TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.
TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.
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DOI：
10.1186/1471-2105-9-358
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发表时间：
2008-08-31
影响因子：
3
通讯作者：
Godzik A
中科院分区：
文献类型：
--
作者：
Veeramalai M;Ye Y;Godzik A
蛋白质结构分析和比较是结构生物信息学的主要挑战。尽管存在许多工具和算法，但其中很少有人能够捕获结构生物学中开发的蛋白质结构的直观理解，特别是在快速数据库搜索的背景下。这种直觉可以帮助加速相似性搜索，并使人们更容易理解这种分析的结果。我们开发了一种TOPS++FATCAT算法，该算法使用流行的TOPS图中捕获的蛋白质结构的直观描述，以限制FATCAT算法执行的蛋白质结构灵活对齐中对齐片段对（AFP）的搜索空间。TOPS++FATCAT算法比FATCAT快一个数量级以上，分类和对齐精度的成本最小。对于富含β的蛋白质，其准确性优于FATCAT，因为TOPS+串模型包含β链SSE（二级结构元件）之间平行和反平行氢键模式的重要信息。我们发现，TOPS++FATCAT错误，罕见的，因为他们是，可以清楚地链接到过度简化的TOPS图，并可以通过更精确的二级结构元素定义的发展得到纠正。用于Linux平台的TOPS++FATCAT程序的基准分析结果和压缩存档可以从以下网站下载：TOPS++FATCAT以与序列比对相当的速度提供FATCAT准确性和对蛋白质结构变化的洞察，开辟了交互式蛋白质结构相似性搜索的可能性。
Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have managed to capture the intuitive understanding of protein structures developed in structural biology, especially in the context of rapid database searches. Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses. We developed a TOPS++FATCAT algorithm that uses an intuitive description of the proteins' structures as captured in the popular TOPS diagrams to limit the search space of the aligned fragment pairs (AFPs) in the flexible alignment of protein structures performed by the FATCAT algorithm. The TOPS++FATCAT algorithm is faster than FATCAT by more than an order of magnitude with a minimal cost in classification and alignment accuracy. For beta-rich proteins its accuracy is better than FATCAT, because the TOPS+ strings models contains important information of the parallel and anti-parallel hydrogen-bond patterns between the beta-strand SSEs (Secondary Structural Elements). We show that the TOPS++FATCAT errors, rare as they are, can be clearly linked to oversimplifications of the TOPS diagrams and can be corrected by the development of more precise secondary structure element definitions. The benchmark analysis results and the compressed archive of the TOPS++FATCAT program for Linux platform can be downloaded from the following web site: TOPS++FATCAT provides FATCAT accuracy and insights into protein structural changes at a speed comparable to sequence alignments, opening up a possibility of interactive protein structure similarity searches.
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影响因子：
14.9
作者：
Chandonia, JM;Walker, NS;Brenner, SE
通讯作者：
Brenner, SE
DOI：
10.2165/00822942-200403020-00009
发表时间：
2004-01-01
期刊：
Applied bioinformatics
影响因子：
--
作者：
Ren, Te;Veeramalai, Mallika;Gilbert, David
通讯作者：
Gilbert, David
影响因子：
5.8
作者：
Torrance, GM;Gilbert, DR;Westhead, DW
通讯作者：
Westhead, DW
DOI：
10.1073/pnas.0404383101
发表时间：
2004-08-17
影响因子：
11.1
作者：
Kolodny, R;Linial, N
通讯作者：
Linial, N
影响因子：
8
作者：
Bradley, AP
通讯作者：
Bradley, AP