The Phenix software for automated determination of macromolecular structures

被引：714

作者：

Adams, Paul D. ^{[1
,2
]}

Afonine, Pavel V. ^{[1
]}

Bunkoczi, Gabor ^{[3
]}

Chen, Vincent B. ^{[4
]}

Echols, Nathaniel ^{[1
]}

Headd, Jeffrey J. ^{[1
]}

Hung, Li-Wei ^{[5
]}

Jain, Swati ^{[4
]}

Kapral, Gary J. ^{[4
]}

Kunstleve, Ralf W. Grosse ^{[1
]}

McCoy, Airlie J. ^{[3
]}

Moriarty, Nigel W. ^{[1
]}

Oeffner, Robert D. ^{[3
]}

Read, Randy J. ^{[3
]}

Richardson, David C. ^{[4
]}

Richardson, Jane S. ^{[4
]}

Terwilliger, Thomas C. ^{[5
]}

Zwart, Peter H. ^{[1
]}

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA

[3] Univ Cambridge, Dept Haematol, Cambridge Inst Med Res, Cambridge CB2 0XY, England

[4] Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA

[5] Los Alamos Natl Lab, Los Alamos, NM 87545 USA

来源：

METHODS | 2011年 / 55卷 / 01期

基金：

英国惠康基金;

关键词：

Macromolecular crystallography; Automation; Phenix; X-ray; Diffraction; Python; MOLECULAR-REPLACEMENT; DENSITY MODIFICATION; MAXIMUM-LIKELIHOOD; PROTEIN-STRUCTURE; CRYSTAL-STRUCTURE; STRUCTURE VALIDATION; MODEL; REFINEMENT; CRYSTALLOGRAPHY; RESOLUTION;

D O I：

10.1016/j.ymeth.2011.07.005

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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 favor 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. (C) 2011 Elsevier Inc. All rights reserved.

引用

页码：94 / 106

页数：13

共 76 条

[1]

Abrahams D., 2003, C/C++ Users Journal, V21, P29

[2]

PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].

Adams, Paul D. ;

Afonine, Pavel V. ;

Bunkoczi, Gabor ;

Chen, Vincent B. ;

Davis, Ian W. ;

Echols, Nathaniel ;

Headd, Jeffrey J. ;

Hung, Li-Wei ;

Kapral, Gary J. ;

Grosse-Kunstleve, Ralf W. ;

McCoy, Airlie J. ;

Moriarty, Nigel W. ;

Oeffner, Robert ;

Read, Randy J. ;

Richardson, David C. ;

Richardson, Jane S. ;

Terwilliger, Thomas C. ;

Zwart, Peter H. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221

[3]

Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement [J].

Adams, PD ;

Pannu, NS ;

Read, RJ ;

Brunger, AT .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1999, 55 :181-190

[4]

Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement [J].

Adams, PD ;

Pannu, NS ;

Read, RJ ;

Brunger, AT .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (10) :5018-5023

[5]

Automatic multiple-zone rigid-body refinement with a large convergence radius [J].

Afonine, Pavel V. ;

Grosse-Kunstleve, Ralf W. ;

Urzhumtsev, Alexandre ;

Adams, Paul D. .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2009, 42 :607-615

[6]

A robust bulk-solvent correction and anisotropic scaling procedure [J].

Afonine, PV ;

Grosse-Kunstleve, RW ;

Adams, PD .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2005, 61 :850-855

[7]

NEW LEAST-SQUARES REFINEMENT TECHNIQUE BASED ON FAST FOURIER-TRANSFORM ALGORITHM [J].

AGARWAL, RC .

ACTA CRYSTALLOGRAPHICA SECTION A, 1978, 34 (SEP) :791-809

[8]

SYSTEMATIC ANALYSIS OF STRUCTURAL DATA AS A RESEARCH TECHNIQUE IN ORGANIC-CHEMISTRY [J].

ALLEN, FH ;

KENNARD, O ;

TAYLOR, R .

ACCOUNTS OF CHEMICAL RESEARCH, 1983, 16 (05) :146-153

[9]

[Anonymous], METHOD ENZYMOL

[10]

Arendall W. Bryan III, 2005, Journal of Structural and Functional Genomics, V6, P1, DOI 10.1007/s10969-005-3138-4

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