메뉴 건너뛰기




Volumn 23, Issue 5, 2013, Pages 707-714

Crystallographic model validation: From diagnosis to healing

Author keywords

[No Author keywords available]

Indexed keywords

GLYCAN; LIGAND; MEMBRANE PROTEIN;

EID: 84885868627     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2013.06.004     Document Type: Review
Times cited : (13)

References (70)
  • 2
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh R.A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr 1991, A47:392-400.
    • (1991) Acta Crystallogr , vol.A47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 6
    • 0000243829 scopus 로고
    • ProCheck-a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. ProCheck-a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993, 26:283-291.
    • (1993) J Appl Crystallogr , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 7
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • Dunbrack R.L. Rotamer libraries in the 21st century. Curr Opin Struct Biol 2002, 12:431-440.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 431-440
    • Dunbrack, R.L.1
  • 8
    • 33846115011 scopus 로고    scopus 로고
    • GlycoMapsDB-a database of the accessible conformational space of glycosidic linkages
    • Frank M., Lütteke T., von der Lieth C.W. GlycoMapsDB-a database of the accessible conformational space of glycosidic linkages. Nucleic Acids Res 2007, 35:287-290.
    • (2007) Nucleic Acids Res , vol.35 , pp. 287-290
    • Frank, M.1    Lütteke, T.2    von der Lieth, C.W.3
  • 11
    • 0027542118 scopus 로고
    • Quality control of protein models-directional atomic contact analysis
    • Vriend G., Sander C. Quality control of protein models-directional atomic contact analysis. J Appl Crystallogr 1993, 26:47-60.
    • (1993) J Appl Crystallogr , vol.26 , pp. 47-60
    • Vriend, G.1    Sander, C.2
  • 14
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald I.K., Thornton N. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994, 238:777-793.
    • (1994) J Mol Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, N.2
  • 15
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
    • Hooft R.W.W., Sander C., Vriend G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins: Struct Funct Genet 1996, 26:363-376.
    • (1996) Proteins: Struct Funct Genet , vol.26 , pp. 363-376
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 16
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine-using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word J.M., Lovell S.C., Richardson J.S., Richardson D.C. Asparagine and glutamine-using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999, 285:1735-1747.
    • (1999) J Mol Biol , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 18
    • 84877785397 scopus 로고    scopus 로고
    • Doing molecular biophysics: Finding, naming, and picturing signal within complexity
    • (available on-line)
    • Richardson J.S., Richardson D.C. Doing molecular biophysics: Finding, naming, and picturing signal within complexity. Annu Rev Biophys 2013, 42:14.1-14.28. (available on-line).
    • (2013) Annu Rev Biophys , vol.42
    • Richardson, J.S.1    Richardson, D.C.2
  • 20
    • 0034013435 scopus 로고    scopus 로고
    • Validation of protein crystal structures
    • Kleywegt G.J. Validation of protein crystal structures. Acta Crystallogr 2000, D56:249-265.
    • (2000) Acta Crystallogr , vol.D56 , pp. 249-265
    • Kleywegt, G.J.1
  • 22
    • 77951938696 scopus 로고    scopus 로고
    • Xtriage and Fest-automatic assessment of X-ray data and substructure structure factor estimation
    • Zwart P.H., Grosse-Kunstleve R.W., Adams P.D. Xtriage and Fest-automatic assessment of X-ray data and substructure structure factor estimation. CCP4 Newsl 2005, 43:99-107.
