메뉴 건너뛰기




Volumn 27, Issue 6, 2009, Pages 706-711

Development of new indices to evaluate protein-protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor

Author keywords

Assembling space volume; Delaunay tessellation; Gap volume; Shape complementarity; Subunit assembly

Indexed keywords

ASSEMBLING SPACE VOLUME; DELAUNAY TESSELLATION; GAP VOLUME; SHAPE COMPLEMENTARITY; SUBUNIT ASSEMBLY;

EID: 58849118376     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2008.11.002     Document Type: Article
Times cited : (6)

References (26)
  • 1
    • 31144467558 scopus 로고    scopus 로고
    • The impact of structural genomics: expectations and outcomes
    • Chandonia J.M., and Brenner S.E. The impact of structural genomics: expectations and outcomes. Science 311 (2006) 347-351
    • (2006) Science , vol.311 , pp. 347-351
    • Chandonia, J.M.1    Brenner, S.E.2
  • 2
    • 0027772959 scopus 로고
    • Shape complementarity at protein/protein interfaces
    • Lawrence M.C., and Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234 (1993) 946-950
    • (1993) J. Mol. Biol. , vol.234 , pp. 946-950
    • Lawrence, M.C.1    Colman, P.M.2
  • 3
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly M.L. Solvent-accessible surfaces of proteins and nucleic acids. Science 221 (1983) 709-713
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 4
    • 0033980458 scopus 로고    scopus 로고
    • QSD Quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock)
    • Goldman B.B., and Wipke W.T. QSD Quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock). Proteins: Struct. Funct. Genet. 38 (2000) 79-94
    • (2000) Proteins: Struct. Funct. Genet. , vol.38 , pp. 79-94
    • Goldman, B.B.1    Wipke, W.T.2
  • 5
    • 2542557409 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
    • Tsuchiya Y., Kinoshita K., and Nakamura H. Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins: Struct. Funct. Genet. 55 (2004) 885-894
    • (2004) Proteins: Struct. Funct. Genet. , vol.55 , pp. 885-894
    • Tsuchiya, Y.1    Kinoshita, K.2    Nakamura, H.3
  • 6
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb H.A., Jackson R.M., and Sternberg M.J.E. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272 (1997) 106-120
    • (1997) J. Mol. Biol. , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 7
    • 0038185277 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • Chen R., and Wing. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins: Struct. Funct. Genet. 51 (2003) 397-408
    • (2003) Proteins: Struct. Funct. Genet. , vol.51 , pp. 397-408
    • Chen, R.1    Wing2
  • 8
    • 0028881975 scopus 로고
    • SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski R.A. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 13 (1995) 323-330
    • (1995) J. Mol. Graph. , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 9
    • 34250831648 scopus 로고    scopus 로고
    • Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites
    • Kawabata T., and Go N. Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites. Proteins: Struct. Funct. Bioinform. 68 (2007) 516-529
    • (2007) Proteins: Struct. Funct. Bioinform. , vol.68 , pp. 516-529
    • Kawabata, T.1    Go, N.2
  • 11
    • 0031736346 scopus 로고    scopus 로고
    • Novel method to detect a motif of local structures in different protein conformations
    • Wako H., and Yamato T. Novel method to detect a motif of local structures in different protein conformations. Protein Eng. 11 (1998) 981-990
    • (1998) Protein Eng. , vol.11 , pp. 981-990
    • Wako, H.1    Yamato, T.2
  • 12
    • 3142661684 scopus 로고    scopus 로고
    • A simple topological representation of protein structure: implications for new, fast, and robust structural classification
    • Bostick D.L., Shen M., and Vaisman I.I. A simple topological representation of protein structure: implications for new, fast, and robust structural classification. Proteins: Struct. Funct. Bioinform. 56 (2004) 487-501
    • (2004) Proteins: Struct. Funct. Bioinform. , vol.56 , pp. 487-501
    • Bostick, D.L.1    Shen, M.2    Vaisman, I.I.3
  • 14
    • 34047129815 scopus 로고    scopus 로고
    • A new protein-protein docking scoring function based on interface residue properties
    • Bernauer J., Azé J., Janin J., and Poupon A. A new protein-protein docking scoring function based on interface residue properties. Bioinfomatics 23 (2007) 555-562
    • (2007) Bioinfomatics , vol.23 , pp. 555-562
    • Bernauer, J.1    Azé, J.2    Janin, J.3    Poupon, A.4
  • 15
    • 23044493886 scopus 로고    scopus 로고
    • New method for protein secondary structure assignment based on a simple topological descriptor
    • Taylor T., Rivera M., Wilson G., and Vaisman I.I. New method for protein secondary structure assignment based on a simple topological descriptor. Proteins: Struct. Funct. Bioinform. 60 (2005) 513-524
    • (2005) Proteins: Struct. Funct. Bioinform. , vol.60 , pp. 513-524
    • Taylor, T.1    Rivera, M.2    Wilson, G.3    Vaisman, I.I.4
  • 17
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design
    • Liang J., Edelsbrunner H., and Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7 (1998) 1884-1897
    • (1998) Protein Sci. , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 18
    • 0000734331 scopus 로고
    • Nouvelles applications des paramètres continus à la théorie des formes quadratiques
    • Voronoi G. Nouvelles applications des paramètres continus à la théorie des formes quadratiques. Journal für die Reine und Angewandte Mathematik 133 (1907) 97-178
    • (1907) Journal für die Reine und Angewandte Mathematik , vol.133 , pp. 97-178
    • Voronoi, G.1
  • 19
    • 1842850600 scopus 로고    scopus 로고
    • Voronoi and Voronoi-related tessellations in studies of protein structure and interaction
    • Poupon A. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr. Opin. Struct. Biol. 14 (2004) 233-241
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 233-241
    • Poupon, A.1
  • 20
    • 0015222647 scopus 로고
    • The interpretation of protein structures: estimation of static accessibility
    • Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55 (1971) 379-400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 22
    • 0034308172 scopus 로고    scopus 로고
    • Discriminating between homodimeric and monomeric proteins in the crystalline state
    • Ponstingl H., Henrick K., and Thornton M. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins: Struct. Funct. Genet. 41 (2000) 47-57
    • (2000) Proteins: Struct. Funct. Genet. , vol.41 , pp. 47-57
    • Ponstingl, H.1    Henrick, K.2    Thornton, M.3
  • 24
    • 0004822706 scopus 로고
    • Structure of recombinant bovine interferon-gamma at 3.0 Å resolution
    • Samudzi C.T., and Rubin J.R. Structure of recombinant bovine interferon-gamma at 3.0 Å resolution. Acta Cryst. D 49 (1993) 513-521
    • (1993) Acta Cryst. D , vol.49 , pp. 513-521
    • Samudzi, C.T.1    Rubin, J.R.2
  • 25
    • 0022511852 scopus 로고
    • Dimeric form of diphtheria toxin: purification and characterization
    • Carroll S.F., Barbieri J.T., and Collier R.J. Dimeric form of diphtheria toxin: purification and characterization. Biochemistry 25 (1986) 2425-2430
    • (1986) Biochemistry , vol.25 , pp. 2425-2430
    • Carroll, S.F.1    Barbieri, J.T.2    Collier, R.J.3
  • 26
    • 0028103275 scopus 로고    scopus 로고
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50 (1994), 760-763.
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50 (1994), 760-763.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.