Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures

IF 2.2 4区生物学 Q3 BIOPHYSICS

European Biophysics Journal Pub Date : 2023-02-28 DOI:10.1007/s00249-023-01636-1

Emre H. Brookes, Mattia Rocco

{"title":"Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures","authors":"Emre H. Brookes, Mattia Rocco","doi":"10.1007/s00249-023-01636-1","DOIUrl":null,"url":null,"abstract":"<div><p>At the 25th International Analytical Ultracentrifugation Workshop and Symposium, we described the recent implementation of the UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF) database, containing hydrodynamic, structural, CD calculations, and other ancillary information, performed on the entire AF v2 database of predicted protein structures, containing more than 1,000,000 entries. The scope of the US-SOMO-AF database was that of providing direct access to pre-calculated physicochemical parameters for rapid assessment against their experimentally determined counterparts to test the compatibility in solution of predicted AlphaFold structures. In the meantime, the AlphaFold consortium has extended its database of predicted structures to an astonishing > 200 million entries, making it quite impractical for their coverage in the US-SOMO-AF database. Therefore, we have created the US-SOMO-Web site, allowing the rapid calculations of all the properties, as present in the US-SOMO-AF database, on user-supplied PDB and mmCIF structures, as well as allowing direct processing of the latest AlphaFold models. Major features on the website are described, along with current limitations and potential future developments.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 4-5","pages":"225 - 232"},"PeriodicalIF":2.2000,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01636-1.pdf","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"European Biophysics Journal","FirstCategoryId":"2","ListUrlMain":"https://link.springer.com/article/10.1007/s00249-023-01636-1","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOPHYSICS","Score":null,"Total":0}

引用次数: 1

Abstract

At the 25th International Analytical Ultracentrifugation Workshop and Symposium, we described the recent implementation of the UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF) database, containing hydrodynamic, structural, CD calculations, and other ancillary information, performed on the entire AF v2 database of predicted protein structures, containing more than 1,000,000 entries. The scope of the US-SOMO-AF database was that of providing direct access to pre-calculated physicochemical parameters for rapid assessment against their experimentally determined counterparts to test the compatibility in solution of predicted AlphaFold structures. In the meantime, the AlphaFold consortium has extended its database of predicted structures to an astonishing > 200 million entries, making it quite impractical for their coverage in the US-SOMO-AF database. Therefore, we have created the US-SOMO-Web site, allowing the rapid calculations of all the properties, as present in the US-SOMO-AF database, on user-supplied PDB and mmCIF structures, as well as allowing direct processing of the latest AlphaFold models. Major features on the website are described, along with current limitations and potential future developments.

Abstract Image

查看原文本刊更多论文

超越US-SOMO-AF数据库:用户提供结构的水动力、结构和圆二色性计算的新网站

在第25届国际分析超离心研讨会和研讨会上，我们描述了UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF)数据库的最新实现，该数据库包含流体动力学、结构、CD计算和其他辅助信息，在整个预测蛋白质结构的AF v2数据库上执行，包含超过1,000,000个记录。US-SOMO-AF数据库的范围是提供直接访问预先计算的物理化学参数，以便根据实验确定的对应参数进行快速评估，以测试预测AlphaFold结构在溶液中的相容性。与此同时，AlphaFold联盟已经将其预测结构的数据库扩展到惊人的2亿个条目，这使得它们在US-SOMO-AF数据库中的覆盖变得非常不切实际。因此，我们创建了US-SOMO-Web站点，允许在用户提供的PDB和mmCIF结构上快速计算US-SOMO-AF数据库中的所有属性，并允许直接处理最新的AlphaFold模型。描述了网站的主要功能，以及当前的限制和潜在的未来发展。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

European Biophysics Journal 生物-生物物理

CiteScore

4.30

自引率

0.00%

发文量

审稿时长

6-12 weeks

期刊介绍： The journal publishes papers in the field of biophysics, which is defined as the study of biological phenomena by using physical methods and concepts. Original papers, reviews and Biophysics letters are published. The primary goal of this journal is to advance the understanding of biological structure and function by application of the principles of physical science, and by presenting the work in a biophysical context. Papers employing a distinctively biophysical approach at all levels of biological organisation will be considered, as will both experimental and theoretical studies. The criteria for acceptance are scientific content, originality and relevance to biological systems of current interest and importance. Principal areas of interest include: - Structure and dynamics of biological macromolecules - Membrane biophysics and ion channels - Cell biophysics and organisation - Macromolecular assemblies - Biophysical methods and instrumentation - Advanced microscopics - System dynamics.