    • (2005) CCP4 Newsl , vol.43 , pp. 99-107
    • Zwart, P.H.1    Grosse-Kunstleve, R.W.2    Adams, P.D.3
  • 23
    • 33644874887 scopus 로고    scopus 로고
    • Intensity statistics in twinned crystals with examples from the PDB
    • Lebedev A.A., Vagin A.A., Murshudov G.N. Intensity statistics in twinned crystals with examples from the PDB. Acta Crystallogr 2006, D62:83-95.
    • (2006) Acta Crystallogr , vol.D62 , pp. 83-95
    • Lebedev, A.A.1    Vagin, A.A.2    Murshudov, G.N.3
  • 25
    • 0001644632 scopus 로고
    • Between objectivity and subjectivity
    • Branden C.-I., Jones T.A. Between objectivity and subjectivity. Nature 1990, 343:687-689.
    • (1990) Nature , vol.343 , pp. 687-689
    • Branden, C.-I.1    Jones, T.A.2
  • 28
    • 34547763220 scopus 로고    scopus 로고
    • Crystallography: crystallographic evidence for deviating C3b structure
    • Janssen B.J.C., Read R.J., Brunger A.T., Gros P. Crystallography: crystallographic evidence for deviating C3b structure. Nature 2007, 448:E1-E3.
    • (2007) Nature , vol.448
    • Janssen, B.J.C.1    Read, R.J.2    Brunger, A.T.3    Gros, P.4
  • 29
    • 84860275453 scopus 로고    scopus 로고
    • Implementing an X-ray validation pipeline for the Protein Data Bank
    • Gore S., Velankar S., Kleywegt G.J. Implementing an X-ray validation pipeline for the Protein Data Bank. Acta Crystallogr 2012, D68:478-483.
    • (2012) Acta Crystallogr , vol.D68 , pp. 478-483
    • Gore, S.1    Velankar, S.2    Kleywegt, G.J.3
  • 30
    • 67650340716 scopus 로고    scopus 로고
    • Retraction: cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0Å resolution
    • Hanson M.A., Stevens R.C. Retraction: cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0Å resolution. Nat Struct Mol Biol 2009, 16:795.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 795
    • Hanson, M.A.1    Stevens, R.C.2
  • 32
    • 0030010605 scopus 로고    scopus 로고
    • Experimentally observed conformation-dependent geometry and hidden strain in proteins
    • Karplus P.A. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 1996, 5:1406-1420.
    • (1996) Protein Sci , vol.5 , pp. 1406-1420
    • Karplus, P.A.1
  • 36
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: a quarter of a million crystal structures and rising
    • Allen F.H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr 2002, B58:380-388.
    • (2002) Acta Crystallogr , vol.B58 , pp. 380-388
    • Allen, F.H.1
  • 38
    • 77952749131 scopus 로고    scopus 로고
    • A novel evaluation of residue and protein volumes by means of Laguerre tesselation
    • Esque J., Oguey C., de Brevern A.G. A novel evaluation of residue and protein volumes by means of Laguerre tesselation. J Chem Inf Model 2010, 50:947-960.
    • (2010) J Chem Inf Model , vol.50 , pp. 947-960
    • Esque, J.1    Oguey, C.2    de Brevern, A.G.3
  • 39
    • 58149463441 scopus 로고    scopus 로고
    • RosettaHoles-rapid assessment of protein core packing for structure prediction, refinement, design, and validation
    • Sheffler W., Baker D. RosettaHoles-rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci 2009, 18:229-239.
    • (2009) Protein Sci , vol.18 , pp. 229-239
    • Sheffler, W.1    Baker, D.2
  • 40
    • 58149464546 scopus 로고    scopus 로고
    • Sorting the chaff from the wheat at the PDB
    • Tronrud D.E., Matthews B.W. Sorting the chaff from the wheat at the PDB. Protein Sci 2009, 18:2-5.
    • (2009) Protein Sci , vol.18 , pp. 2-5
    • Tronrud, D.E.1    Matthews, B.W.2
  • 41
    • 84877773919 scopus 로고    scopus 로고
    • Influences of membrane mimetic environments on membrane protein structures
