The Phenix software for automated determination of macromolecular structures.
The Phenix software for automated determination of macromolecular structures.
复制标题
用于自动确定大分子结构的Phenix软件。
DOI：
10.1016/j.ymeth.2011.07.005
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发表时间：
2011-09
期刊：
影响因子：
4.8
通讯作者：
Zwart, Peter H.
中科院分区：
文献类型：
--
作者：
Adams, Paul D.;Afonine, Pavel V.;Bunkoczi, Gabor;Chen, Vincent B.;Echols, Nathaniel;Headd, Jeffrey J.;Hung, Li-Wei;Jain, Swati;Kapral, Gary J.;Kunstleve, Ralf W. Grosse;McCoy, Airlie J.;Moriarty, Nigel W.;Oeffner, Robert D.;Read, Randy J.;Richardson, David C.;Richardson, Jane S.;Terwilliger, Thomas C.;Zwart, Peter H.
x射线晶体学是研究生物系统的重要工具。它能够提供信息，这是理解生命基本原理的先决条件。它也是开发人类疾病新疗法的核心方法。确定和优化许多大分子结构需要大量的时间和精力，因为需要手动解释复杂的数值数据，通常使用许多不同的软件包，并且反复使用交互式三维图形。开发了Phenix软件包，为大分子晶体结构解决方案提供了一个全面的系统，重点是自动化。这就要求开发新的算法，以最大限度地减少或消除主观输入，支持内置的专家系统知识，传统上手工执行的程序的自动化，以及允许算法之间紧密集成的计算框架的开发。自动化方法的应用特别适用于结构蛋白质组学领域，在那里需要高通量。描述了Phenix中用于实验阶段自动化的功能，包括随后的模型构建、分子替换、结构优化和验证，并给出了从命令行和图形用户界面运行Phenix的示例。
X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.
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DOI：
10.1107/s0907444910051218
发表时间：
2011-04
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Bunkóczi G;Read RJ
通讯作者：
Read RJ
DOI：
10.1107/s0907444908020039
发表时间：
2009-02
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Das, Rhiju;Baker, David
通讯作者：
Baker, David
DOI：
10.1107/s090744490200118x
发表时间：
2002-03-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Dauter, Z;Dauter, M;Dodson, E
通讯作者：
Dodson, E
DOI：
10.1107/s0907444903018043
发表时间：
2003-11-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Grosse-Kunstleve, RW;Adams, PD
通讯作者：
Adams, PD
DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K