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

The majority of previously deposited X-ray structures can be improved by applying current refinement methods.

[1]  S. French,et al.  On the treatment of negative intensity observations , 1978 .

[2]  Martin Hofmann-Apitius,et al.  Virtual screening on large scale grids , 2007, Parallel Comput..

[3]  Marian Bubak,et al.  2nd IEEE International Conference on e-Science and Grid Computing , 2006 .

[4]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

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

[6]  Haruki Nakamura,et al.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..

[7]  P. Bryan,et al.  Large increases in general stability for subtilisin BPN' through incremental changes in the free energy of unfolding. , 1989, Biochemistry.

[8]  G. Sheldrick.  Phase annealing in SHELX-90: direct methods for larger structures , 1990 .

[9]  Janet M. Thornton,et al.  PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids , 2004, Nucleic Acids Res..

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

[11]  David W. Smith,et al.  Macromolecular Crystallography conventional and high-throughput methods , 2007 .

[12]  Gert Vriend,et al.  Making optimal use of empirical energy functions: Force‐field parameterization in crystal space , 2004, Proteins.

[13]  Gerard J Kleywegt,et al.  Homo crystallographicus--quo vadis? , 2002, Structure.

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

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

[16]  V. Rich.  Personal communication , 1989, Nature.

[17]  Clifford A Goudey,et al.  Aquaculture in Offshore Zones , 2006, Science.

[18]  A. Brunger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[19]  Chandra S Verma,et al.  Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin. , 2002, Biochemistry.

[20]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[21]  Miron Livny,et al.  RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank , 2005, Proteins.

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

[23]  Tim Salditt,et al.  Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments. , 2007, Biophysical journal.

[24]  Abstracts: Annual Meeting , 1984, Pediatric Research.

[25]  Markus Wagener,et al.  A flexible approach to induced fit docking. , 2007, Journal of medicinal chemistry.

[26]  Mark R. Sanderson,et al.  Macromolecular crystallography : conventional and high-throughput methods , 2007 .

[27]  BMC Bioinformatics , 2005 .

[28]  Alexander Tomasz,et al.  Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. , 2002, Structure.

[29]  G. Bricogne.  [23] Bayesian statistical viewpoint on structure determination: Basic concepts and examples. , 1997, Methods in enzymology.

[30]  Alexandre M J J Bonvin,et al.  DRESS: a database of REfined solution NMR structures , 2004, Proteins.

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