메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

The LabelHash algorithm for substructure matching

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC SITES; NON-REDUNDANT; NOVEL ALGORITHM; PARTIAL MATCHES; PROTEIN DATA BANK; PROTEIN FUNCTIONS; PROTEIN STRUCTURES; SEQUENCE IDENTITY;

EID: 78149332085     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-555     Document Type: Article
Times cited : (33)

References (68)
  • 2
    • 0037305974 scopus 로고    scopus 로고
    • Overview of structural genomics: from structure to function
    • Zhang C, Kim SH. Overview of structural genomics: from structure to function. Current Opinion in Chemical Biology 2003, 7:28-32.
    • (2003) Current Opinion in Chemical Biology , vol.7 , pp. 28-32
    • Zhang, C.1    Kim, S.H.2
  • 3
    • 31144467558 scopus 로고    scopus 로고
    • The impact of structural genomics: expectations and outcomes
    • Chandonia JM, Brenner SE. The impact of structural genomics: expectations and outcomes. Science 2006, 311(5759):347-351.
    • (2006) Science , vol.311 , Issue.5759 , pp. 347-351
    • Chandonia, J.M.1    Brenner, S.E.2
  • 6
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22(22):4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 7
    • 0029937428 scopus 로고    scopus 로고
    • Hidden Markov models
    • Eddy SR. Hidden Markov models. Curr Opin Struct Biol 1996, 6(3):361-365.
    • (1996) Curr Opin Struct Biol , vol.6 , Issue.3 , pp. 361-365
    • Eddy, S.R.1
  • 12
    • 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, 233:123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 13
    • 12944271968 scopus 로고    scopus 로고
    • FAST: a novel protein structure alignment algorithm
    • Zhu J, Weng Z. FAST: a novel protein structure alignment algorithm. Proteins 2005, 58(3):618-627.
    • (2005) Proteins , vol.58 , Issue.3 , pp. 618-627
    • Zhu, J.1    Weng, Z.2
  • 14
    • 3242883091 scopus 로고    scopus 로고
    • PvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
    • Binkowski TA, Freeman P, Liang J. pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. Nucleic Acids Res 2004, 32:W555-W558.
    • (2004) Nucleic Acids Res , vol.32
    • Binkowski, T.A.1    Freeman, P.2    Liang, J.3
  • 15
    • 33747818007 scopus 로고    scopus 로고
    • CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    • Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Research 2006, 34(Web Server issue):W116-W118.
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB SERVER ISSUE
    • Dundas, J.1    Ouyang, Z.2    Tseng, J.3    Binkowski, A.4    Turpaz, Y.5    Liang, J.6
  • 16
    • 0028881975 scopus 로고
    • SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13(5):323-330.
    • (1995) J Mol Graph , vol.13 , Issue.5 , pp. 323-330
    • Laskowski, R.A.1
  • 18
    • 12944257228 scopus 로고    scopus 로고
    • The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures
    • Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 2005, 58(3):610-617.
    • (2005) Proteins , vol.58 , Issue.3 , pp. 610-617
    • Glaser, F.1    Rosenberg, Y.2    Kessel, A.3    Pupko, T.4    Ben-Tal, N.5
  • 19
    • 33845924786 scopus 로고    scopus 로고
    • Analysis and prediction of functionally important sites in proteins
    • Chakrabarti S, Lanczycki C. Analysis and prediction of functionally important sites in proteins. Protein Science 2007, 16:4.
    • (2007) Protein Science , vol.16 , pp. 4
    • Chakrabarti, S.1    Lanczycki, C.2
  • 20
    • 0030724039 scopus 로고    scopus 로고
    • TESS: A geometric hashing algorithm for deriving 3 D coordinate templates for searching structural databases. Application to enzyme active sites
    • Wallace AC, Borkakoti N, Thornton JM. TESS: A geometric hashing algorithm for deriving 3 D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Science 1997, 6(11):2308.
