메뉴 건너뛰기




Volumn 23, Issue 23, 2007, Pages 3139-3146

Moment invariants as shape recognition technique for comparing protein binding sites

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CLUSTER ANALYSIS; DATA BASE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; ROC CURVE; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS;

EID: 36549048871     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm503     Document Type: Article
Times cited : (52)

References (45)
  • 2
    • 15944411037 scopus 로고    scopus 로고
    • Graph theoretic methods for the analysis of structural relationships in biological macromolecules
    • Artymiuk,P.J. et al. (2005) Graph theoretic methods for the analysis of structural relationships in biological macromolecules. J. Am. Soc. Inf. Sci. Technol., 56, 518-528.
    • (2005) J. Am. Soc. Inf. Sci. Technol , vol.56 , pp. 518-528
    • Artymiuk, P.J.1
  • 3
    • 34547260921 scopus 로고    scopus 로고
    • Ultrafast shape recognition to search compound databases for similar molecular shapes
    • Ballester,P.J. and Richards,W.G. (2007) Ultrafast shape recognition to search compound databases for similar molecular shapes. J. Comput. Chem., 28, 1711-1723.
    • (2007) J. Comput. Chem , vol.28 , pp. 1711-1723
    • Ballester, P.J.1    Richards, W.G.2
  • 5
    • 34248382877 scopus 로고    scopus 로고
    • Discovery of similar regions on protein surfaces
    • Bock,M.E. et al. (2007) Discovery of similar regions on protein surfaces. J. Comput. Biol., 14, 285-299.
    • (2007) J. Comput. Biol , vol.14 , pp. 285-299
    • Bock, M.E.1
  • 6
    • 0036135747 scopus 로고    scopus 로고
    • Protein-ligand recognition using spherical harmonic molecular surfaces: Towards a fast and efficient filter for large virtual throughput screening
    • Cai,W. et al. (2002) Protein-ligand recognition using spherical harmonic molecular surfaces: Towards a fast and efficient filter for large virtual throughput screening. J. Mol. Graph. Model., 20 313-328.
    • (2002) J. Mol. Graph. Model , vol.20 , pp. 313-328
    • Cai, W.1
  • 7
    • 33748171998 scopus 로고    scopus 로고
    • Revisiting the voronoi description of protein-protein interfaces
    • Cazals,F. et al. (2006) Revisiting the voronoi description of protein-protein interfaces. Protein Sci., 15, 2082-2092.
    • (2006) Protein Sci , vol.15 , pp. 2082-2092
    • Cazals, F.1
  • 8
    • 0016606973 scopus 로고
    • Structural invariants in protein folding
    • Chothia,C. (1975) Structural invariants in protein folding. Nature 254, 304-308.
    • (1975) Nature , vol.254 , pp. 304-308
    • Chothia, C.1
  • 9
    • 12944273003 scopus 로고    scopus 로고
    • A barcode shape descriptor for curve point cloud data
    • Alexa,M. and Rusinkiewicz,S, eds
    • Collins,A. et al. (2004) A barcode shape descriptor for curve point cloud data. In Alexa,M. and Rusinkiewicz,S. (eds.) Eurographics Symposium on Point-Based Graphics http://graphics.ethz.ch/events/pbg/.
    • (2004) Eurographics Symposium on Point-Based Graphics
    • Collins, A.1
  • 11
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett,T. (2006) An introduction to ROC analysis. Pattern Recognit. Lett., 27, 861-874.
    • (2006) Pattern Recognit. Lett , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 12
    • 0037325956 scopus 로고    scopus 로고
    • Moment forms invariant to rotation and blur in arbitrary number of dimensions
    • Flusser,J. et al. (2003) Moment forms invariant to rotation and blur in arbitrary number of dimensions. IEEE Trans. Pattern Anal. Mach. Intell., 25, 234-245.
    • (2003) IEEE Trans. Pattern Anal. Mach. Intell , vol.25 , pp. 234-245
    • Flusser, J.1
  • 13
    • 0001109246 scopus 로고    scopus 로고
    • A fast method of molecular shape comparison: A simple application of a gaussian description of molecular shape
    • Grant,J.A. et al. (1996) A fast method of molecular shape comparison: A simple application of a gaussian description of molecular shape. J. Comput. Chem., 17, 1653-1666.
    • (1996) J. Comput. Chem , vol.17 , pp. 1653-1666
    • Grant, J.A.1
  • 14
    • 18344364321 scopus 로고    scopus 로고
    • Sh2 binding site comparison: A new application of the surfcomp method
