메뉴 건너뛰기




Volumn 84, Issue 4, 2003, Pages 2553-2561

Atom depth as a descriptor of the protein interior

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN; PROTEIN; SOLVENT;

EID: 0037382258     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75060-7     Document Type: Article
Times cited : (53)

References (30)
  • 1
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • Blom, N., S. Gammeltoft, and S. Brunak. 1999. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294:1351-1362.
    • (1999) J. Mol. Biol. , vol.294 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 2
    • 0026697940 scopus 로고
    • Mechanistic studies on rhodopsin kinase. Light-dependent phosphorylation of C-terminal peptides of rhodopsin
    • Brown, N. G., C. Fowles, R. Sharma, and M. Akhtar. 1992. Mechanistic studies on rhodopsin kinase. Light-dependent phosphorylation of C-terminal peptides of rhodopsin. Eur. J. Biochem. 208:659-667.
    • (1992) Eur. J. Biochem. , vol.208 , pp. 659-667
    • Brown, N.G.1    Fowles, C.2    Sharma, R.3    Akhtar, M.4
  • 3
    • 0036304230 scopus 로고    scopus 로고
    • Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison
    • Carugo, O., and S. Pongor. 2002. Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. J. Mol. Biol. 315:887-898.
    • (2002) J. Mol. Biol. , vol.315 , pp. 887-898
    • Carugo, O.1    Pongor, S.2
  • 4
    • 0026539511 scopus 로고
    • Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds
    • Casari, G., and M. J. Sippl. 1992. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J. Mol. Biol. 224:725-732.
    • (1992) J. Mol. Biol. , vol.224 , pp. 725-732
    • Casari, G.1    Sippl, M.J.2
  • 5
    • 0033565815 scopus 로고    scopus 로고
    • Residue depth: A novel parameter for the analysis of protein structure and stability
    • Chakravarty, S., and R. Varadarajan. 1999. Residue depth: a novel parameter for the analysis of protein structure and stability. Struct. Fold. Des. 7:723-732.
    • (1999) Struct. Fold. Des. , vol.7 , pp. 723-732
    • Chakravarty, S.1    Varadarajan, R.2
  • 6
    • 0017187836 scopus 로고
    • The nature of the accessible and buried surfaces in proteins
    • Chothia, C. 1976. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105:1-12.
    • (1976) J. Mol. Biol. , vol.105 , pp. 1-12
    • Chothia, C.1
  • 7
    • 0021691817 scopus 로고
    • Analysis of membrane and surface protein sequences with the hydrophobic moment plot
    • Eisenberg, D., E. Schwarz, M. Komaromy, and R. Wall. 1984. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179:125-142.
    • (1984) J. Mol. Biol. , vol.179 , pp. 125-142
    • Eisenberg, D.1    Schwarz, E.2    Komaromy, M.3    Wall, R.4
  • 8
    • 0034595515 scopus 로고    scopus 로고
    • Protein packing: Dependence on protein size, secondary structure and amino acid composition
    • Fleming, P. J., and F. M. Richards. 2000. Protein packing: dependence on protein size, secondary structure and amino acid composition. J. Mol. Biol. 299:487-498.
    • (2000) J. Mol. Biol. , vol.299 , pp. 487-498
    • Fleming, P.J.1    Richards, F.M.2
  • 9
    • 0031057146 scopus 로고    scopus 로고
    • Autophosphorylation-inactivation site of hexokinase 2 in Saccharomyces cerevisiae
    • Heidrich, K., A. Otto, J. Behlke, J. Rush, K. W. Wenzel, and T. Kriegel. 1997. Autophosphorylation-inactivation site of hexokinase 2 in Saccharomyces cerevisiae. Biochemistry. 36:1960-1964.
    • (1997) Biochemistry , vol.36 , pp. 1960-1964
    • Heidrich, K.1    Otto, A.2    Behlke, J.3    Rush, J.4    Wenzel, K.W.5    Kriegel, T.6
  • 10
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm, U., and C. Sander. 1994. Enlarged representative set of protein structures. Protein Sci. 3:522-524.
    • (1994) Protein Sci. , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 11
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L., and C. Sander. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 12
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm, L., and C. Sander. 1996. Mapping the protein universe. Science. 273:595-603.