    • (1997) Protein Science , vol.6 , Issue.11 , pp. 2308
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 21
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • Kleywegt GJ. Recognition of spatial motifs in protein structures. J Mol Biol 1999, 285(4):1887-1897.
    • (1999) J Mol Biol , vol.285 , Issue.4 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 22
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt S, Kuhn D, Klebe G. A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 2002, 323(2):387-406.
    • (2002) J Mol Biol , vol.323 , Issue.2 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 23
    • 0036288284 scopus 로고    scopus 로고
    • Identification of protein functions from a molecular surface database, eF-site
    • Kinoshita K, Furui J, Nakamura H. Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics 2002, 2:9-22.
    • (2002) J Struct Funct Genomics , vol.2 , pp. 9-22
    • Kinoshita, K.1    Furui, J.2    Nakamura, H.3
  • 24
    • 0038128338 scopus 로고    scopus 로고
    • Searching for patterns of amino acids in 3 D protein structures
    • Spriggs RV, Artymiuk PJ, Willett P. Searching for patterns of amino acids in 3 D protein structures. J Chem Inf Comput Sci 2003, 43(2):412-21.
    • (2003) J Chem Inf Comput Sci , vol.43 , Issue.2 , pp. 412-421
    • Spriggs, R.V.1    Artymiuk, P.J.2    Willett, P.3
  • 25
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
    • Stark A, Russell RB. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Research 2003, 31(13):3341-3344.
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 26
    • 0141850386 scopus 로고    scopus 로고
    • An algorithm for constraint-based structural template matching: application to 3 D templates with statistical analysis
    • Barker JA, Thornton JM. An algorithm for constraint-based structural template matching: application to 3 D templates with statistical analysis. Bioinformatics 2003, 19(13):1644-1649.
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 27
    • 0037661398 scopus 로고    scopus 로고
    • A new bioinformatic approach to detect common 3 D sites in protein structures
    • Jambon M, Imberty A, Deléage G, Geourjon C. A new bioinformatic approach to detect common 3 D sites in protein structures. Proteins 2003, 52(2):137-45.
    • (2003) Proteins , vol.52 , Issue.2 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Deléage, G.3    Geourjon, C.4
  • 28
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shulman-Peleg A, Nussinov R, Wolfson HJ. Recognition of functional sites in protein structures. J Mol Biol 2004, 339(3):607-633.
    • (2004) J Mol Biol , vol.339 , Issue.3 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 29
    • 33947201695 scopus 로고    scopus 로고
    • Query3d: a new method for high-throughput analysis of functional residues in protein structures
    • Ausiello G, Via A, Helmer-Citterich M. Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics 2005, 6(Suppl 4):S5.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL 4
    • Ausiello, G.1    Via, A.2    Helmer-Citterich, M.3
  • 31
    • 11844292002 scopus 로고    scopus 로고
    • Inference of protein function from protein structure
    • Pal D, Eisenberg D. Inference of protein function from protein structure. Structure 2005, 13:121-130.
    • (2005) Structure , vol.13 , pp. 121-130
    • Pal, D.1    Eisenberg, D.2
  • 32
    • 29444457054 scopus 로고    scopus 로고
    • Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships
    • Gold ND, Jackson RM. Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J Mol Biol 2006, 355(5):1112-1124.
    • (2006) J Mol Biol , vol.355 , Issue.5 , pp. 1112-1124
    • Gold, N.D.1    Jackson, R.M.2
  • 33
    • 38149096341 scopus 로고    scopus 로고
    • Similarity search for local protein structures at atomic resolution by exploiting a database management system
    • Kinjo AR, Nakamura H. Similarity search for local protein structures at atomic resolution by exploiting a database management system. Biophysics 2007, 3:75-84.
    • (2007) Biophysics , vol.3 , pp. 75-84
    • Kinjo, A.R.1    Nakamura, H.2
  • 35
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • Xie L, Bourne PE. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natli Acad Sci USA 2008, 105(14):5441-5446.
