Pub Date : 2023-02-28Epub Date: 2023-03-08DOI: 10.5940/jcrsj.65.10
Vanessa Bijak, Michal Gucwa, Joanna Lenkiewicz, Krzysztof Murzyn, David R Cooper, Wladek Minor
The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence.
{"title":"Continuous Validation Across Macromolecular Structure Determination Process.","authors":"Vanessa Bijak, Michal Gucwa, Joanna Lenkiewicz, Krzysztof Murzyn, David R Cooper, Wladek Minor","doi":"10.5940/jcrsj.65.10","DOIUrl":"10.5940/jcrsj.65.10","url":null,"abstract":"<p><p>The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence.</p>","PeriodicalId":74311,"journal":{"name":"Nihon Kessho Gakkai shi","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10321142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9806868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Function of X-ray Crystallography in Modern Structural Biology","authors":"Masaki Yamamoto","doi":"10.5940/jcrsj.65.55","DOIUrl":"https://doi.org/10.5940/jcrsj.65.55","url":null,"abstract":"","PeriodicalId":74311,"journal":{"name":"Nihon Kessho Gakkai shi","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85478418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Advantages of X-ray Crystallography in Drug Discovery Research","authors":"M. Takimoto-Kamimura","doi":"10.5940/jcrsj.65.51","DOIUrl":"https://doi.org/10.5940/jcrsj.65.51","url":null,"abstract":"","PeriodicalId":74311,"journal":{"name":"Nihon Kessho Gakkai shi","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85986639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structure and Function of a Plant Silicic Acid Channel","authors":"Y. Saitoh, M. Suga","doi":"10.5940/jcrsj.64.265","DOIUrl":"https://doi.org/10.5940/jcrsj.64.265","url":null,"abstract":"","PeriodicalId":74311,"journal":{"name":"Nihon Kessho Gakkai shi","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90535499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cryo-electron microscopy(cryo-EM)is a powerful method to visualize high resolution structures of biomolecules under physiological condition. Since cryo-EM images represent conformational ensemble of the target biomolecule, cryo-EM is applicable to analyze the biomolecular dynamics such as metastable conformations and/or free-energy landscape in conformational changes. Here, we briefly introduce our method to deduce free-energy landscape of biomolecules from cryo-EM images and compare it with other existing methods.
{"title":"Deducing Free-Energy Landscape of Biomolecular Dynamics from Cryo-Electron Microscopy Images","authors":"Mao Oide, M. Nakasako","doi":"10.5940/jcrsj.64.300","DOIUrl":"https://doi.org/10.5940/jcrsj.64.300","url":null,"abstract":"Cryo-electron microscopy(cryo-EM)is a powerful method to visualize high resolution structures of biomolecules under physiological condition. Since cryo-EM images represent conformational ensemble of the target biomolecule, cryo-EM is applicable to analyze the biomolecular dynamics such as metastable conformations and/or free-energy landscape in conformational changes. Here, we briefly introduce our method to deduce free-energy landscape of biomolecules from cryo-EM images and compare it with other existing methods.","PeriodicalId":74311,"journal":{"name":"Nihon Kessho Gakkai shi","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88051889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Conventional X-ray protein crystallography captures only “static” structures due to the limitation of temporal resolution. Recently
由于时间分辨率的限制，传统的x射线蛋白质晶体学只能捕获“静态”结构。最近
{"title":"Molecular Movies using X-ray Free Electron Lasers: Recent Advances and Future Prospects","authors":"E. Nango, Takaaki Fujiwara, Luo Fangjia, S. Iwata","doi":"10.5940/jcrsj.64.290","DOIUrl":"https://doi.org/10.5940/jcrsj.64.290","url":null,"abstract":"Conventional X-ray protein crystallography captures only “static” structures due to the limitation of temporal resolution. Recently","PeriodicalId":74311,"journal":{"name":"Nihon Kessho Gakkai shi","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85453144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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