated modeling choices regarding molecular representations, generation capabilities, prevailing heuristics, as well as key limitations and forthcoming refinements. We also provide best practices around evaluation procedures to help establish rigorous benchmarking and evaluation. The review is intended to provide a fresh view into the state-of-the-art as well as highlight its potentials and current challenges of recent generative techniques in computational structural biology.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 2","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1711","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140351592","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