Overview of the CCP4 suite and current developments

被引:10410
作者
Winn, Martyn D. [1 ]
Ballard, Charles C. [2 ]
Cowtan, Kevin D. [3 ]
Dodson, Eleanor J. [3 ]
Emsley, Paul [4 ]
Evans, Phil R. [5 ]
Keegan, Ronan M. [2 ]
Krissinel, Eugene B. [2 ]
Leslie, Andrew G. W. [5 ]
McCoy, Airlie [6 ]
McNicholas, Stuart J. [3 ]
Murshudov, Garib N. [3 ]
Pannu, Navraj S. [7 ]
Potterton, Elizabeth A. [3 ]
Powell, Harold R. [5 ]
Read, Randy J. [6 ]
Vagin, Alexei [3 ]
Wilson, Keith S. [3 ]
机构
[1] STFC Daresbury Lab, Warrington WA4 4AD, Cheshire, England
[2] STFC Rutherford Appleton Lab, Didcot OX11 0QX, Oxon, England
[3] Univ York, Dept Chem, York Struct Biol Lab, York YO10 5YW, N Yorkshire, England
[4] Univ Oxford, Dept Biochem, Oxford OX1 3QU, England
[5] MRC, Mol Biol Lab, Cambridge CB2 0QH, England
[6] Univ Cambridge, Dept Haematol, Cambridge Inst Med Res, Cambridge CB2 2XY, England
[7] Leiden Univ, NL-2300 RA Leiden, Netherlands
来源
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2011年 / 67卷
基金
英国惠康基金; 英国生物技术与生命科学研究理事会; 英国医学研究理事会;
关键词
MACROMOLECULAR STRUCTURES; MOLECULAR-REPLACEMENT; PHASE INFORMATION; CRYSTALLOGRAPHY; REFINEMENT; KNOWLEDGE; SOFTWARE; EXAMPLES; PROGRAM; MOLREP;
D O I
10.1107/S0907444910045749
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. After giving a brief description of the evolution of CCP4 over the last 30 years, an overview of the current suite is given. While detailed descriptions are given in the accompanying articles, here it is shown how the individual programs contribute to a complete software package.
引用
收藏
页码:235 / 242
页数:8
相关论文
共 50 条
[1]   Methods used in the structure determination of bovine mitochondrial F-1 ATPase [J].
Abrahams, JP ;
Leslie, AGW .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1996, 52 :30-42
[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]   THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY [J].
BAILEY, S .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :760-763
[4]   General quadratic functions in real and reciprocal space and their application to likelihood phasing [J].
Cowtan, K .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2000, 56 :1612-1621
[5]  
Cowtan K., 2001, INT TABLES CRYSTALLO
[6]  
Cowtan K., 2003, IUCR COMPUTING COMMI, V2, P4
[7]   Fitting molecular fragments into electron density [J].
Cowtan, Kevin .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2008, 64 :83-89
[8]   The Buccaneer software for automated model building.: 1.: Tracing protein chains [J].
Cowtan, Kevin .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2006, 62 :1002-1011
[9]   Recent developments in classical density modification [J].
Cowtan, Kevin .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 :470-478
[10]   Matrix methods for solving protein substructures of chlorine and sulfur from anomalous data [J].
de Graaff, RAG ;
Hilge, M ;
van der Plas, JL ;
Abrahams, JP .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2001, 57 :1857-1862