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Volumn 11, Issue SUPPL. 11, 2010, Pages

Improved protein surface comparison and application to low-resolution protein structure data

Author keywords

[No Author keywords available]

Indexed keywords

COMPACT REPRESENTATION; CONVENTIONAL APPROACH; EXPERIMENTAL TECHNIQUES; LOW-RESOLUTION PROTEIN STRUCTURES; PROTEIN TERTIARY STRUCTURES; RETRIEVAL PERFORMANCE; STRUCTURE COMPARISONS; SURFACE REPRESENTATION;

EID: 78650810394     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S11-S2     Document Type: Article
Times cited : (21)

References (35)
  • 2
    • 18044397545 scopus 로고    scopus 로고
    • Progress of structural genomics initiatives: an analysis of solved target structures
    • Todd AE, Marsden RL, Thornton JM, Orengo CA. Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol 2005, 348:1235-1260.
    • (2005) J Mol Biol , vol.348 , pp. 1235-1260
    • Todd, A.E.1    Marsden, R.L.2    Thornton, J.M.3    Orengo, C.A.4
  • 4
    • 0029164708 scopus 로고
    • Seeking significance in three-dimensional protein structure comparisons
    • Mizuguchi K, Go N. Seeking significance in three-dimensional protein structure comparisons. Curr Opin Struct Biol 1995, 5:377-382.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 377-382
    • Mizuguchi, K.1    Go, N.2
  • 5
    • 0242720595 scopus 로고    scopus 로고
    • The PDB is a covering set of small protein structures
    • Kihara D, Skolnick J. The PDB is a covering set of small protein structures. J Mol Biol 2003, 793-802.
    • (2003) J Mol Biol , pp. 793-802
    • Kihara, D.1    Skolnick, J.2
  • 6
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998, 11:739-47.
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 7
    • 38949092920 scopus 로고    scopus 로고
    • Protein structure fitting and refinement guided by cryo-EM density
    • 2409374, 18275820
    • Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 2008, 16:295-307. 2409374, 18275820.
    • (2008) Structure , vol.16 , pp. 295-307
    • Topf, M.1    Lasker, K.2    Webb, B.3    Wolfson, H.4    Chiu, W.5    Sali, A.6
  • 8
    • 1942521664 scopus 로고    scopus 로고
    • Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization
    • Ceulemans H, Russell RB. Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. J Mol Biol 2004, 338:783-793.
    • (2004) J Mol Biol , vol.338 , pp. 783-793
    • Ceulemans, H.1    Russell, R.B.2
  • 9
    • 58149293674 scopus 로고    scopus 로고
    • Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model
    • 2576401, 18708469
    • Kawabata T. Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model. Biophys J 2008, 95:4643-4658. 2576401, 18708469.
    • (2008) Biophys J , vol.95 , pp. 4643-4658
    • Kawabata, T.1
  • 10
    • 68949187842 scopus 로고    scopus 로고
    • Refinement of protein structures into low-resolution density maps using rosetta
    • DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D. Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol 2009, 392:181-190.
    • (2009) J Mol Biol , vol.392 , pp. 181-190
    • DiMaio, F.1    Tyka, M.D.2    Baker, M.L.3    Chiu, W.4    Baker, D.5
  • 11
    • 33847266703 scopus 로고    scopus 로고
    • ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage
    • Garzon JI, Kovacs J, Abagyan R, Chacon P. ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics 2007, 23:427-433.
    • (2007) Bioinformatics , vol.23 , pp. 427-433
    • Garzon, J.I.1    Kovacs, J.2    Abagyan, R.3    Chacon, P.4
  • 13
    • 40649089098 scopus 로고    scopus 로고
    • An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison
    • Mak L, Grandison S, Morris RJ. An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. J Mol Graph Model 2007, 26:1035-1045.
    • (2007) J Mol Graph Model , vol.26 , pp. 1035-1045
    • Mak, L.1    Grandison, S.2    Morris, R.J.3
  • 14
    • 51349090017 scopus 로고    scopus 로고
    • Fast protein tertiary structure retrieval based on global surface shape similarity
    • Sael L, Li B, La D, Fang Y, Ramani K, Rustamov R, Kihara D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins 2008, 72:1259-1273.
    • (2008) Proteins , vol.72 , pp. 1259-1273
    • Sael, L.1    Li, B.2    La, D.3    Fang, Y.4    Ramani, K.5    Rustamov, R.6    Kihara, D.7
  • 15
    • 84862297227 scopus 로고    scopus 로고
    • Protein surface representation and comparison: New approaches in structural proteomics
    • Boca Raton, Florida, USA: Chapman & Hall/CRC Press, Chen J, Lonardi S
    • Sael L, Kihara D. Protein surface representation and comparison: New approaches in structural proteomics. Biological Data Mining 2009, 89-109. Boca Raton, Florida, USA: Chapman & Hall/CRC Press, Chen J, Lonardi S.
    • (2009) Biological Data Mining , pp. 89-109
    • Sael, L.1    Kihara, D.2
  • 16
    • 50849126111 scopus 로고    scopus 로고
    • Rapid comparison of properties on protein surface
    • 2574582, 18618695
