Towards complete validated models in the next generation of ARP/wARP

被引:146
作者
Cohen, SX
Morris, RJ
Fernandez, FJ
Ben Jelloul, M
Kakaris, M
Parthasarathy, V
Lamzin, VS
Kleywegt, GJ
Perrakis, A
机构
[1] Netherlands Canc Inst, Dept Mol Carcinogenesis, NL-1066 CX Amsterdam, Netherlands
[2] EMBL, European Bioinformat Inst, Hinxton CB10 1SD, England
[3] DESY, European Mol Biol Lab, D-22603 Hamburg, Germany
[4] Uppsala Univ, Biomed Ctr, Dept Cell & Mol Biol, SE-75124 Uppsala, Sweden
来源
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2004年 / 60卷
关键词
D O I
10.1107/S0907444904027556
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The design of a new versatile control system that will underlie future releases of the automated model-building package ARP/wARP is presented. A sophisticated expert system is under development that will transform ARP/wARP from a very useful model-building aid to a truly automated package capable of delivering complete, well refined and validated models comparable in quality to the result of intensive manual checking, rebuilding, hypothesis testing, refinement and validation cycles of an experienced crystallographer. In addition to the presentation of this control system, recent advances, ideas and future plans for improving the current model-building algorithms, especially for completing partially built models, are presented. Furthermore, a concept for integrating validation routines into the iterative model-building process is also presented.
引用
收藏
页码:2222 / 2229
页数:8
相关论文
共 30 条
  • [1] An evaluation of automated model-building procedures for protein crystallography
    Badger, J
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2003, 59 : 823 - 827
  • [2] Modified phased translation functions and their application to molecular-fragment location
    Cowtan, K
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 : 750 - 756
  • [3] Determining protein structure from electron-density maps using pattern matching
    Holton, T
    Ioerger, TR
    Christopher, JA
    Sacchettini, JC
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2000, 56 : 722 - 734
  • [4] Ioerger T R, 1999, Proc Int Conf Intell Syst Mol Biol, P130
  • [5] Automatic modeling of protein backbones in electron-density maps via prediction of Cα coordinates
    Ioerger, TR
    Sacchettini, JC
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2002, 58 : 2043 - 2054
  • [6] CRYSTALLOGRAPHIC REFINEMENT OF MACROMOLECULES HAVING NON-CRYSTALLOGRAPHIC SYMMETRY
    JONES, TA
    LILJAS, L
    [J]. ACTA CRYSTALLOGRAPHICA SECTION A, 1984, 40 (JAN): : 50 - 57
  • [7] IMPROVED METHODS FOR BUILDING PROTEIN MODELS IN ELECTRON-DENSITY MAPS AND THE LOCATION OF ERRORS IN THESE MODELS
    JONES, TA
    ZOU, JY
    COWAN, SW
    KJELDGAARD, M
    [J]. ACTA CRYSTALLOGRAPHICA SECTION A, 1991, 47 : 110 - 119
  • [8] Template convolution to enhance or detect structural features in macromolecular electron-density maps
    Kleywegt, GJ
    Jones, TA
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 1997, 53 : 179 - 185
  • [9] Validation of protein crystal structures
    Kleywegt, GJ
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2000, 56 : 249 - 265
  • [10] The Uppsala Electron-Density Server
    Kleywegt, GJ
    Harris, MR
    Zou, JY
    Taylor, TC
    Wählby, A
    Jones, TA
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2004, 60 : 2240 - 2249