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Graph neural networks for conditional de novo drug design 有条件从头药物设计的图神经网络
IF 11.4 2区 化学
Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2023-01-12 DOI: 10.1002/wcms.1651
Carlo Abate, Sergio Decherchi, Andrea Cavalli
{"title":"Graph neural networks for conditional de novo drug design","authors":"Carlo Abate,&nbsp;Sergio Decherchi,&nbsp;Andrea Cavalli","doi":"10.1002/wcms.1651","DOIUrl":"https://doi.org/10.1002/wcms.1651","url":null,"abstract":"<p>Drug design is costly in terms of resources and time. Generative deep learning techniques are using increasing amounts of biochemical data and computing power to pave the way for a new generation of tools and methods for drug discovery and optimization. Although early methods used SMILES strings, more recent approaches use molecular graphs to naturally represent chemical entities. Graph neural networks (GNNs) are learning models that can natively process graphs. The use of GNNs in drug discovery is growing exponentially. GNNs for drug design are often coupled with conditioning techniques to steer the generation process towards desired chemical and biological properties. These conditioned graph-based generative models and frameworks hold promise for the routine application of GNNs in drug discovery.</p><p>This article is categorized under:\u0000 </p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 4","pages":""},"PeriodicalIF":11.4,"publicationDate":"2023-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6195716","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: 1
Rational design of catalysts with earth-abundant elements 富土元素催化剂的合理设计
IF 11.4 2区 化学
Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-30 DOI: 10.1002/wcms.1654
Gaomou Xu, Cheng Cai, Wanghui Zhao, Yonghua Liu, Tao Wang
{"title":"Rational design of catalysts with earth-abundant elements","authors":"Gaomou Xu,&nbsp;Cheng Cai,&nbsp;Wanghui Zhao,&nbsp;Yonghua Liu,&nbsp;Tao Wang","doi":"10.1002/wcms.1654","DOIUrl":"https://doi.org/10.1002/wcms.1654","url":null,"abstract":"<p>Catalysis has played a crucial role in energy sustainability, environment control, and chemical production, while the design of high-performance catalysts is a key scientific question. In nature, biological organisms carry out catalysis with earth-abundant metals, whereas modern industrial processes rely heavily on precious metals. This points out the necessity of designing state-of-the-art catalysts with earth-abundant elements to maintain sustainable catalysis. In this review, we will start with the fact that nature uses earth-abundant metals to feed the planet, followed by a few successful examples of catalyst design for water oxidation. Then, we will systematically introduce the practical methods in computational catalyst design and their applications in the rational modification of EAM catalysts for various reactions. In addition, the roles of high-throughput computations and artificial intelligence in this framework are summarized and discussed. We will also discuss the potential limitations of the framework and the strategies to overcome these challenges. Finally, we emphasize the importance of the synergistic efforts between theory and experiments in rational catalyst design with earth-abundant elements.</p><p>This article is categorized under:\u0000 </p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 4","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6108357","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
Combining machine-learning and molecular-modeling methods for drug-target affinity predictions 结合机器学习和分子建模方法进行药物靶标亲和力预测
IF 11.4 2区 化学
Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-27 DOI: 10.1002/wcms.1653
Carles Perez-Lopez, Alexis Molina, Estrella Lozoya, Victor Segarra, Marti Municoy, Victor Guallar
{"title":"Combining machine-learning and molecular-modeling methods for drug-target affinity predictions","authors":"Carles Perez-Lopez,&nbsp;Alexis Molina,&nbsp;Estrella Lozoya,&nbsp;Victor Segarra,&nbsp;Marti Municoy,&nbsp;Victor Guallar","doi":"10.1002/wcms.1653","DOIUrl":"https://doi.org/10.1002/wcms.1653","url":null,"abstract":"<p>Machine learning (ML) techniques offer a novel and exciting approach in the drug discovery field. One might even argue that their current expansion may push traditional MM modeling techniques to a secondary role in modeling methods. In this review article, we advocate that a combination of both techniques could be the most efficient implementation in the coming years. Focusing on drug-target affinity predictions, we first review pure ML approaches. Then, we introduced recent developments in mixing ML and MM methods in a single combined manner. Finally, we show the detailed implementation of a real industrial prospective study where nanomolar hits, on a kinase target, were obtained by combination of state of the art Monte Carlo MM simulations (PELE) with a ML ranking function.</p><p>This article is categorized under:\u0000 </p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 4","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6065019","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: 1
