Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank.

The RCSB Protein Data Bank (PDB) has a number of options for deposition of structural data and has developed software tools to facilitate the process. In addition to ADIT and the PDB Validation Suite, a new software application, pdb_extract, has been designed to promote automatic data deposition of structures solved by X-ray diffraction. The pdb_extract software can extract information about data reduction, phasing, molecular replacement, density modification and refinement from the output files produced by many X-ray crystallographic applications. The options, procedures and tools for accurate and automated PDB data deposition are described here.

[1]  D E Tronrud,et al.  TNT refinement package. , 1997, Methods in enzymology.

[2]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[3]  R. Huber,et al.  Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .

[4]  G. Bricogne,et al.  [27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. , 1997, Methods in enzymology.

[5]  W Furey,et al.  PHASES-95: a program package for processing and analyzing diffraction data from macromolecules. , 1997, Methods in enzymology.

[6]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[7]  J. Davenport.  Editor , 1960 .

[8]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[9]  W. Hendrickson.  Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. , 1991, Science.

[10]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[11]  Ian W. Davis,et al.  Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.

[12]  G. Sheldrick,et al.  SHELXL: high-resolution refinement. , 1997, Methods in enzymology.

[13]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[14]  H. Berman,et al.  Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents , 1996 .

[15]  Philip E. Bourne,et al.  [30] Macromolecular crystallographic information file , 1997 .

[16]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[17]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[18]  Robert H. Blessing,et al.  Towards automated protein structure determination: BnP, the SnB-PHASES interface , 2002 .

[19]  A. Sali,et al.  Structural genomics: beyond the Human Genome Project , 1999, Nature Genetics.

[20]  A. R. Srinivasan,et al.  Geometric parameters in nucleic acids: Nitrogenous bases , 1996 .

[21]  Zukang Feng,et al.  Validation of protein structures for protein data bank. , 2003, Methods in enzymology.

[22]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[23]  C. Sander,et al.  Errors in protein structures , 1996, Nature.