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Volumn 8, Issue 11, 2013, Pages

Maximum allowed solvent accessibilites of residues in proteins

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTALLOGRAPHY, X-RAY; PROTEIN CONFORMATION; PROTEINS; SOLVENTS;

EID: 84888331478     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080635     Document Type: Article
Times cited : (303)

References (40)
  • 1
    • 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 : 1-14.
    • (1976) J Mol Biol , pp. 1-14
    • Chothia, C.1
  • 3
  • 4
    • 1342310510 scopus 로고    scopus 로고
    • Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins
    • Moelbert S, Emberly E, Tang C (2004) Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins. Prot Sci : 752-762.
    • (2004) Prot Sci , pp. 752-762
    • Moelbert, S.1    Emberly, E.2    Tang, C.3
  • 5
    • 66149109184 scopus 로고    scopus 로고
    • Solvent accessible surface area of amino acid residues in globular proteins: Correlations of apparent transfer free engergies with experimental hydrophobicity scales
    • Shaytan AK, Shaitan KV, Khokhlov AR (2009) Solvent accessible surface area of amino acid residues in globular proteins: Correlations of apparent transfer free engergies with experimental hydrophobicity scales. Biomacromolecules 10: 1224-1237.
    • (2009) Biomacromolecules , vol.10 , pp. 1224-1237
    • Shaytan, A.K.1    Shaitan, K.V.2    Khokhlov, A.R.3
  • 6
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman N, Thorne JL, Jones DT (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445-458.
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 7
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23: 1751-1761.
    • (2006) Mol Biol Evol , vol.23 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilke, C.O.4
  • 8
    • 70349911882 scopus 로고    scopus 로고
    • Structural determinants of protein evolution are context-sensitive at the residue level
    • Franzosa EA, Xia Y (2009) Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol 26: 2387-2395.
    • (2009) Mol Biol Evol , vol.26 , pp. 2387-2395
    • Franzosa, E.A.1    Xia, Y.2
  • 9
    • 67649356943 scopus 로고    scopus 로고
    • Translationally optimal codons associate with structurally sensitive sites in proteins
    • Zhou T, Weems M, Wilke CO (2009) Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol 26: 1571-1580.
    • (2009) Mol Biol Evol , vol.26 , pp. 1571-1580
    • Zhou, T.1    Weems, M.2    Wilke, C.O.3
  • 10
    • 84867090988 scopus 로고    scopus 로고
    • Independent effects of protein core size and expression on structure-evolution relationships at the residue level
    • Franzosa EA, Xia Y (2012) Independent effects of protein core size and expression on structure-evolution relationships at the residue level. PLoS One 7: e46602.
    • (2012) PLoS One , vol.7
    • Franzosa, E.A.1    Xia, Y.2
  • 11
    • 84866021249 scopus 로고    scopus 로고
    • Modeling coding-sequence evolution within the context of residue solvent accessibility
    • Scherrer MP, Meyer AG, Wilke CO (2012) Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol Biol 12: 179.
    • (2012) BMC Evol Biol , vol.12 , pp. 179
    • Scherrer, M.P.1    Meyer, A.G.2    Wilke, C.O.3
  • 12
    • 84873445018 scopus 로고    scopus 로고
    • Integrating sequence variation and protein structure to identify sites under selection
    • Meyer AG, Wilke CO (2012) Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol.
    • (2012) Mol Biol Evol
    • Meyer, A.G.1    Wilke, C.O.2
  • 13
    • 65349140199 scopus 로고    scopus 로고
    • Solvent exposure imparts similar selective pressures across a range of yeast proteins
    • Contant GC, Stadler PF (2009) Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol 26: 1155-1161.
    • (2009) Mol Biol Evol , vol.26 , pp. 1155-1161
    • Contant, G.C.1    Stadler, P.F.2
  • 14
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost B, Sander C (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20: 216-226.
    • (1994) Proteins , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 15
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • Pollastri G, Baldi P, Fariselli P, Casadio R (2002) Prediction of coordination number and relative solvent accessibility in proteins. Proteins 47: 142-153.
    • (2002) Proteins , vol.47 , pp. 142-153
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 16
    • 1042268067 scopus 로고    scopus 로고
    • Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor
    • Kim H, Park H (2004) Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor. Proteins 54: 557-562.
    • (2004) Proteins , vol.54 , pp. 557-562
    • Kim, H.1    Park, H.2
  • 18
    • 14644440766 scopus 로고    scopus 로고
    • Prediction of protein relative solvent accessibility with a two-stage SVM approach
    • Nguyen MN, Rajapakse JC (2005) Prediction of protein relative solvent accessibility with a two-stage SVM approach. Proteins 59: 30-37.
    • (2005) Proteins , vol.59 , pp. 30-37
    • Nguyen, M.N.1    Rajapakse, J.C.2
  • 19
    • 68949213019 scopus 로고    scopus 로고
    • A generic method for assignment of reliability scores applied to solvent accessibility predictions