    • Sael L, La D, Li B, Rustamov R, Kihara D. Rapid comparison of properties on protein surface. Proteins 2008, 73:1-10. 2574582, 18618695.
    • (2008) Proteins , vol.73 , pp. 1-10
    • Sael, L.1    La, D.2    Li, B.3    Rustamov, R.4    Kihara, D.5
  • 17
    • 68549104171 scopus 로고    scopus 로고
    • Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors
    • Venkatraman V, Sael L, Kihara D. Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors. Cell Biochem Biophys 2009, 54:23-32.
    • (2009) Cell Biochem Biophys , vol.54 , pp. 23-32
    • Venkatraman, V.1    Sael, L.2    Kihara, D.3
  • 18
    • 0027490298 scopus 로고
    • Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics
    • Masek BB, Merchant A, Matthew JB. Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics. Proteins 1993, 17:193-202.
    • (1993) Proteins , vol.17 , pp. 193-202
    • Masek, B.B.1    Merchant, A.2    Matthew, J.B.3
  • 20
    • 26444578248 scopus 로고    scopus 로고
    • Identifying similar surface patches on proteins using a spin-image surface representation
    • Identifying similar surface patches on proteins using a spin-image surface representation. Lecture Notes in Comp Sci 2005, 3537:417-428., http://www.springerlink.com/content/uxtrp55q6y9q3j08/
    • (2005) Lecture Notes in Comp Sci , vol.3537 , pp. 417-428
  • 21
    • 74049092313 scopus 로고    scopus 로고
    • Protein-protein docking using region-based 3D Zernike descriptors
    • 2800122, 20003235
    • Venkatraman V, Yang YD, Sael L, Kihara D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics 2009, 10:407. 2800122, 20003235.
    • (2009) BMC Bioinformatics , vol.10 , pp. 407
    • Venkatraman, V.1    Yang, Y.D.2    Sael, L.3    Kihara, D.4
  • 22
    • 74049098905 scopus 로고    scopus 로고
    • Characterization and classification of local protein surfaces using self-organizing map
    • Sael L, Kihara D. Characterization and classification of local protein surfaces using self-organizing map. International Journal of Knowledge Discovery in Bioinformatics (IJKDB) 2010, 1:32-47., http://www.igi-global.com/bookstore/Article.aspx?TitleId=40970
    • (2010) International Journal of Knowledge Discovery in Bioinformatics (IJKDB) , vol.1 , pp. 32-47
    • Sael, L.1    Kihara, D.2
  • 23
    • 77953587057 scopus 로고    scopus 로고
    • Real-time ligand binding pocket database search using local surface descriptors.
    • Chikhi R, Sael L, Kihara D. Real-time ligand binding pocket database search using local surface descriptors. Proteins 2010, 78:2007-2028.
    • (2010) Proteins , vol.78 , pp. 2007-2028
    • Chikhi, R.1    Sael, L.2    Kihara, D.3
  • 24
    • 76749110379 scopus 로고    scopus 로고
    • Application of 3D Zernike descriptors to shape-based ligand similarity searching
    • Venkatraman V, Chakravarthy PR, Kihara D. Application of 3D Zernike descriptors to shape-based ligand similarity searching. J Cheminform. 2009, 17(1):19.
    • (2009) J Cheminform. , vol.17 , Issue.1 , pp. 19
    • Venkatraman, V.1    Chakravarthy, P.R.2    Kihara, D.3
  • 26
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993, 233:123-38.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 28
    • 78650849574 scopus 로고    scopus 로고
    • Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking
    • Kihara D, Sael L, Chikhi R, Esquivel-Rodriguez J. Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. Curr Protein Pept Sci 2010,
    • (2010) Curr Protein Pept Sci
    • Kihara, D.1    Sael, L.2    Chikhi, R.3    Esquivel-Rodriguez, J.4
  • 29
    • 0037779312 scopus 로고    scopus 로고
    • 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition
    • Canterakis N. 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. Proc 11th Scandinavian Conference on Image Analysis 1999, 85-93.
    • (1999) Proc 11th Scandinavian Conference on Image Analysis , pp. 85-93
    • Canterakis, N.1
  • 32
    • 55249097443 scopus 로고    scopus 로고
    • Radius of gyration is indicator of compactness of protein structure
    • 18856071
    • Lobanov MI, Bogatyreva NS, Galzitskaia OV. Radius of gyration is indicator of compactness of protein structure. Mol Biol (Mosk) 2008, 42:701-706. 18856071.
    • (2008) Mol Biol (Mosk) , vol.42 , pp. 701-706
    • Lobanov, M.I.1    Bogatyreva, N.S.2    Galzitskaia, O.V.3
  • 33
    • 0033377664 scopus 로고    scopus 로고
    • EMAN: semiautomated software for high-resolution single-particle reconstructions
    • Ludtke SJ, Baldwin PR, Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 1999, 128:82-97.
    • (1999) J Struct Biol , vol.128 , pp. 82-97
    • Ludtke, S.J.1    Baldwin, P.R.2    Chiu, W.3
  • 34
    • 39849102970 scopus 로고    scopus 로고
    • Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy
    • Jiang W, Baker ML, Jakana J, Weigele PR, King J, Chiu W. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 2008, 451:1130-1134.
    • (2008) Nature , vol.451 , pp. 1130-1134
    • Jiang, W.1    Baker, M.L.2    Jakana, J.3    Weigele, P.R.4    King, J.5    Chiu, W.6


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