메뉴 건너뛰기




Volumn 60, Issue 1, 2005, Pages 139-147

Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?

Author keywords

Accessible surface area; Hydrogen bonds; Interresidue contacts; Structural alignment; X ray and NMR protein structures

Indexed keywords

PROTEIN;

EID: 19544370004     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20491     Document Type: Article
Times cited : (79)

References (23)
  • 1
    • 0033027208 scopus 로고    scopus 로고
    • Completeness of NOEs in protein structure: A statistical analysis of NMR
    • Doreleijers JF, Raves ML, Rullmann T, Kaptein R. Completeness of NOEs in protein structure: a statistical analysis of NMR. J Biomol NMR 1999;14:123-132.
    • (1999) J Biomol NMR , vol.14 , pp. 123-132
    • Doreleijers, J.F.1    Raves, M.L.2    Rullmann, T.3    Kaptein, R.4
  • 2
    • 0032707718 scopus 로고    scopus 로고
    • Validation of nuclear magnetic resonance structures of proteins and nucleic acids: Hydrogen geometry and nomenclature
    • Doreleijers JF, Vriend G, Raves ML, Kaptein R. Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature. Proteins Struct Funct Genet 1999;37:404-416.
    • (1999) Proteins Struct Funct Genet , vol.37 , pp. 404-416
    • Doreleijers, J.F.1    Vriend, G.2    Raves, M.L.3    Kaptein, R.4
  • 3
    • 0035427382 scopus 로고    scopus 로고
    • How to guarantee optimal stability for most representative structures in the Protein Data Bank
    • Bastolla U, Farwer J, Knapp EW, Vendruscolo M. How to guarantee optimal stability for most representative structures in the Protein Data Bank. Proteins Struct Funct Genet 2001;44:79-96.
    • (2001) Proteins Struct Funct Genet , vol.44 , pp. 79-96
    • Bastolla, U.1    Farwer, J.2    Knapp, E.W.3    Vendruscolo, M.4
  • 4
    • 0036219167 scopus 로고    scopus 로고
    • Improving the quality of protein structures derived by NMR spectroscopy
    • Spronk CA, Linge JP, Hilbers CW, Vuister GW. Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 2002;22:281-289.
    • (2002) J Biomol NMR , vol.22 , pp. 281-289
    • Spronk, C.A.1    Linge, J.P.2    Hilbers, C.W.3    Vuister, G.W.4
  • 6
    • 0027062751 scopus 로고
    • Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals
    • Billeter M. Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Q Rev Biophys 1992;25:325-377.
    • (1992) Q Rev Biophys , vol.25 , pp. 325-377
    • Billeter, M.1
  • 7
    • 0032478518 scopus 로고    scopus 로고
    • Determination of the structure of oxidized Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure
    • Davy SL, Osborne MJ, Moore GR. Determination of the structure of oxidized Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure. J Mol Biol 1998;277:683-706.
    • (1998) J Mol Biol , vol.277 , pp. 683-706
    • Davy, S.L.1    Osborne, M.J.2    Moore, G.R.3
  • 8
    • 0344096565 scopus 로고    scopus 로고
    • Validation of NMR side-chain conformations by packing calculations
    • Chung SY, Subbiah S. Validation of NMR side-chain conformations by packing calculations. Proteins Struct Funct Genet 1999;35: 184-194.
    • (1999) Proteins Struct Funct Genet , vol.35 , pp. 184-194
    • Chung, S.Y.1    Subbiah, S.2
  • 9
    • 0035207954 scopus 로고    scopus 로고
    • The X-ray structure of a recombinant major urinary protein at 1.75 Å resolution. A comparative study of X-ray and NMR-derived structures
    • Kuser PR, Franzoni L, Ferrari E, Spisni A, Polikarpov I. The X-ray structure of a recombinant major urinary protein at 1.75 Å resolution. A comparative study of X-ray and NMR-derived structures. Acta Crystallogr D 2001;57:1863-1869.
    • (2001) Acta Crystallogr D , vol.57 , pp. 1863-1869
    • Kuser, P.R.1    Franzoni, L.2    Ferrari, E.3    Spisni, A.4    Polikarpov, I.5
  • 10
    • 0028892389 scopus 로고
    • Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
    • Godzik A, Kolinski A, Skolnick J. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci 1995;4:2107-2117.
    • (1995) Protein Sci , vol.4 , pp. 2107-2117
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
  • 13
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 16
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 17
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000;16:776-785.
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4
  • 18
    • 19544385738 scopus 로고
    • Pushchino: Institute of Protein Research, Russian Academy of Sciences
    • Finkelstein AV. Program FITT for rmsd calculation. Pushchino: Institute of Protein Research, Russian Academy of Sciences; 1987.
    • (1987) Program FITT for rmsd Calculation
    • Finkelstein, A.V.1
  • 19
    • 0009171171 scopus 로고
    • A toolkit for computational molecular biology. II. On the optimal superposition of two sets of coordinates
    • Lesk AM. A toolkit for computational molecular biology. II. On the optimal superposition of two sets of coordinates. Acta Crystallogr A 1986;42:110-113.
    • (1986) Acta Crystallogr A , vol.42 , pp. 110-113
    • Lesk, A.M.1
  • 21
    • 0034595515 scopus 로고    scopus 로고
    • Protein packing: Dependence on protein size, secondary structure and amino acid composition
    • Fleming PJ, Richards FM. Protein packing: dependence on protein size, secondary structure and amino acid composition. J Mol Biol 2000;299:487-498.
    • (2000) J Mol Biol , vol.299 , pp. 487-498
    • Fleming, P.J.1    Richards, F.M.2
  • 22
    • 0037005883 scopus 로고    scopus 로고
    • The direct determination of protein structure by NMR without assignment
    • Atkinson RA, Saudek V. The direct determination of protein structure by NMR without assignment. FEBS Lett 2002;510:1-4.
    • (2002) FEBS Lett , vol.510 , pp. 1-4
    • Atkinson, R.A.1    Saudek, V.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.