Desktop and Web-based Gesamt Software for Fast and Accurate Structural Queries in the PDB
Desktop and Web-based Gesamt Software for Fast and Accurate Structural Queries in the PDB
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DOI：
10.15226/2474-9257/2/2/00114
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发表时间：
2017-04
期刊：
影响因子：
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通讯作者：
E. Krissinel;V. Uski
中科院分区：
文献类型：
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作者：
E. Krissinel;V. Uski
介绍了一种新的蛋白质数据库三维快速筛选软件。该软件代表了Gesamt算法的多线程版本，在单独的出版物中进行了描述。该软件被实现为一个Qt驱动的桌面应用程序QtGesamt，在新的CCP 4网络应用程序“jsCoFE”（http：//ccp4serv6.rcharwell.ac.uk/jscofe/）中专用的“结构对齐”任务，以及一个Restful API，用于从连接到互联网的普通PC执行远程PDB搜索。该软件利用了所有现代计算平台的典型多核架构，用于在PDB中进行快速结构搜索以及在3D中进行蛋白质结构的成对和多重比对。并行化和数据缩减技术的结合使得在现代笔记本电脑上执行结构化查询成为可能，其速度以前只能从专门的Web服务器上获得。给出了QtGesamt的详细性能分析。QtGesamt和相应的Restful API可从http://ccp4serv7.rc-harwell.ac.uk/gesamt下载。
New software for fast screening of the Protein Data Bank in 3 dimensions is presented. The software represents a multi-threaded version of the Gesamt algorithm, described in a separate publication. The software is implemented as a Qt-powered desktop application QtGesamt, dedicated "Structural Alignment" task in the new CCP4 web-application "jsCoFE" (http://ccp4serv6.rcharwell.ac.uk/jscofe/), as well as a Restful API for performing remote PDB searches from ordinary PC connected to the internet. The software takes advantage of multi-core architectures, typical for all modern computational platforms, for making fast structural searches in the PDB as well as pairwise and multiple alignments of protein structures in 3d. A combination of parallelization and data reduction techniques made it possible to perform structural queries on modern laptops with speeds that were previously obtainable only from specialized web-servers. A detail performance analysis of QtGesamt is given. QtGesamt and the corresponding Restful API are available for download from http://ccp4serv7.rc-harwell.ac.uk/gesamt.