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 13
    • 0004180464 scopus 로고
    • Department of Biochemistry and Molecular Biology, University College, London
    • Hubbard, S. J., and J. M. Thornton. 1993. Naccess Version 2.1.1. Department of Biochemistry and Molecular Biology, University College, London.
    • (1993) Naccess Version 2.1.1
    • Hubbard, S.J.1    Thornton, J.M.2
  • 14
    • 0034717183 scopus 로고    scopus 로고
    • Structure and function of a human TAFII250 double bromodomain module
    • Jacobson, R. H., A. G. Ladurner, D. S. King, and R. Tjian. 2000. Structure and function of a human TAFII250 double bromodomain module. Science. 288:1422-1425.
    • (2000) Science , vol.288 , pp. 1422-1425
    • Jacobson, R.H.1    Ladurner, A.G.2    King, D.S.3    Tjian, R.4
  • 15
    • 0018784438 scopus 로고
    • Surface and inside volumes in globular proteins
    • Janin, J. 1979. Surface and inside volumes in globular proteins. Nature. 277:491-492.
    • (1979) Nature , vol.277 , pp. 491-492
    • Janin, J.1
  • 16
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 17
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J., and R. F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 18
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 19
    • 0036127198 scopus 로고    scopus 로고
    • Mass spectrometric analysis of the kinetics of in vivo rhodopsin phosphorylation
    • Lee, K. A., K. B. Craven, G. A. Niemi, and J. B. Hurley. 2002. Mass spectrometric analysis of the kinetics of in vivo rhodopsin phosphorylation. Protein Sci. 11:862-874.
    • (2002) Protein Sci. , vol.11 , pp. 862-874
    • Lee, K.A.1    Craven, K.B.2    Niemi, G.A.3    Hurley, J.B.4
  • 21
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
    • Mirny, L. A., and E. I. Shakhnovich. 1999. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291:177-196.
    • (1999) J. Mol. Biol. , vol.291 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 23
    • 0029411262 scopus 로고
    • Occluded molecular surface: Analysis of protein packing
    • Pattabiraman, N., K. B. Ward, and P. J. Fleming. 1995. Occluded molecular surface: analysis of protein packing. J. Mol. Recognit. 8:334-344.
    • (1995) J. Mol. Recognit. , vol.8 , pp. 334-344
    • Pattabiraman, N.1    Ward, K.B.2    Fleming, P.J.3
  • 25
    • 0036328545 scopus 로고    scopus 로고
    • CX, an algorithm that identifies protruding atoms in proteins
    • Pintar, A., O. Carugo, and S. Pongor. 2002. CX, an algorithm that identifies protruding atoms in proteins. Bioinformatics. 18:980-984.
    • (2002) Bioinformatics , vol.18 , pp. 980-984
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 26
    • 0037316590 scopus 로고    scopus 로고
    • DPX: For the analysis of the protein core
    • Pintar, A., O. Carugo, and S. Pongor. 2003. DPX: for the analysis of the protein core. Bioinformatics. 19:313-314.
    • (2003) Bioinformatics , vol.19 , pp. 313-314
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 27
    • 0021112868 scopus 로고
    • Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure
    • Sweet, R. M., and D. Eisenberg. 1983. Correlation of sequence hydrophobicities measures similarity in three- dimensional protein structure. J. Mol. Biol. 171:479-488.
    • (1983) J. Mol. Biol. , vol.171 , pp. 479-488
    • Sweet, R.M.1    Eisenberg, D.2
  • 28
  • 29
    • 0033753811 scopus 로고    scopus 로고
    • Domain size distributions can predict domain boundaries
    • Wheelan, S. J., A. Marchler-Bauer, and S. H. Bryant. 2000. Domain size distributions can predict domain boundaries. Bioinformatics. 16:613-618.
    • (2000) Bioinformatics , vol.16 , pp. 613-618
    • Wheelan, S.J.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 30
    • 0031932170 scopus 로고    scopus 로고
    • Favorable domain size in proteins
    • Xu, D., and R. Nussinov. 1998. Favorable domain size in proteins. Fold. Des. 3:11-17.
    • (1998) Fold. Des. , vol.3 , pp. 11-17
    • Xu, D.1    Nussinov, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.