메뉴 건너뛰기




Volumn 6, Issue 4, 2009, Pages 639-651

Protein structure classification based on conserved hydrophobic residues

Author keywords

Bioinformatics (genome or protein) databases; Data mining; Hydrophobicity scales; Protein folding; Structural classification; Subgraph mining

Indexed keywords

BIOINFORMATICS (GENOME OR PROTEIN) DATABASE; BIOINFORMATICS (GENOME OR PROTEIN) DATABASES; HYDROPHOBICITY SCALE; HYDROPHOBICITY SCALES; STRUCTURAL CLASSIFICATION; SUBGRAPH MINING;

EID: 75449113406     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.77     Document Type: Article
Times cited : (9)

References (23)
  • 1
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • C.S. Leslie, E. Eskin, A. Cohen, J. Weston, and W.S. Noble, "Mismatch String Kernels for Discriminative Protein Classification," Bioinformatics, vol.20, no.4, pp. 467-476, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 467-476
    • Leslie, C.S.1    Eskin, E.2    Cohen, A.3    Weston, J.4    Noble, W.S.5
  • 2
    • 29144444567 scopus 로고    scopus 로고
    • Search for folding nuclei in native protein structures
    • A. Shmygelska, "Search for Folding Nuclei in Native Protein Structures," Bioinformatics, vol.21, no.1, pp. 394-402, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.1 , pp. 394-402
    • Shmygelska, A.1
  • 3
    • 0008863560 scopus 로고
    • Factors in the interpretation of protein denaturation
    • W.Z. Kauzmann, "Factors in the Interpretation of Protein Denaturation," Advanced Protein Chemistry, vol.14, pp. 1-63, 1959.
    • (1959) Advanced Protein Chemistry , vol.14 , pp. 1-63
    • Kauzmann, W.Z.1
  • 4
    • 7244238406 scopus 로고    scopus 로고
    • Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, Pyridoxal-5′-phosphate- dependent enzymes
    • A. Paiardini, F. Bossa, and S. Pascarella, "Evolutionarily Conserved Regions and Hydrophobic Contacts at the Superfamily Level: The Case of the Fold-Type I, Pyridoxal-5′-Phosphate-Dependent Enzymes," Protein Sciences, vol.13, pp. 2992-3005, 2004.
    • (2004) Protein Sciences , vol.13 , pp. 2992-3005
    • Paiardini, A.1    Bossa, F.2    Pascarella, S.3
  • 5
    • 0035254936 scopus 로고    scopus 로고
    • Conserved Key Amino Acid Positions (CKAAPs) derived from the analysis of common substructures in proteins
    • B.V.B. Reddy, W.W. Li, I.N. Shindyalov, and P.E. Bourne, "Conserved Key Amino Acid Positions (CKAAPs) Derived from the Analysis of Common Substructures in Proteins," PROTEINS: Structure, Function, and Genetics, vol.42, pp. 148-163, 2001.
    • (2001) PROTEINS: Structure, Function, and Genetics , vol.42 , pp. 148-163
    • Reddy, B.V.B.1    Li, W.W.2    Shindyalov, I.N.3    Bourne, P.E.4
  • 6
    • 0031012563 scopus 로고    scopus 로고
    • Hydrophobic folding units derived from dissimilar monomer structures and their interactions
    • C.-J. Tsai and R. Nussinov, "Hydrophobic Folding Units Derived from Dissimilar Monomer Structures and Their Interactions," Protein Science, vol.6, no.1, pp. 24-42, 1997.
    • (1997) Protein Science , vol.6 , Issue.1 , pp. 24-42
    • Tsai, C.-J.1    Nussinov, R.2
  • 7
    • 33745698176 scopus 로고    scopus 로고
    • A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues
    • U.K. Muppirala and Z. Li, "A Simple Approach for Protein Structure Discrimination Based on the Network Pattern of Conserved Hydrophobic Residues," Protein Eng., Design, and Selection, vol.19, no.6, pp. 265-275, 2006.
    • (2006) Protein Eng., Design, and Selection , vol.19 , Issue.6 , pp. 265-275
    • Muppirala, U.K.1    Li, Z.2
  • 8
    • 0029101826 scopus 로고
    • Recognizing native folds by the arrangement of hydrophobic and polar residues
    • E.S. Huang, S. Subbiah, and M. Levitt, "Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues," J. Molecular Biology, vol.252, pp. 709-720, 1995.
    • (1995) J. Molecular Biology , vol.252 , pp. 709-720
    • Huang, E.S.1    Subbiah, S.2    Levitt, M.3
  • 9
    • 0038777517 scopus 로고    scopus 로고
    • Evaluation of methods for measuring amino acid hydrophobicities and interactions
    • K.M. Biswas, D.R. DeVido, and J.G. Dorsey, "Evaluation of Methods for Measuring Amino Acid Hydrophobicities and Interactions," J. Chromatography A, vol.1000, no.1, pp. 637-655, 2003.
    • (2003) J. Chromatography A , vol.1000 , Issue.1 , pp. 637-655
    • Biswas, K.M.1    Vido De, D.R.2    Dorsey, J.G.3
  • 10
    • 0023645034 scopus 로고
    • Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins
    • J.L. Cornette, K.B. Cease, H. Margalit, J.L. Spounge, J.A. Berzofsky, and C. DeLisi, "Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic Structures in Proteins," J. Molecular Biology, vol.195, no.3, pp. 659-685, 1987.
    • (1987) J. Molecular Biology , vol.195 , Issue.3 , pp. 659-685
    • Cornette, J.L.1    Cease, K.B.2    Margalit, H.3    Spounge, J.L.4    Berzofsky, J.A.5    De Lisi, C.6
  • 11
    • 0000154810 scopus 로고