Perspective: Simultaneous treatment of relativity, correlation, and QED 观点:同时处理相对性、相关性和QED
IF 11.4 2区 化学
Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-22 DOI: 10.1002/wcms.1652
Wenjian Liu
{"title":"Perspective: Simultaneous treatment of relativity, correlation, and QED","authors":"Wenjian Liu","doi":"10.1002/wcms.1652","DOIUrl":"https://doi.org/10.1002/wcms.1652","url":null,"abstract":"<p>Electronic structure calculations of many-electron systems should in principle treat relativistic, correlation, and quantum electrodynamics (QED) effects simultaneously to a high precision, so as to match experimental measurements as close as possible. While both relativistic and QED effects can readily be built into the many-electron Hamiltonian, electron correlation is more difficult to describe due to the exponential growth of the number of parameters in the wave function. Compared with the spin-free case, spin–orbit interaction results in the loss of spin symmetry and concomitant complex algebra, thereby rendering the treatment of electron correlation even more difficult. Possible solutions to these issues are highlighted here.</p><p>This article is categorized under:\u0000 </p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 4","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5744339","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: 2
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,&nbsp;Lane W. Votapka,&nbsp;Rommie E. Amaro,&nbsp;Rebecca C. Wade","doi":"10.1002/wcms.1649","DOIUrl":"https://doi.org/10.1002/wcms.1649","url":null,"abstract":"<p>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.</p><p>This article is categorized under:\u0000 </p>","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,&nbsp;Xiao He","doi":"10.1002/wcms.1650","DOIUrl":"https://doi.org/10.1002/wcms.1650","url":null,"abstract":"<p>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<sup>+</sup>(H<sub>2</sub>O)<sub>21</sub> 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.</p><p>This article is categorized under:\u0000 </p>","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,&nbsp;Patrick Eschenbach,&nbsp;Moritz Bensberg,&nbsp;Johannes T?lle,&nbsp;Lars Hellmann,&nbsp;Lukas Lampe,&nbsp;Anja Massolle,&nbsp;Anton Rikus,&nbsp;David Schnieders,&nbsp;Jan P. Unsleber,&nbsp;Johannes Neugebauer","doi":"10.1002/wcms.1647","DOIUrl":"https://doi.org/10.1002/wcms.1647","url":null,"abstract":"<p>SERENITY [J Comput Chem<i>.</i> 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.</p><p>This article is categorized under:\u0000 </p>","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
{"title":"Growing Spicy ONIOMs: Extending and generalizing concepts of ONIOM and many body expansions","authors":"Phillip Seeber,&nbsp;Sebastian Seidenath,&nbsp;Johannes Steinmetzer,&nbsp;Stefanie Gr?fe","doi":"10.1002/wcms.1644","DOIUrl":"https://doi.org/10.1002/wcms.1644","url":null,"abstract":"<p>The ONIOM method and many extensions to it provide capabilities to treat challenging multiscale problems in catalysis and material science. Our open-source program <i>Spicy</i> is a flexible toolkit for ONIOM and fragment methods. <i>Spicy</i> includes a generalization of multicenter-ONIOM, a higher-order multipole embedding scheme, and fragment methods as useful extensions of our own <i>n</i>-layered integrated molecular orbital and molecular mechanics (ONIOM), which allow applying ONIOM and high accuracy calculations to a wider range of systems. A calculation on the metallo-protein hemoglobin demonstrates the versatility of the implementation.</p><p>This article is categorized under:\u0000 </p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1644","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5754567","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: 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,&nbsp;Tristan Cragnolini,&nbsp;Manaz Kaleel,&nbsp;Thomas Mulvaney,&nbsp;Aaron Sweeney,&nbsp;Maya Topf","doi":"10.1002/wcms.1642","DOIUrl":"https://doi.org/10.1002/wcms.1642","url":null,"abstract":"<p>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.</p><p>This article is categorized under:\u0000 </p>","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
{"title":"Cover Image, Volume 12, Issue 6","authors":"Xin He,&nbsp;Baihua Wu,&nbsp;Youhao Shang,&nbsp;Bingqi Li,&nbsp;Xiangsong Cheng,&nbsp;Jian Liu","doi":"10.1002/wcms.1648","DOIUrl":"https://doi.org/10.1002/wcms.1648","url":null,"abstract":"<p>The cover image is based on the Focus Article <i>New phase space formulations and quantum dynamics approaches</i> by Xin He et al., https://doi.org/10.1002/wcms.1619.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"12 6","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.1648","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5763163","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
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