    • Hofbauer,C. and Aszodi,A. (2005) Sh2 binding site comparison: A new application of the surfcomp method. J. Chem. Inf. Model., 45 414-421.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 414-421
    • Hofbauer, C.1    Aszodi, A.2
  • 15
    • 2942708194 scopus 로고    scopus 로고
    • Surfcomp: A novel graph-based approach to molecular surface comparison
    • Hofbauer,C. et al. (2004) Surfcomp: A novel graph-based approach to molecular surface comparison. J. Chem. Inf. Comput. Sci., 44 837-847.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 837-847
    • Hofbauer, C.1
  • 16
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Hohn,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
    • (1993) J. Mol. Biol , vol.233 , pp. 123-138
    • Hohn, L.1    Sander, C.2
  • 17
    • 0021618665 scopus 로고
    • Extended Gaussian images
    • Horn,B. (1984) Extended Gaussian images. Proc. IEEE., 72, 1671-1686.
    • (1984) Proc. IEEE , vol.72 , pp. 1671-1686
    • Horn, B.1
  • 18
    • 84937655864 scopus 로고
    • Visual pattern recognition by moment invatiants
    • Hu,M.-K. (1962) Visual pattern recognition by moment invatiants. IRE. Tran. Inf. Theory, 8, 179-187.
    • (1962) IRE. Tran. Inf. Theory , vol.8 , pp. 179-187
    • Hu, M.-K.1
  • 19
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka,R. and Gentleman,R. (1996) R: A language for data analysis and graphics. J. Comput. Graph. Stat., 5, 299-314.
    • (1996) J. Comput. Graph. Stat , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 20
    • 27544512084 scopus 로고    scopus 로고
    • The SuMo server: 3D search for protein functional sites
    • Jambon,M. et al. (2005) The SuMo server: 3D search for protein functional sites. Bioinformatics, 21, 3929-3930.
    • (2005) Bioinformatics , vol.21 , pp. 3929-3930
    • Jambon, M.1
  • 21
    • 33846052595 scopus 로고    scopus 로고
    • SNAPPI-DB: A database and api of structures, interfaces and alignments for protein-protein interactions
    • Jefferson,E.R. et al. (2007) SNAPPI-DB: A database and api of structures, interfaces and alignments for protein-protein interactions. Nucleic Acids Res., 35, D580-D589.
    • (2007) Nucleic Acids Res , vol.35
    • Jefferson, E.R.1
  • 22
    • 0029109468 scopus 로고
    • Protein-protein interactions: A review of protein dirner structures
    • Jones,S. and Thornton J.M. (1995) Protein-protein interactions: A review of protein dirner structures. Prog. Biophys. Mol. Biol., 63, 31-65.
    • (1995) Prog. Biophys. Mol. Biol , vol.63 , pp. 31-65
    • Jones, S.1    Thornton, J.M.2
  • 23
    • 85089921422 scopus 로고    scopus 로고
    • Rotation invariant spherical harmonic representation of 3D shape descriptors
    • Kobbelt,L, Schröder,P. and Hoppe,H, eds
    • Kazhdan,M. et al. (2003) Rotation invariant spherical harmonic representation of 3D shape descriptors. In Kobbelt,L., Schröder,P. and Hoppe,H. (eds.) Eurographics Symposium on Geometry Processing, http://www-i8.informatik.rwth-aachen.de/old-site/SGP/sgp03/.
    • (2003) Eurographics Symposium on Geometry Processing
    • Kazhdan, M.1
  • 24
    • 1842507022 scopus 로고    scopus 로고
    • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
    • Keskin,O. et al. (2004) A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci., 13, 1043-1055.
    • (2004) Protein Sci , vol.13 , pp. 1043-1055
    • Keskin, O.1
  • 25
    • 28644448657 scopus 로고    scopus 로고
    • Survey of the geometric association of domain-domain interfaces
    • Kim,W.K. and Ison J.C. (2005) Survey of the geometric association of domain-domain interfaces. Proteins, 61, 1075-1088.
    • (2005) Proteins , vol.61 , pp. 1075-1088
    • Kim, W.K.1    Ison, J.C.2
  • 26
    • 33749337098 scopus 로고    scopus 로고
    • The many faces of protein-protein interactions: A compendium of interface geometry
    • Kim,W.K. et al. (2006) The many faces of protein-protein interactions: A compendium of interface geometry. PLoS. Comput. Biol. 2, 1151-1164.
    • (2006) PLoS. Comput. Biol , vol.2 , pp. 1151-1164
    • Kim, W.K.1
  • 27
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • Kleywegt,G. (1999) Recognition of spatial motifs in protein structures. J. Mol. Biol., 285, 1887-1997.
    • (1999) J. Mol. Biol , vol.285 , pp. 1887-1997
