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Volumn 8, Issue , 2012, Pages 79-94

GIRAF: A method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

Author keywords

Hungarian algorithm; Protein structure comparison; Protein ligand interaction; Relational database

Indexed keywords


EID: 84864270309     PISSN: None     EISSN: 13492942     Source Type: Journal    
DOI: 10.2142/biophysics.8.79     Document Type: Article
Times cited : (4)

References (60)
  • 1
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor, W. R. & Orengo, C. A. Protein structure alignment. J. Mol. Biol. 208, 1-22 (1989).
    • (1989) J. Mol. Biol , vol.208 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2
  • 2
    • 0025275776 scopus 로고
    • Use of techniques derived from graph theory to compare secondary structure motifs in proteins
    • Mitchell, E. M., Artymiuk, P. J., Rice, D.W. & Willett, P. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J. Mol. Biol. 212, 151-166 (1990).
    • (1990) J. Mol. Biol , vol.212 , pp. 151-166
    • Mitchell, E.M.1    Artymiuk, P.J.2    Rice, D.W.3    Willett, P.4
  • 3
    • 0025719208 scopus 로고
    • Efficient detection of threedimensional structural motifs in biological macromolecules by computer vision techniques
    • Nussinov, R. & Wolfson, H. J. Efficient detection of threedimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. USA 88, 10495-10499 (1991).
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.J.2
  • 4
    • 0026587854 scopus 로고
    • Common spatial arrangements of backbone fragments in homologous and nonhomologous proteins
    • Alexandrov, N. N., Takahashi, K. & Go, N. Common spatial arrangements of backbone fragments in homologous and nonhomologous proteins. J. Mol. Biol. 225, 5-9 (1992).
    • (1992) J. Mol. Biol , vol.225 , pp. 5-9
    • Alexandrov, N.N.1    Takahashi, K.2    Go, N.3
  • 5
    • 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. 233, 123-138 (1993).
    • (1993) J. Mol. Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 6
    • 0029061843 scopus 로고
    • Comparison of spatial arrangements of secondary structural elements in proteins
    • Mizuguchi, K. & Go, N. Comparison of spatial arrangements of secondary structural elements in proteins. Protein Eng. 8, 353-362 (1995).
    • (1995) Protein Eng , vol.8 , pp. 353-362
    • Mizuguchi, K.1    Go, N.2
  • 7
    • 0034308164 scopus 로고    scopus 로고
    • Protein tertiary structure comparison using the markov transition model of evolution
    • Kawabata, T. & Nishikawa, K. Protein tertiary structure comparison using the markov transition model of evolution. Proteins 41, 108-122 (2000).
    • (2000) Proteins , vol.41 , pp. 108-122
    • Kawabata, T.1    Nishikawa, K.2
  • 8
    • 0036545421 scopus 로고    scopus 로고
    • Protein structure comparison using bipartite graph matching and its application to protein structure classification
    • Taylor, W.R. Protein structure comparison using bipartite graph matching and its application to protein structure classification. Mol. Cell Proteomics 1, 334-339 (2002).
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 334-339
    • Taylor, W.R.1
  • 10
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540 (1995).
    • (1995) J. Mol. Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 12
    • 0031032662 scopus 로고    scopus 로고
    • ATP binding proteins with different folds share a common ATP-binding structural motif
    • Kobayashi, N. & Go, N. ATP binding proteins with different folds share a common ATP-binding structural motif. Nat. Struct. Biol. 4, 6-7 (1997).
    • (1997) Nat. Struct. Biol , vol.4 , pp. 6-7
    • Kobayashi, N.1    Go, N.2
  • 13
    • 0030826293 scopus 로고    scopus 로고
    • A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition
    • Kobayashi, N. & Go, N. A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition. Eur. Biophys. J. 26, 135-144 (1997).
    • (1997) Eur. Biophys. J , vol.26 , pp. 135-144
    • Kobayashi, N.1    Go, N.2
  • 14
    • 0032568859 scopus 로고    scopus 로고
    • Detection of protein three-dimensional sidechain patterns: New examples of convergent evolution
    • Russell, R. B. Detection of protein three-dimensional sidechain patterns: New examples of convergent evolution. J. Mol. Biol. 279, 1211-1227 (1998).
    • (1998) J. Mol. Biol , vol.279 , pp. 1211-1227
    • Russell, R.B.1
  • 15
    • 0032972775 scopus 로고    scopus 로고
    • Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of proteinmononucleotide complexes
