CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
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DOI：
10.1371/journal.pcbi.1002708
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发表时间：
2012
影响因子：
4.3
通讯作者：
Damborsky J
中科院分区：
文献类型：
--
作者：
Chovancova E;Pavelka A;Benes P;Strnad O;Brezovsky J;Kozlikova B;Gora A;Sustr V;Klvana M;Medek P;Biedermannova L;Sochor J;Damborsky J
隧道和通道促进各种蛋白质中小分子、离子和水溶剂的运输。单个转运途径的特征，包括它们的几何形状、物理化学性质和动力学，有助于理解这些蛋白质的结构-功能关系，用于设计新的抑制剂和构建改进的生物催化剂。CAVER是一种软件工具，广泛用于静态大分子结构中转运途径的识别和表征。在这里，我们提出了一个新版本的CAVER，使自动分析隧道和通道的蛋白质构象的大合奏。CAVER 3.0实现了用于路径计算和聚类的新算法。来自分子动力学模拟的轨迹作为典型的输入，而输出中提供了各个途径的时间演变的详细特征和汇总统计。为了说明CAVER 3.0的功能，该工具被应用于微生物酶卤代烷脱卤酶DhaA的分子动力学模拟分析。CAVER 3.0安全地识别并可靠地估计了所有先前发表的DhaA隧道的重要性，包括DhaA晶体结构中封闭的隧道。得到的结果清楚地表明，分子动力学模拟分析是必不可少的通道特性的估计和阐明的结构基础的隧道门控。CAVER 3.0为研究分子转运、分子识别和酶催化领域的重要生物化学现象铺平了道路。该软件作为多平台命令行应用程序在http://www.caver.cz上免费提供。
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.
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影响因子：
56.9
作者：
Doyle, DA;Cabral, JM;MacKinnon, R
通讯作者：
MacKinnon, R
影响因子：
2.7
作者：
Barber, CB;Dobkin, DP;Huhdanpaa, H
通讯作者：
Huhdanpaa, H
影响因子：
3.8
作者：
Fishman, A;Tao, Y;Wood, TK
通讯作者：
Wood, TK
影响因子：
3.4
作者：
Coleman, Ryan G.;Sharp, Kim A.
通讯作者：
Sharp, Kim A.
影响因子：
2.9
作者：
Huang, XY;Raushel, FM
通讯作者：
Raushel, FM