    • Petersen B, Nordahl Petersen T, Andersen P, Nielsen M, Lundegaard C (2009) A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol 9: 51.
    • (2009) BMC Struct Biol , vol.9 , pp. 51
    • Petersen, B.1    Nordahl Petersen, T.2    Andersen, P.3    Nielsen, M.4    Lundegaard, C.5
  • 20
    • 66149176906 scopus 로고    scopus 로고
    • Context dependent reference states of solvent accessibility derived from native protein sturctures and assessed by predictability analysis
    • Singh H, Ahmad S (2009) Context dependent reference states of solvent accessibility derived from native protein sturctures and assessed by predictability analysis. BMC Struct Biol 9: 25.
    • (2009) BMC Struct Biol , vol.9 , pp. 25
    • Singh, H.1    Ahmad, S.2
  • 21
    • 77957921373 scopus 로고    scopus 로고
    • A simple definition of structural regions in proteins and its use in analyzing interface evolution
    • Levy ED (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 403: 660-670.
    • (2010) J Mol Biol , vol.403 , pp. 660-670
    • Levy, E.D.1
  • 22
    • 33745101459 scopus 로고    scopus 로고
    • DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks
    • Cheng J, Sweredoski MJ, Baldi P (2006) DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Mining and Knowledge Discovery 13: 1-10.
    • (2006) Data Mining and Knowledge Discovery , vol.13 , pp. 1-10
    • Cheng, J.1    Sweredoski, M.J.2    Baldi, P.3
  • 23
    • 20144377620 scopus 로고    scopus 로고
    • Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    • Chen H, Zhou HX (2005) Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucl Acids Res 33: 3193-3199.
    • (2005) Nucl Acids Res , vol.33 , pp. 3193-3199
    • Chen, H.1    Zhou, H.X.2
  • 24
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang G, Dunbrack RL (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 27
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF (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
  • 28
    • 0000484499 scopus 로고
    • Hydrophobic parameters of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides
    • Fauchere JL, Pliska VE (1983) Hydrophobic parameters of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur J Med Chem 18: 369-375.
    • (1983) Eur J Med Chem , vol.18 , pp. 369-375
    • Fauchere, J.L.1    Pliska, V.E.2
  • 29
    • 33845280446 scopus 로고
    • Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
    • Radzicka A, Wolfenden R (1988) Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochem 27: 1664-1670.
    • (1988) Biochem , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 30
    • 34247626293 scopus 로고    scopus 로고
    • Partitioning of amino acid side chains into lipid bilayers: Results from computer simulations and comparison to experiment
    • MacCallum JL, Bennett WFD, Tieleman DP (2007) Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J Gen Physiol 129: 371-377.
    • (2007) J Gen Physiol , vol.129 , pp. 371-377
    • MacCallum, J.L.1    Bennett, W.F.D.2    Tieleman, D.P.3
  • 31
    • 79959928058 scopus 로고    scopus 로고
    • Side chain hydrophobicity scales derived from transmembrane protein folding into lipid bilayers
    • Moon CP, Fleming KG (2011) Side chain hydrophobicity scales derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci USA 108: 10174-10177.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 10174-10177
    • Moon, C.P.1    Fleming, K.G.2
  • 32
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
    • Wimley WC, Creamer TP, White SH (1996) Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochem 35: 5109-5124.
    • (1996) Biochem , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 33
    • 0037340834 scopus 로고    scopus 로고
    • Real-value prediction of solvent accessibility from amino acid sequence
    • Ahmad S, Gromiha MM, Sarai A (2003) Real-value prediction of solvent accessibility from amino acid sequence. Proteins 50: 629-635.
    • (2003) Proteins , vol.50 , pp. 629-635
    • Ahmad, S.1    Gromiha, M.M.2    Sarai, A.3
  • 34
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (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
  • 35
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B, Richards FM (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
  • 37
    • 0029922443 scopus 로고    scopus 로고
    • Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
    • Tomii K, Kanehisa M (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 9: 27-36.
    • (1996) Protein Eng , vol.9 , pp. 27-36
    • Tomii, K.1    Kanehisa, M.2
  • 39
    • 0000243829 scopus 로고
    • PROCHECK - A program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J App Cryst 26: 283-291.
    • (1993) J App Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 40
    • 84885098469 scopus 로고    scopus 로고
    • PeptideBuilder: A simple Python library to generate model peptides
    • Tien MZ, Sydykova DK, Meyer AG, Wilke CO (2013) PeptideBuilder: a simple Python library to generate model peptides. PeerJ 1: e80.
    • (2013) PeerJ , vol.1
    • Tien, M.Z.1    Sydykova, D.K.2    Meyer, A.G.3    Wilke, C.O.4


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