PDB_REDO: automated re-refinement of X-ray structure models in the PDB

被引：171

作者：

Joosten, Robbie P. ^{[1
]}

Salzemann, Jean ^{[2
]}

Bloch, Vincent ^{[2
]}

Stockinger, Heinz ^{[3
]}

Berglund, Ann-Charlott ^{[4
]}

Blanchet, Christophe ^{[5
]}

Bongcam-Rudloff, Erik ^{[4
]}

Combet, Christophe ^{[5
]}

Da Costa, Ana L. ^{[2
]}

Deleage, Gilbert ^{[5
]}

Diarena, Matteo ^{[2
]}

Fabbretti, Roberto ^{[3
]}

Fettahi, Geraldine ^{[2
]}

Flegel, Volker ^{[3
]}

Gisel, Andreas ^{[6
]}

Kasam, Vinod ^{[7
]}

Kervinen, Timo ^{[8
]}

Korpelainen, Eija ^{[8
]}

Mattila, Kimmo ^{[8
]}

Pagni, Marco ^{[3
]}

Reichstadt, Matthieu ^{[2
]}

Breton, Vincent ^{[2
]}

Tickle, Ian J. ^{[9
]}

Vriend, Gert ^{[1
]}

机构：

[1] Radboud Univ Nijmegen, Ctr Mol & Biomol Informat, NCMLS, Med Ctr, NL-6525 ED Nijmegen, Netherlands

[2] Univ Blaise Pascal, CNRS, IN2P3, Phys Corpusculaire Lab, Clermont Ferrand, France

[3] Swiss Inst Bioinformat, Vital IT Grp, Lausanne, Switzerland

[4] Uppsala Univ, SLV, Uppsala, Sweden

[5] Univ Lyon 1, IBCP, CNRS, IFR Biosci Lyon Gerland 128, F-69365 Lyon, France

[6] CNR, Inst Biomed Technol Bari, I-70126 Bari, Italy

[7] Fraunhofer Inst Algorithms & Sci Comp, St Augustin, Germany

[8] Finnish IT Ctr Sci, CSC, Espoo, Finland

[9] Astex Therapeut Ltd, Cambridge, England

来源：

JOURNAL OF APPLIED CRYSTALLOGRAPHY | 2009年 / 42卷

关键词：

PROTEIN DATA-BANK; PARAMETERS; DATABASE; ARCHIVE; VALUES; ENERGY; BOND;

D O I：

10.1107/S0021889809008784

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

引用

页码：376 / 384

页数：9

共 44 条

[1]

ADAMS P, 2009, PERSONAL COMMUN

[2]

[Anonymous], [No title captured]

[3]

BEERNINK P, 2009, IN PREPARATION

[4] Announcing the worldwide Protein Data Bank [J].

Berman, H ;

Henrick, K ;

Nakamura, H .

NATURE STRUCTURAL BIOLOGY, 2003, 10 (12) :980-980

[5] The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data [J].

Berman, Helen ;

Henrick, Kim ;

Nakamura, Haruki ;

Markley, John L. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D301-D303

[6] Bayesian statistical viewpoint on structure determination: Basic concepts and examples [J].

Bricogne, G .

MACROMOLECULAR CRYSTALLOGRAPHY, PT A, 1997, 276 :361-423

[7] FREE R-VALUE - A NOVEL STATISTICAL QUANTITY FOR ASSESSING THE ACCURACY OF CRYSTAL-STRUCTURES [J].

BRUNGER, AT .

NATURE, 1992, 355 (6359) :472-475

[8] Structure of MsbA from E. coli:: A homolog of the multidrug resistance ATP binding cassette (ABC) transporters (Retraction of vol 293, pg 1793, 2001) [J].

Chang, Geoffrey ;

Roth, Christopher B. ;

Reyes, Christopher L. ;

Pornillos, Owen ;

Chen, Yen-Ju ;

Chen, Andy P. .

SCIENCE, 2006, 314 (5807) :1875-1875

[9] ACCURATE BOND AND ANGLE PARAMETERS FOR X-RAY PROTEIN-STRUCTURE REFINEMENT [J].

ENGH, RA ;

HUBER, R .

ACTA CRYSTALLOGRAPHICA SECTION A, 1991, 47 :392-400

[10] TREATMENT OF NEGATIVE INTENSITY OBSERVATIONS [J].

FRENCH, S ;

WILSON, K .

ACTA CRYSTALLOGRAPHICA SECTION A, 1978, 34 (JUL) :517-525

← 1 2 3 4 5 →