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Volumn 27, Issue 24, 2011, Pages 3392-3398

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN;

EID: 83355177227     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr590     Document Type: Article
Times cited : (87)

References (27)
  • 1
    • 76449098262 scopus 로고    scopus 로고
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution
    • Adams, P.D. et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr., 66, 213-221.
    • (2010) Acta Crystallogr. D. Biol. Crystallogr. , vol.66 , pp. 213-221
    • Adams, P.D.1
  • 2
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
    • Berman, H. et al. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
    • (2007) Nucleic Acids Res. , vol.35
    • Berman, H.1
  • 3
    • 0017411710 scopus 로고
    • The Protein Data Bank: a computer-based archival file for macromolecular structures
    • Bernstein, F.C. et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
    • (1977) J. Mol. Biol. , vol.112 , pp. 535-542
    • Bernstein, F.C.1
  • 4
    • 16644377724 scopus 로고    scopus 로고
    • Towards complete validated models in the next generation of ARP/wARP
    • Cohen, S.X. et al. (2004) Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr. D. Biol. Crystallogr., 60, 2222-2229.
    • (2004) Acta Crystallogr. D. Biol. Crystallogr. , vol.60 , pp. 2222-2229
    • Cohen, S.X.1
  • 5
    • 28544438059 scopus 로고    scopus 로고
    • The Clipper C++ libraries for x-ray crystallography
    • Cowtan, K. (2003) The Clipper C++ libraries for x-ray crystallography, IUCr Comput. Comission Newsl. 2, 4-9.
    • (2003) IUCr Comput. Comission Newsl. , vol.2 , pp. 4-9
    • Cowtan, K.1
  • 6
    • 33748337934 scopus 로고    scopus 로고
    • The Buccaneer software for automated model building. 1. Tracing protein chains
    • Cowtan, K. (2006) The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D. Biol. Crystallogr., 62, 1002-1011.
    • (2006) Acta Crystallogr. D. Biol. Crystallogr. , vol.62 , pp. 1002-1011
    • Cowtan, K.1
  • 7
    • 34547592557 scopus 로고    scopus 로고
    • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    • Davis, I.W. et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res., 35, W375-W383.
    • (2007) Nucleic Acids Res. , vol.35
    • Davis, I.W.1
  • 9
    • 60849104394 scopus 로고    scopus 로고
    • Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place
    • Headd, J.J. et al. (2009) Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. J. Struct. Funct. Genomics, 10, 83-93.
    • (2009) J. Struct. Funct. Genomics , vol.10 , pp. 83-93
    • Headd, J.J.1
  • 10
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
    • Hooft, R.W. et al. (1996a) Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins, 26, 363-376.
    • (1996) Proteins , vol.26 , pp. 363-376
    • Hooft, R.W.1
  • 11
    • 0344186399 scopus 로고    scopus 로고
    • Errors in protein structures
    • Hooft, R.W. et al. (1996b) Errors in protein structures. Nature, 381, 272.
    • (1996) Nature , vol.381 , pp. 272
    • Hooft, R.W.1
  • 12
    • 0030870075 scopus 로고    scopus 로고
    • Objectively judging the quality of a protein structure from a Ramachandran plot
    • Hooft, R.W. et al. (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Appl. Biosci., 13, 425-430.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 425-430
    • Hooft, R.W.1
  • 13
    • 84889120137 scopus 로고
    • Improved methods for the building of protein models in electron density maps and the location of errors in these models
    • Jones, T.A. et al. (1991) Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallographica. Section A, 47, 110-119.
    • (1991) Acta Crystallographica. Section A , vol.47 , pp. 110-119
    • Jones, T.A.1
  • 14
    • 41949122355 scopus 로고    scopus 로고
    • A knowledge-driven approach for crystallographic protein model completion
    • Joosten, K. et al. (2008) A knowledge-driven approach for crystallographic protein model completion. Acta Crystallogr. D. Biol. Crystallogr., 64, 416-424.
    • (2008) Acta Crystallogr. D. Biol. Crystallogr. , vol.64 , pp. 416-424
    • Joosten, K.1
  • 15
    • 66249103704 scopus 로고    scopus 로고
    • PDB_REDO: automated re-refinement of X-ray structure models in the PDB
    • Joosten, R.P. et al. (2009) PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J. Appl. Crystallogr., 42, 376-384.
    • (2009) J. Appl. Crystallogr. , vol.42 , pp. 376-384
    • Joosten, R.P.1
  • 19
    • 50249136103 scopus 로고    scopus 로고
    • Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
    • Langer, G. et al. (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc., 3, 1171-1179.
    • (2008) Nat. Protoc. , vol.3 , pp. 1171-1179
    • Langer, G.1
  • 20
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski, R.A. et al. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291.
    • (1993) J. Appl. Cryst. , vol.26 , pp. 283-291
    • Laskowski, R.A.1
  • 21
    • 0034663722 scopus 로고    scopus 로고
    • The penultimate rotamer library
    • Lovell, S.C. et al. (2000) The penultimate rotamer library. Proteins, 40, 389-408.
    • (2000) Proteins , vol.40 , pp. 389-408
    • Lovell, S.C.1
  • 22
    • 13244253766 scopus 로고    scopus 로고
    • pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files
    • Lutteke, T. and von der Lieth, C.W. (2004) pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinformatics, 5, 69.
    • (2004) BMC Bioinformatics , vol.5 , pp. 69
    • Lutteke, T.1    von der Lieth, C.W.2
  • 23
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G.N. et al. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D. Biol. Crystallogr., 53, 240-255.
    • (1997) Acta Crystallogr. D. Biol. Crystallogr. , vol.53 , pp. 240-255
    • Murshudov, G.N.1
  • 24
    • 77957687159 scopus 로고    scopus 로고
    • Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists
    • Peng, Y.H. et al. (2010) Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists. ChemMedChem, 5, 1707-1716.
    • (2010) Chem Med Chem , vol.5 , pp. 1707-1716
    • Peng, Y.H.1
  • 25
    • 0037237545 scopus 로고    scopus 로고
    • Automated main-chain model building by template matching and iterative fragment extension
    • Terwilliger, T.C. (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D. Biol. Crystallogr., 59, 38-44.
    • (2003) Acta Crystallogr. D. Biol. Crystallogr. , vol.59 , pp. 38-44
    • Terwilliger, T.C.1
  • 26
    • 0017087147 scopus 로고
    • The structure of Paracoccus denitrificans cytochrome c550
    • Timkovich, R. and Dickerson, R.E. (1976) The structure of Paracoccus denitrificans cytochrome c550. J. Biol. Chem., 251, 4033-4046.
    • (1976) J. Biol. Chem. , vol.251 , pp. 4033-4046
    • Timkovich, R.1    Dickerson, R.E.2
  • 27
    • 0013461295 scopus 로고    scopus 로고
    • Macromolecular TLS refinement in REFMAC at moderate resolutions
    • Winn, M.D. et al. (2003) Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol., 374, 300-321.
    • (2003) Methods Enzymol. , vol.374 , pp. 300-321
    • Winn, M.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.