GTOP: a database of protein structures predicted from genome sequences
GTOP: a database of protein structures predicted from genome sequences
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DOI：
10.1093/nar/30.1.294
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发表时间：
2002-01-01
影响因子：
14.9
通讯作者：
Nishikawa, K
中科院分区：
文献类型：
--
作者：
Kawabata, T;Fukuchi, S;Nishikawa, K
大规模的基因组计划产生了前所未有数量的蛋白质序列，其中大多数是实验上未表征的。预测序列的三维结构为了解它们的功能提供了重要线索。我们构建了基因组TO蛋白质结构和功能（GTOP）数据库，包含大量序列的蛋白质折叠预测。预测主要是进行同源性搜索程序PSI-BLAST，目前最流行的高灵敏度的轮廓搜索方法。GTOP还包括其他分析的结果，例如同源性和基序搜索，跨膜螺旋和重复序列的检测。我们已经完成了41种生物的序列分析，蛋白质总数超过12万。GTOP使用图形查看器以“彩条”格式在一页中显示每个ORF的分析结果。指定的3D结构由Chime插件或RasMol呈现。还包括配体的结合位点，提供功能信息。GTOP服务器可在http://spock.genes.nig.ac.jp/similar togene/gtop.html上找到。
Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 3D structures of sequences provides important clues as to their functions. We constructed the Genomes TO Protein structures and functions (GTOP) database, containing protein fold predictions of a huge number of sequences. Predictions are mainly carried out with the homology search program PSI-BLAST, currently the most popular among high-sensitivity profile search methods. GTOP also includes the results of other analyses, e.g. homology and motif search, detection of transmembrane helices and repetitive sequences. We have completed analyzing the sequences of 41 organisms, with the number of proteins exceeding 120 000 in total. GTOP uses a graphical viewer to present the analytical results of each ORF in one page in a 'color-bar' format. The assigned 3D structures are presented by Chime plug-in or RasMol. The binding sites of ligands are also included, providing functional information. The GTOP server is available at http://spock.genes.nig.ac.jp/similar togenome/gtop.html.