    • Physicochemical basis of amino acid hydrophobicity scales: Evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides
    • M.C.J. Wilce, M.-I. Aguilar, and M.T. Hearn, "Physicochemical Basis of Amino Acid Hydrophobicity Scales: Evaluation of Four New Scales of Amino Acid Hydrophobicity Coefficients Derived from RP-HPLC of Peptides," Analytical Chemistry, vol.67, no.7, pp. 1210-1219, 1995.
    • (1995) Analytical Chemistry , vol.67 , Issue.7 , pp. 1210-1219
    • Wilce, M.C.J.1    Aguilar, M.-I.2    Hearn, M.T.3
  • 12
    • 29144474447 scopus 로고    scopus 로고
    • Mining coherent dense subgraphs across massive biological networks for functional discovery
    • H. Hu, X. Yan, Y. Huang, J. Han, and X.J. Zhou, "Mining Coherent Dense Subgraphs across Massive Biological Networks for Functional Discovery," Bioinformatics, vol.21, pp. i213-i221, suppl. 1, 2005
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Hu, H.1    Yan, X.2    Huang, Y.3    Han, J.4    Zhou, X.J.5
  • 13
    • 0042889108 scopus 로고    scopus 로고
    • Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
    • B. Krishnamoorthy and A. Torpsha, "Development of a Four-Body Statistical Pseudo-Potential to Discriminate Native from Non-Native Protein Conformations," Bioinformatics, vol.19, no.12, pp. 1540-1548, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1540-1548
    • Krishnamoorthy, B.1    Torpsha, A.2
  • 15
    • 0036470527 scopus 로고    scopus 로고
    • Residue packing in proteins: Uniform distribution on a coarse-grained scale
    • Z. Bagci, R.L. Jernigan, and I. Bahar, "Residue Packing in Proteins: Uniform Distribution on a Coarse-Grained Scale," J. Chemical Physics, vol.116, no.5, pp. 2269-2276, 2002.
    • (2002) J. Chemical Physics , vol.116 , Issue.5 , pp. 2269-2276
    • Bagci, Z.1    Jernigan, R.L.2    Bahar, I.3
  • 16
    • 33646338456 scopus 로고    scopus 로고
    • Graph theoretic properties of networks formed by the delaunay tessellation of protein structures
    • Apr.
    • T.J. Taylor and I.I. Vaisman, "Graph Theoretic Properties of Networks Formed by the Delaunay Tessellation of Protein Structures," Physical Rev. E, vol.73, no.4, pp. 041925-1-041925-13, Apr. 2006.
    • (2006) Physical Rev. e , vol.73 , Issue.4 , pp. 0419251-04192513
    • Taylor, T.J.1    Vaisman, I.I.2
  • 17
    • 0001790593 scopus 로고
    • Depth-first search and linear graph algorithms
    • R. Tarjan, "Depth-First Search and Linear Graph Algorithms," SIAM J. Computing, vol.1, no.2, pp. 146-160, 1972.
    • (1972) SIAM J. Computing , vol.1 , Issue.2 , pp. 146-160
    • Tarjan, R.1
  • 18
    • 32144447952 scopus 로고    scopus 로고
    • "Protein Peeling": An approach for splitting a 3D protein structure into compact fragments
    • J.-C. Gelly, A.G. de Brevern, and S. Hazout, ""Protein Peeling": An Approach for Splitting a 3D Protein Structure into Compact Fragments," Bioinformatics, vol.22, no.2, pp. 129-133, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.2 , pp. 129-133
    • Gelly, J.-C.1    Brevern De, A.G.2    Hazout, S.3
  • 19
    • 0019042107 scopus 로고
    • Prediction of the surface interior diagram of globular proteins by an empirical method
    • K. Nishikawa and T. Ooi, "Prediction of the Surface Interior Diagram of Globular Proteins by an Empirical Method," Int'l J. Peptide and Protein Research, vol.16, no.1, pp. 19-32, 1980.
    • (1980) Int'l J. Peptide and Protein Research , vol.16 , Issue.1 , pp. 19-32
    • Nishikawa, K.1    Ooi, T.2
  • 20
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • B. Lee and F.M. Richards, "The Interpretation of Protein Structures: Estimation of Static Accessibility," J. Molecular Biology, vol.55, no.3, pp. 379-400, 1971.
    • (1971) J. Molecular Biology , vol.55 , Issue.3 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 21
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Oct.
    • L. Breiman, "Random Forests," Machine Learning, vol.45, pp. 5-32, Oct. 2001.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 22
    • 34147112346 scopus 로고    scopus 로고
    • LFMPro: A tool for detecting significant local structural sites in proteins
    • A. Sacan, O. Ozturk, H. Ferhatosmanoglu, and Y. Wang, "LFMPro: A Tool for Detecting Significant Local Structural Sites in Proteins," Bioinformatics, vol.23, no.6, pp. 709-716, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 709-716
    • Sacan, A.1    Ozturk, O.2    Ferhatosmanoglu, H.3    Wang, Y.4
  • 23
    • 12944331949 scopus 로고    scopus 로고
    • Predicting protein function from structure: Unique structural features of proteases
    • E.W. Stawiski, A.E. Baucom, S.C. Lohr, and L.M. Gregoret, "Predicting Protein Function from Structure: Unique Structural Features of Proteases," Proc. Nat'l Academy of Sciences USA, vol.97, no.8, p. 3954, 2000.
    • (2000) Proc. Nat'l Academy of Sciences USA , vol.97 , Issue.8 , pp. 3954
    • Stawiski, E.W.1    Baucom, A.E.2    Lohr, S.C.3    Gregoret, L.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.