Michelle Philipp, Christopher W Moth, Nikola Ristic, Johanna K S Tiemann, Florian Seufert, Aleksandra Panfilova, Jens Meiler, Peter W Hildebrand, Amelie Stein, Daniel Wiegreffe, René Staritzbichler
{"title":"MutationExplorer- 用于蛋白质变异和能量影响三维可视化的网络服务器。","authors":"Michelle Philipp, Christopher W Moth, Nikola Ristic, Johanna K S Tiemann, Florian Seufert, Aleksandra Panfilova, Jens Meiler, Peter W Hildebrand, Amelie Stein, Daniel Wiegreffe, René Staritzbichler","doi":"10.1101/2023.03.23.533926","DOIUrl":null,"url":null,"abstract":"<p><p>The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format.</p>","PeriodicalId":48200,"journal":{"name":"Research in Higher Education","volume":"10 1","pages":""},"PeriodicalIF":1.9000,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10925206/pdf/","citationCount":"0","resultStr":"{\"title\":\"MUTATIONEXPLORER- A WEBSERVER FOR MUTATION OF PROTEINS AND 3D VISUALIZATION OF ENERGETIC IMPACTS.\",\"authors\":\"Michelle Philipp, Christopher W Moth, Nikola Ristic, Johanna K S Tiemann, Florian Seufert, Aleksandra Panfilova, Jens Meiler, Peter W Hildebrand, Amelie Stein, Daniel Wiegreffe, René Staritzbichler\",\"doi\":\"10.1101/2023.03.23.533926\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format.</p>\",\"PeriodicalId\":48200,\"journal\":{\"name\":\"Research in Higher Education\",\"volume\":\"10 1\",\"pages\":\"\"},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2024-02-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10925206/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Research in Higher Education\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1101/2023.03.23.533926\",\"RegionNum\":3,\"RegionCategory\":\"教育学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"EDUCATION & EDUCATIONAL RESEARCH\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Research in Higher Education","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2023.03.23.533926","RegionNum":3,"RegionCategory":"教育学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EDUCATION & EDUCATIONAL RESEARCH","Score":null,"Total":0}
引用次数: 0
摘要
只有在蛋白质三维结构的背景下，才能了解突变对蛋白质稳定性和功能可能产生的影响。M utation E xplorer 网络服务器将序列变化映射到蛋白质结构上，允许用户通过输入序列变化来研究变异。当用户输入变异时，三维模型会发生变化，并突出显示能量的估计变化。除了基本的按残基输入格式外，M utation E xplorer 还可以上传整个替换序列。这种上载方式以前属于桌面应用程序的范畴，只需一步即可将 PDB 结构反向变异为野生型序列。另一个支持的变异源是人类单核苷酸多态性（SNPs），以 VCF 格式输入基因组坐标。结构可灵活着色，不仅可根据能量差异着色，还可根据疏水性、序列保护或其他生化分析着色。按界面得分着色可显示突变对结合表面的影响。M utation E xplorer 致力于提高用户体验的效率。例如，我们已经准备了 45,000 个 PDB 文库，用于即时检索和初始显示。所有建模步骤均由 Rosetta 执行。可视化利用 MDsrv/Mol*。M utation E xplorer 的网址为：http://proteinformatics.org/mutation_explorer/。
MUTATIONEXPLORER- A WEBSERVER FOR MUTATION OF PROTEINS AND 3D VISUALIZATION OF ENERGETIC IMPACTS.
The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format.
期刊介绍：
Research in Higher Education publishes studies that examine issues pertaining to postsecondary education. The journal is open to studies using a wide range of methods, but has particular interest in studies that apply advanced quantitative research methods to issues in postsecondary education or address postsecondary education policy issues. Among the topics of interest to the journal are: access and retention; student success; equity; faculty issues; institutional productivity and assessment; postsecondary education governance; curriculum and instruction; state and federal higher education policy; and financing of postsecondary education. The journal encourages submissions from scholars in disciplines outside of higher education, and studies from outside the United States that address issues that are of interest to the readership. The journal will on occasion publish short notes of a methodological nature, literature reviews of topics pertaining to postsecondary research, and “research and practice” studies illustrating how postsecondary research can inform decision making.
京公网安备 11010802042870号
京ICP备2023020795号-1
分享
求助内容：
应助结果提醒方式：
扫码关注我们