    • Kinoshita, K., Sadanami, K., Kidera, A. & Go, N. Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of proteinmononucleotide complexes. Protein Eng. 12, 11-14 (1999).
    • (1999) Protein Eng , vol.12 , pp. 11-14
    • Kinoshita, K.1    Sadanami, K.2    Kidera, A.3    Go, N.4
  • 16
    • 0041842509 scopus 로고    scopus 로고
    • Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    • Kinoshita, K. & Nakamura, H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci. 12, 1589-1595 (2003).
    • (2003) Protein Sci , vol.12 , pp. 1589-1595
    • Kinoshita, K.1    Nakamura, H.2
  • 17
    • 0037661398 scopus 로고    scopus 로고
    • A new bioinformatic approach to detect common 3D sites in protein structures
    • Jambon, M., Imberty, A., Deléage, G. & Geourjon, C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 52, 137-145 (2003).
    • (2003) Proteins , vol.52 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Deléage, G.3    Geourjon, C.4
  • 18
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • Aloy, P., Ceulemans, H., Stark, A. & Russell, R. B. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 332, 989-998 (2003).
    • (2003) J. Mol. Biol , vol.332 , pp. 989-998
    • Aloy, P.1    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 19
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter, C.T., Bartlett, G. J. & Thornton, J. M. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res. 32, D129-D133 (2004).
    • (2004) Nucleic Acids Res , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 20
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shulman-Peleg, A., Nussinov, R. & Wolfson, H. J. Recognition of functional sites in protein structures. J. Mol. Biol. 339, 607-633 (2004).
    • (2004) J. Mol. Biol , vol.339 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 21
    • 3042809615 scopus 로고    scopus 로고
    • Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching
    • Brakoulias, A. & Jackson, R.M. Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins 56, 250-260 (2004).
    • (2004) Proteins , vol.56 , pp. 250-260
    • Brakoulias, A.1    Jackson, R.M.2
  • 22
    • 1842507022 scopus 로고    scopus 로고
    • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
    • Keskin, O., Tsai, C. J., Wolfson, H. & Nussinov, R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci. 13, 1043-1055 (2004).
    • (2004) Protein Sci , vol.13 , pp. 1043-1055
    • Keskin, O.1    Tsai, C.J.2    Wolfson, H.3    Nussinov, R.4
  • 23
    • 33644852029 scopus 로고    scopus 로고
    • Equivalent binding sites reveal convergently evolved interaction motifs
    • Henschel, A., Kim, W. K. & Schroeder, M. Equivalent binding sites reveal convergently evolved interaction motifs. Bioinformatics 22, 550-555 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 550-555
    • Henschel, A.1    Kim, W.K.2    Schroeder, M.3
  • 24
    • 33749337098 scopus 로고    scopus 로고
    • The many faces of protein-protein interactions: A compendium of interface geometry
    • Kim, W. K., Henschel, A., Winter, C. & Schroeder, M. The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput. Biol. 2, e124 (2006).
    • (2006) PLoS Comput. Biol , vol.2
    • Kim, W.K.1    Henschel, A.2    Winter, C.3    Schroeder, M.4
  • 25
    • 29444457054 scopus 로고    scopus 로고
    • Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships
    • Gold, N. D. & Jackson, R. M. Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J. Mol. Biol. 355, 1112-1124 (2006).
    • (2006) J. Mol. Biol , vol.355 , pp. 1112-1124
    • Gold, N.D.1    Jackson, R.M.2
  • 26
    • 33644876493 scopus 로고    scopus 로고
    • SCOPPI: A structural classification of protein-protein interfaces
    • Winter, C., Henschel, A., Kim, W. K. & Schroeder, M. SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res. 34, D310-D314 (2006).
    • (2006) Nucleic Acids Res , vol.34
    • Winter, C.1    Henschel, A.2    Kim, W.K.3    Schroeder, M.4
  • 27
    • 46049099795 scopus 로고    scopus 로고
    • PPiClust: Efficient clustering of 3D protein-protein interaction interfaces
    • Aung, Z., Tan, S.-H., Ng, S.-K. & Tan, K.-L. PPiClust: efficient clustering of 3D protein-protein interaction interfaces. J. Bioinform. Comput. Biol. 6, 415-433 (2008).
    • (2008) J. Bioinform. Comput. Biol , vol.6 , pp. 415-433
    • Aung, Z.1    Tan, S.-H.2    Ng, S.-K.3    Tan, K.-L.4
  • 28
    • 44949110143 scopus 로고    scopus 로고
    • Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
