Towards index-based similarity search for protein structure databases.

Orhan Camoğlu, Tamer Kahveci, Ambuj K Singh
{"title":"Towards index-based similarity search for protein structure databases.","authors":"Orhan Camoğlu,&nbsp;Tamer Kahveci,&nbsp;Ambuj K Singh","doi":"","DOIUrl":null,"url":null,"abstract":"<p><p>We propose two methods for finding similarities in protein structure databases. Our techniques extract feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins. These feature vectors are then indexed using a multidimensional index structure. Our first technique considers the problem of finding proteins similar to a given query protein in a protein dataset. This technique quickly finds promising proteins using the index structure. These proteins are then aligned to the query protein using a popular pairwise alignment tool such as VAST. We also develop a novel statistical model to estimate the goodness of a match using the SSEs. Our second technique considers the problem of joining two protein datasets to find an all-to-all similarity. Experimental results show that our techniques improve the pruning time of VAST 3 to 3.5 times while keeping the sensitivity similar.</p>","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"148-58"},"PeriodicalIF":0.0000,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings. IEEE Computer Society Bioinformatics Conference","FirstCategoryId":"1085","ListUrlMain":"","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

Abstract

We propose two methods for finding similarities in protein structure databases. Our techniques extract feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins. These feature vectors are then indexed using a multidimensional index structure. Our first technique considers the problem of finding proteins similar to a given query protein in a protein dataset. This technique quickly finds promising proteins using the index structure. These proteins are then aligned to the query protein using a popular pairwise alignment tool such as VAST. We also develop a novel statistical model to estimate the goodness of a match using the SSEs. Our second technique considers the problem of joining two protein datasets to find an all-to-all similarity. Experimental results show that our techniques improve the pruning time of VAST 3 to 3.5 times while keeping the sensitivity similar.

基于索引的蛋白质结构数据库相似性搜索研究。
我们提出了在蛋白质结构数据库中寻找相似性的两种方法。我们的技术在蛋白质的二级结构元件(ses)的三联体上提取特征向量。然后使用多维索引结构对这些特征向量进行索引。我们的第一种技术考虑了在蛋白质数据集中寻找与给定查询蛋白质相似的蛋白质的问题。该技术使用索引结构快速找到有希望的蛋白质。然后使用流行的成对比对工具(如VAST)将这些蛋白质与查询蛋白质对齐。我们还开发了一种新的统计模型来估计使用sse的匹配优度。我们的第二种技术考虑的问题是连接两个蛋白质数据集以找到所有的相似性。实验结果表明,该技术在保持灵敏度不变的情况下,将VAST的剪枝时间提高了3 ~ 3.5倍。
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
自引率
0.00%
发文量
0
×
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:604180095
Book学术官方微信