    • Kleywegt, G.1
  • 28
    • 0032141278 scopus 로고    scopus 로고
    • n-dimensional moment invariants and conceptual mathematical theory of recognition of n-dimensional data sets
    • Mamistvalov,A. (1998) n-dimensional moment invariants and conceptual mathematical theory of recognition of n-dimensional data sets. IEEE. Trans. Pattern Anal. Mach. Intell., 20, 819-831.
    • (1998) IEEE. Trans. Pattern Anal. Mach. Intell , vol.20 , pp. 819-831
    • Mamistvalov, A.1
  • 30
    • 19544389524 scopus 로고    scopus 로고
    • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    • Morris,R.J. et al. (2005) Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics, 21, 2347-2355.
    • (2005) Bioinformatics , vol.21 , pp. 2347-2355
    • Morris, R.J.1
  • 32
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1
  • 34
  • 35
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 36
    • 35048856940 scopus 로고    scopus 로고
    • Protein-protein interfaces: Recognition of similar spatial and chemical organizations
    • Jonassen,I. and Kim,J, eds, Algorithms in Bioinformatics: 4th International Workshop, WABI 2004, Bergen, Norway, 2004, of, Springer Verlag, Berlin, Heidelberg, pp
    • Shulman-Peleg,A. et al. (2004a) Protein-protein interfaces: recognition of similar spatial and chemical organizations. In Jonassen,I. and Kim,J. (eds.) Algorithms in Bioinformatics: 4th International Workshop, WABI 2004, Bergen, Norway, 2004, Volume 3240 of Lecture Notes in Computer Science. Springer Verlag, Berlin, Heidelberg, pp. 194-205.
    • (2004) Lecture Notes in Computer Science , vol.3240 , pp. 194-205
    • Shulman-Peleg, A.1
  • 37
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shuhnan-Peleg,A. et al. (2004b) Recognition of functional sites in protein structures. J. Mol. Biol., 339, 607-633.
    • (2004) J. Mol. Biol , vol.339 , pp. 607-633
    • Shuhnan-Peleg, A.1
  • 38
    • 23144456254 scopus 로고    scopus 로고
    • SiteEngines: Recognition and comparison of binding sites and protein-protein interfaces, Web Server issue, W337-W341
    • Shulman-Peleg,A. et al. (2005) SiteEngines: Recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res., 33 (Web Server issue), W337-W341.
    • (2005) Nucleic Acids Res , vol.33
    • Shulman-Peleg, A.1
  • 39
    • 9944251424 scopus 로고    scopus 로고
    • Déjí vu an over again: Finding and analyzing protein structure similarities
    • Sierk,M.L. and Kleywegt,G.J. (2004) Déjí vu an over again: Finding and analyzing protein structure similarities. Structure, 12 (12), 2103-2111.
    • (2004) Structure , vol.12 , Issue.12 , pp. 2103-2111
    • Sierk, M.L.1    Kleywegt, G.J.2
  • 40
    • 27544491192 scopus 로고    scopus 로고
    • ROCR: Visualizing classifier performance in R
    • Sing,T. et al. (2005) ROCR: Visualizing classifier performance in R. Bioinformatics, 21 (20), 3940-3941.
    • (2005) Bioinformatics , vol.21 , Issue.20 , pp. 3940-3941
    • Sing, T.1
  • 41
    • 0037424601 scopus 로고    scopus 로고
    • A model for statistical significance of local similarities in structure
    • Stark,A. et al. (2003) A model for statistical significance of local similarities in structure. J. Mol. Biol., 326, 1307-1316.
    • (2003) J. Mol. Biol , vol.326 , pp. 1307-1316
    • Stark, A.1
  • 42
    • 0034489092 scopus 로고    scopus 로고
    • Protein surface similarities: A survey of methods to describe and compare protein surfaces
    • Via,A. et al. (2000) Protein surface similarities: A survey of methods to describe and compare protein surfaces. Cell. Mol Life Sci. 57, 1970-1977.
    • (2000) Cell. Mol Life Sci , vol.57 , pp. 1970-1977
    • Via, A.1
  • 43
    • 33644876493 scopus 로고    scopus 로고
    • Scoppi: A structural classification of protein-protein interfaces
    • Winter,C. et al. (2006) Scoppi: A structural classification of protein-protein interfaces. Nucleic Acids Res., 34, D310-D314.
    • (2006) Nucleic Acids Res , vol.34
    • Winter, C.1
  • 45
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • Zhang,Y. and Skolnick,J. (2005) The protein structure prediction problem could be solved using the current PDB library. Proc. Natl. Acad. Sci. USA, 102, 1029-1034.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.