预测模型和 CCP4。

IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS
Adam J Simpkin, Iracema Caballero, Stuart McNicholas, Kyle Stevenson, Elisabet Jiménez, Filomeno Sánchez Rodríguez, Maria Fando, Ville Uski, Charles Ballard, Grzegorz Chojnowski, Andrey Lebedev, Eugene Krissinel, Isabel Usón, Daniel J Rigden, Ronan M Keegan
{"title":"预测模型和 CCP4。","authors":"Adam J Simpkin, Iracema Caballero, Stuart McNicholas, Kyle Stevenson, Elisabet Jiménez, Filomeno Sánchez Rodríguez, Maria Fando, Ville Uski, Charles Ballard, Grzegorz Chojnowski, Andrey Lebedev, Eugene Krissinel, Isabel Usón, Daniel J Rigden, Ronan M Keegan","doi":"10.1107/S2059798323006289","DOIUrl":null,"url":null,"abstract":"<p><p>In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 9","pages":"806-819"},"PeriodicalIF":2.6000,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478639/pdf/","citationCount":"0","resultStr":"{\"title\":\"Predicted models and CCP4.\",\"authors\":\"Adam J Simpkin, Iracema Caballero, Stuart McNicholas, Kyle Stevenson, Elisabet Jiménez, Filomeno Sánchez Rodríguez, Maria Fando, Ville Uski, Charles Ballard, Grzegorz Chojnowski, Andrey Lebedev, Eugene Krissinel, Isabel Usón, Daniel J Rigden, Ronan M Keegan\",\"doi\":\"10.1107/S2059798323006289\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.</p>\",\"PeriodicalId\":7116,\"journal\":{\"name\":\"Acta Crystallographica. Section D, Structural Biology\",\"volume\":\"79 Pt 9\",\"pages\":\"806-819\"},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2023-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478639/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Acta Crystallographica. Section D, Structural Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1107/S2059798323006289\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2023/8/17 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Acta Crystallographica. Section D, Structural Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1107/S2059798323006289","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/8/17 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

摘要

2020 年底,CASP14(评估计算蛋白质结构预测方法最新发展的系列竞赛的第 14 项赛事)的结果显示,谷歌的 Deepmind 在解决预测问题方面取得了巨大进步。他们预测的准确度是首次有参赛者在所有难度类别的全球距离测试中得分超过 90 分。这一成就对实验结构生物学领域来说既是挑战也是机遇。对于通过大分子 X 射线晶体学确定结构而言,获得高精度的结构预测非常有益,尤其是在解决相位问题时。本文详细介绍了 CCP4 套件中的新实用程序和增强型应用程序,这些程序和应用程序旨在让用户利用预测模型从 X 射线衍射数据中确定大分子结构。重点主要放在可用于通过分子置换解决相问题的应用程序上。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Predicted models and CCP4.

Predicted models and CCP4.

Predicted models and CCP4.

Predicted models and CCP4.

In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Acta Crystallographica. Section D, Structural Biology
Acta Crystallographica. Section D, Structural Biology BIOCHEMICAL RESEARCH METHODSBIOCHEMISTRY &-BIOCHEMISTRY & MOLECULAR BIOLOGY
CiteScore
4.50
自引率
13.60%
发文量
216
期刊介绍: Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信