Phillip Seeber, Sebastian Seidenath, Johannes Steinmetzer, Stefanie Gr?fe
The ONIOM method and many extensions to it provide capabilities to treat challenging multiscale problems in catalysis and material science. Our open-source program Spicy is a flexible toolkit for ONIOM and fragment methods. Spicy includes a generalization of multicenter-ONIOM, a higher-order multipole embedding scheme, and fragment methods as useful extensions of our own n-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.
{"title":"Growing Spicy ONIOMs: Extending and generalizing concepts of ONIOM and many body expansions","authors":"Phillip Seeber, Sebastian Seidenath, Johannes Steinmetzer, 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":null,"pages":null},"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}
Joseph George Beton, Tristan Cragnolini, Manaz Kaleel, Thomas Mulvaney, Aaron Sweeney, Maya Topf
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.
{"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":"<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":null,"pages":null},"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}
The cover image is based on the Focus Article New phase space formulations and quantum dynamics approaches by Xin He et al., https://doi.org/10.1002/wcms.1619.