    • Minai, R., Matsuo, Y., Onuki, H. & Hirota, H. Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins 72, 367-381 (2008).
    • (2008) Proteins , vol.72 , pp. 367-381
    • Minai, R.1    Matsuo, Y.2    Onuki, H.3    Hirota, H.4
  • 29
    • 38149096341 scopus 로고    scopus 로고
    • Similarity search for local protein structures at atomic resolution by exploiting a database management system
    • doi: 10.2142/biophysics.3.75
    • Kinjo, A. R. & Nakamura, H. Similarity search for local protein structures at atomic resolution by exploiting a database management system. BIOPHYSICS 3, 75-84 (2007). doi: 10.2142/biophysics.3.75.
    • (2007) BIOPHYSICS , vol.3 , pp. 75-84
    • Kinjo, A.R.1    Nakamura, H.2
  • 30
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • Xie, L. & Bourne, P.E. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl. Acad. Sci. USA 105, 5441-5446 (2008).
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 31
    • 47849091218 scopus 로고    scopus 로고
    • Architectures and functional coverage of protein-protein interfaces
    • Tuncbag, N., Gursoy, A., Guney, E., Nussinov, R. & Keskin, O. Architectures and functional coverage of protein-protein interfaces. J. Mol. Biol. 381, 785-802 (2008).
    • (2008) J. Mol. Biol , vol.381 , pp. 785-802
    • Tuncbag, N.1    Gursoy, A.2    Guney, E.3    Nussinov, R.4    Keskin, O.5
  • 32
    • 40049089622 scopus 로고    scopus 로고
    • SCOWLP classification: Structural comparison and analysis of protein binding regions
    • Teyra, J., Paszkowski-Rogacz, M., Anders, G. & Pisabarro, M.T. SCOWLP classification: structural comparison and analysis of protein binding regions. BMC Bioinformatics 9, 9 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 9
    • Teyra, J.1    Paszkowski-Rogacz, M.2    Anders, G.3    Pisabarro, M.T.4
  • 33
    • 59649095965 scopus 로고    scopus 로고
    • Comprehensive structural classification of ligand binding motifs in proteins
    • Kinjo, A. R. & Nakamura, H. Comprehensive structural classification of ligand binding motifs in proteins. Structure 17, 234-246 (2009).
    • (2009) Structure , vol.17 , pp. 234-246
    • Kinjo, A.R.1    Nakamura, H.2
  • 34
    • 77954759220 scopus 로고    scopus 로고
    • Geometric similarities of proteinprotein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study
    • Kinjo, A. R. & Nakamura, H. Geometric similarities of proteinprotein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. J. Mol. Biol. 399, 526-540 (2010).
    • (2010) J. Mol. Biol , vol.399 , pp. 526-540
    • Kinjo, A.R.1    Nakamura, H.2
  • 35
    • 78149332085 scopus 로고    scopus 로고
    • The LabelHash algorithm for substructure matching
    • Moll, M., Bryant, D. H. & E., K. L. The LabelHash algorithm for substructure matching. BMC Bioinformatics 11, 555 (2010).
    • (2010) BMC Bioinformatics , vol.11 , pp. 555
    • Moll, M.1    Bryant, D.H.2
  • 36
    • 77954185430 scopus 로고    scopus 로고
    • Ligand-binding site prediction of proteins based on known fragment-fragment interactions
    • Kasahara, K., Kinoshita, K. & Takagi, T. Ligand-binding site prediction of proteins based on known fragment-fragment interactions. Bioinformatics 26, 1493-1499 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 1493-1499
    • Kasahara, K.1    Kinoshita, K.2    Takagi, T.3
  • 37
    • 79960903496 scopus 로고    scopus 로고
    • Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners
    • Dasgupta, B., Nakamura, H. & Kinjo, A. R. Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners. J. Mol. Biol. 411, 713-727 (2011).
    • (2011) J. Mol. Biol , vol.411 , pp. 713-727
    • Dasgupta, B.1    Nakamura, H.2    Kinjo, A.R.3
  • 38
    • 84856768585 scopus 로고    scopus 로고
    • PDBscale analysis of known and putative ligand binding sites with structural sketches
    • Ito, J., Tabei, Y., Shimizu, K., Tomii, K. & Tsuda, K. PDBscale analysis of known and putative ligand binding sites with structural sketches. Proteins 80, 747-763 (2012).
    • (2012) Proteins , vol.80 , pp. 747-763
    • Ito, J.1    Tabei, Y.2    Shimizu, K.3    Tomii, K.4    Tsuda, K.5
  • 39
    • 84856707787 scopus 로고    scopus 로고
    • Composite structural motifs of binding sites for delineating biological functions of proteins
    • Kinjo, A. R. & Nakamura, H. Composite structural motifs of binding sites for delineating biological functions of proteins. PLoS One 7, e31437 (2012).
    • (2012) PLoS One , vol.7
    • Kinjo, A.R.1    Nakamura, H.2
  • 40
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35, D301-D303 (2007).