    • (available on-line)
    • Zhou H.-F., Cross T.A. Influences of membrane mimetic environments on membrane protein structures. Annu Rev Biophys 2013, 42. (available on-line).
    • (2013) Annu Rev Biophys , vol.42
    • Zhou, H.-F.1    Cross, T.A.2
  • 42
    • 38549146892 scopus 로고    scopus 로고
    • Glycoconjugate data bank: structures-an annotated glycan structure database and N-glycan primary structure verification service
    • Nakahara T., Hashimoto R., Nakagawa H., Monde K., Miura N., Nishimura S. Glycoconjugate data bank: structures-an annotated glycan structure database and N-glycan primary structure verification service. Nucleic Acids Res 2008, 36:D368-D371.
    • (2008) Nucleic Acids Res , vol.36
    • Nakahara, T.1    Hashimoto, R.2    Nakagawa, H.3    Monde, K.4    Miura, N.5    Nishimura, S.6
  • 43
    • 58849162321 scopus 로고    scopus 로고
    • Analysis and validation of carbohydrate three-dimensional structures
    • Lütteke T. Analysis and validation of carbohydrate three-dimensional structures. Acta Crystallogr 2009, D65:156-168.
    • (2009) Acta Crystallogr , vol.D65 , pp. 156-168
    • Lütteke, T.1
  • 45
    • 84875995416 scopus 로고    scopus 로고
    • Glycan fragment database: a database of PDB-based glycan 3D structures
    • Jo S., Im W. Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res 2013, 41:D470-D474.
    • (2013) Nucleic Acids Res , vol.41
    • Jo, S.1    Im, W.2
  • 47
    • 48849104435 scopus 로고    scopus 로고
    • Data mining of metal ion environments present in protein structures
    • Zheng H., Chruszcz M., Lasota P., Lebioda L., Minor W. Data mining of metal ion environments present in protein structures. J Inorg Biochem 2008, 102:1765-1776.
    • (2008) J Inorg Biochem , vol.102 , pp. 1765-1776
    • Zheng, H.1    Chruszcz, M.2    Lasota, P.3    Lebioda, L.4    Minor, W.5
  • 49
    • 0032896079 scopus 로고    scopus 로고
    • Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structure
    • van den Akker F., Hol W.G.J. Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structure. Acta Crystallogr 1999, D55:206-218.
    • (1999) Acta Crystallogr , vol.D55 , pp. 206-218
    • van den Akker, F.1    Hol, W.G.J.2
  • 51
    • 84865704697 scopus 로고    scopus 로고
    • Detection of alternative conformations by unrestrained refinement
    • Sobolev O.V., Lunin V.Y. Detection of alternative conformations by unrestrained refinement. Acta Crystallogr 2012, D68:1118-1127.
    • (2012) Acta Crystallogr , vol.D68 , pp. 1118-1127
    • Sobolev, O.V.1    Lunin, V.Y.2
  • 52
    • 77954609748 scopus 로고    scopus 로고
    • Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model
    • Ting D., Wang G., Shapovalov M., Mitra R., Jordan M.I., Dunbrack R.L. Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol 2010, 6:e1000763.
    • (2010) PLoS Comput Biol , vol.6
    • Ting, D.1    Wang, G.2    Shapovalov, M.3    Mitra, R.4    Jordan, M.I.5    Dunbrack, R.L.6
  • 53
    • 84864609682 scopus 로고    scopus 로고
    • Correlation between protein secondary structure, backbone angles, and sidechain orientations
    • Lundgren M., Niemi A.J. Correlation between protein secondary structure, backbone angles, and sidechain orientations. Physical Review 2012, E86:021904.
    • (2012) Physical Review , vol.E86 , pp. 021904
    • Lundgren, M.1    Niemi, A.J.2
  • 56
    • 32044456003 scopus 로고    scopus 로고
    • The backrub motion: how protein backbone shrugs when a sidechain dances
    • Davis I.W., Arendall W.B., Richardson J.S., Richardson D.C. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 2006, 14:265-274.
    • (2006) Structure , vol.14 , pp. 265-274