    • (2007) Nucleic Acids Res , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 42
    • 0028015988 scopus 로고
    • The protein threading problem with sequence amino acid interaction preferences is NP-complete
    • Lathrop, R.H. The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059-1068 (1994).
    • (1994) Protein Eng , vol.7 , pp. 1059-1068
    • Lathrop, R.H.1
  • 43
    • 16344364140 scopus 로고    scopus 로고
    • PDBML: The representation of archival macromolecular structure data in XML
    • Westbrook, J., Ito, N., Nakamura, H., Henrick, K. & Berman, H.M. PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21, 988-992 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 988-992
    • Westbrook, J.1    Ito, N.2    Nakamura, H.3    Henrick, K.4    Berman, H.M.5
  • 46
    • 0001382861 scopus 로고
    • A note on the rotational superposition problem
    • Diamond, R. A note on the rotational superposition problem. Acta Cryst. A 44, 211-216 (1988).
    • (1988) Acta Cryst. A , vol.44 , pp. 211-216
    • Diamond, R.1
  • 50
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • Ooi, T., Oobatake, M., Némethy, G. & Scheraga, H. A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. USA 84, 3086-3090 (1987).
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Némethy, G.3    Scheraga, H.A.4
  • 51
    • 79951985476 scopus 로고    scopus 로고
    • Conformational flexibility of the ligand-binding domain dimer in kainate receptor gating and desensitization
    • Nayeem, N., Mayans, O. & Green, T. Conformational flexibility of the ligand-binding domain dimer in kainate receptor gating and desensitization. J. Neurosci. 31, 2916-2924 (2011).
    • (2011) J. Neurosci , vol.31 , pp. 2916-2924
    • Nayeem, N.1    Mayans, O.2    Green, T.3
  • 52
    • 33644999815 scopus 로고    scopus 로고
    • Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists
    • Mayer, M. L., Ghosal, A., Dolman, N. P. & Jane, D. E. Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists. J. Neurosci. 26, 2852-2861 (2006).
    • (2006) J. Neurosci , vol.26 , pp. 2852-2861
    • Mayer, M.L.1    Ghosal, A.2    Dolman, N.P.3    Jane, D.E.4
  • 53
    • 33644868582 scopus 로고    scopus 로고
    • Cofactor-containing antibodies: Crystal structure of the original yellow antibody
    • Zhu, X., Wentworth, P., Kyle, R. A., Lerner, R. A. & Wilson, I. A. Cofactor-containing antibodies: Crystal structure of the original yellow antibody. Proc. Natl. Acad. Sci. USA 103, 3581-3585 (2006).
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 3581-3585
    • Zhu, X.1    Wentworth, P.2    Kyle, R.A.3    Lerner, R.A.4    Wilson, I.A.5
  • 55
    • 33748644877 scopus 로고    scopus 로고
    • Structure of a bacterial multidrug ABC transporter
    • Dawson, R. J. & Locher, K. P. Structure of a bacterial multidrug ABC transporter. Nature 443, 180-185 (2006).
    • (2006) Nature , vol.443 , pp. 180-185
    • Dawson, R.J.1    Locher, K.P.2
  • 56
    • 35348865444 scopus 로고    scopus 로고
    • Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols
    • Gledhill, J. R., Montgomery, M.G., Leslie, A.G.W. & Walker, J.E. Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols. Proc. Natl. Acad. Sci. USA 104, 13632-13637 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 13632-13637
    • Gledhill, J.R.1    Montgomery, M.G.2    Leslie, A.G.W.3    Walker, J.E.4
  • 58
    • 84864273208 scopus 로고    scopus 로고
    • Graduate Studies in Mathematics. (American Mathematical Society, Providence, Rhode Island, U.S.A
    • Burago, D., Burago, Y. & Ivanov, S. A course in metric geometry, volume 33 of Graduate Studies in Mathematics. (American Mathematical Society, Providence, Rhode Island, U.S.A. 2001).
    • (2001) A Course In Metric Geometry , vol.33
    • Burago, D.1    Burago, Y.2    Ivanov, S.3
  • 59
    • 77953285264 scopus 로고    scopus 로고
    • On the use of Gromov-Hausdorff distances for shape comparison
    • (Botsch, M. and Pajarola, R. eds). The Eurographics Association, 2007
    • Mémoli, F. On the use of Gromov-Hausdorff distances for shape comparison. in Eurographics Symposium on Pointbased Graphics (2007). (Botsch, M. and Pajarola, R. eds). The Eurographics Association, 2007.
    • (2007) Eurographics Symposium On Pointbased Graphics
    • Mémoli, F.1
  • 60
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang, Y. & Skolnick, J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33, 2302-2309 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


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