    • Davis, I.W.1    Arendall, W.B.2    Richardson, J.S.3    Richardson, D.C.4
  • 57
    • 84860284066 scopus 로고    scopus 로고
    • PDB_REDO: constructive validation, more than just looking for errors
    • Joosten R.P., Joosten K., Murshudov G.N., Perrakis A. PDB_REDO: constructive validation, more than just looking for errors. Acta Crystallogr 2012, D68:484-496.
    • (2012) Acta Crystallogr , vol.D68 , pp. 484-496
    • Joosten, R.P.1    Joosten, K.2    Murshudov, G.N.3    Perrakis, A.4
  • 59
    • 84871957573 scopus 로고    scopus 로고
    • Correcting pervasive errors in RNA crystallography through enumerative structure prediction
    • Chou F.-C., Sripakdeevong P., Dibrov S.M., Hermann T., Das R. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat Methods 2013, 10:74-76.
    • (2013) Nat Methods , vol.10 , pp. 74-76
    • Chou, F.-C.1    Sripakdeevong, P.2    Dibrov, S.M.3    Hermann, T.4    Das, R.5
  • 61
    • 77951623055 scopus 로고    scopus 로고
    • Super-resolution biomolecular crystallography with low-resolution data
    • Schroeder G.F., Levitt M., Brunger A.T. Super-resolution biomolecular crystallography with low-resolution data. Nature 2010, 464:1218-1222.
    • (2010) Nature , vol.464 , pp. 1218-1222
    • Schroeder, G.F.1    Levitt, M.2    Brunger, A.T.3
  • 64
    • 70349603852 scopus 로고    scopus 로고
    • Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    • van den Bedem H., Dhanik A., Latombe J.-C., Deacon A.M. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers. Acta Crystallogr 2009, D65:1107-1117.
    • (2009) Acta Crystallogr , vol.D65 , pp. 1107-1117
    • van den Bedem, H.1    Dhanik, A.2    Latombe, J.-C.3    Deacon, A.M.4
  • 65
    • 84863307801 scopus 로고    scopus 로고
    • Computational models of protein kinematics and dynamics: beyond simulation
    • Gipson B., Hsu D., Kavraki L.E., Latombe J.-C. Computational models of protein kinematics and dynamics: beyond simulation. Annu Rev Anal Chem 2012, 5:273-291.
    • (2012) Annu Rev Anal Chem , vol.5 , pp. 273-291
    • Gipson, B.1    Hsu, D.2    Kavraki, L.E.3    Latombe, J.-C.4
  • 66
    • 2342525085 scopus 로고    scopus 로고
    • Heterogeneity and inaccuracy in protein structures solved by protein crystallography
    • Depristo M.A., de Bakker P.I.W., Blundell T.L. Heterogeneity and inaccuracy in protein structures solved by protein crystallography. Structure 2004, 12:831-838.
    • (2004) Structure , vol.12 , pp. 831-838
    • Depristo, M.A.1    de Bakker, P.I.W.2    Blundell, T.L.3
  • 68
    • 34548387498 scopus 로고    scopus 로고
    • Ensemble refinement of protein crystal structures: validation and application
    • Levin E.J., Kondrashov D.A., Wesenberg G.E., Phillips G.N. Ensemble refinement of protein crystal structures: validation and application. Structure 2007, 15:1040-1052.
    • (2007) Structure , vol.15 , pp. 1040-1052
    • Levin, E.J.1    Kondrashov, D.A.2    Wesenberg, G.E.3    Phillips, G.N.4
  • 69
    • 0025173665 scopus 로고
    • Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics
    • Gros P., van Gunsteren W.F., Hol W.G. Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. Science 1990, 249:1149-1152.
    • (1990) Science , vol.249 , pp. 1149-1152
    • Gros, P.1    van Gunsteren, W.F.2    Hol, W.G.3
  • 70
    • 77951553486 scopus 로고    scopus 로고
    • Mapping the conformations of biological assemblies
    • 035007
    • Schwander P., Fung R., Phillips G.N., Ourmazd A. Mapping the conformations of biological assemblies. New J Phys 2010, 12:035007. (15pp.).
    • (2010) New J Phys , vol.12 , pp. 15
    • Schwander, P.1    Fung, R.2    Phillips, G.N.3    Ourmazd, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.