    • (2008) Proc Natli Acad Sci USA , vol.105 , Issue.14 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 36
    • 66349119013 scopus 로고    scopus 로고
    • A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery
    • Xie L, Xie L, Bourne PE. A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics 2009, 25(12):i305-312.
    • (2009) Bioinformatics , vol.25 , Issue.12
    • Xie, L.1    Xie, L.2    Bourne, P.E.3
  • 37
    • 52249116089 scopus 로고    scopus 로고
    • The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications
    • Halperin I, Glazer DS, Wu S, Altman RB. The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. BMC Genomics 2008, 9(Suppl 2):S2.
    • (2008) BMC Genomics , vol.9 , Issue.SUPPL 2
    • Halperin, I.1    Glazer, D.S.2    Wu, S.3    Altman, R.B.4
  • 38
    • 61649106689 scopus 로고    scopus 로고
    • Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns
    • Tseng YY, Dundas J, Liang J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol 2009, 387(2):451-464.
    • (2009) J Mol Biol , vol.387 , Issue.2 , pp. 451-464
    • Tseng, Y.Y.1    Dundas, J.2    Liang, J.3
  • 40
    • 0025719208 scopus 로고
    • Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
    • Nussinov R, Wolfson HJ. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc Natl Acad Sci USA 1991, 88(23):10495-10499.
    • (1991) Proc Natl Acad Sci USA , vol.88 , Issue.23 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.J.2
  • 41
    • 3242889058 scopus 로고    scopus 로고
    • ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures
    • Chang DTH, Chen CY, Chung WC, Oyang YJ, Juan HF, Huang HC. ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. Nucleic Acids Res 2004, 32(Web Server issue):W76-82.
    • (2004) Nucleic Acids Res , vol.32 , Issue.WEB SERVER ISSUE
    • Chang, D.T.H.1    Chen, C.Y.2    Chung, W.C.3    Oyang, Y.J.4    Juan, H.F.5    Huang, H.C.6
  • 42
    • 0037424601 scopus 로고    scopus 로고
    • A Model for Statistical Significance of Local Similarities in Structure
    • Stark A, Sunyaev S, Russell RB. A Model for Statistical Significance of Local Similarities in Structure. Journal of Molecular Biology 2003, 326(5):1307-1316.
    • (2003) Journal of Molecular Biology , vol.326 , Issue.5 , pp. 1307-1316
    • Stark, A.1    Sunyaev, S.2    Russell, R.B.3
  • 45
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996, 257(2):342-358.
    • (1996) J Mol Biol , vol.257 , Issue.2 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 46
    • 0027967593 scopus 로고
    • A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures
    • Artymiuk PJ, Poirrette AR, Grindley HM, Rice DW, Willett P. A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures. Journal of Molecular Biology 1994, 243(2):327-344.
    • (1994) Journal of Molecular Biology , vol.243 , Issue.2 , pp. 327-344
    • Artymiuk, P.J.1    Poirrette, A.R.2    Grindley, H.M.3    Rice, D.W.4    Willett, P.5
  • 47
    • 78649778563 scopus 로고    scopus 로고
    • Statistical Models in Protein Structural Alignments
    • Department of Statistics, Rice University, Houston, TX
    • Fofanov VY. Statistical Models in Protein Structural Alignments. PhD thesis 2008, Department of Statistics, Rice University, Houston, TX.
    • (2008) PhD thesis
    • Fofanov, V.Y.1
  • 49
    • 84870561903 scopus 로고    scopus 로고
    • The HDF Group
    • The HDF Group Hierarchical data format version 5 2000-2010. The HDF Group., http://www.hdfgroup.org/HDF5
    • Hierarchical data format version 5 , pp. 2000-2010
  • 51
    • 84893482610 scopus 로고
    • A solution of the best rotation to relate two sets of vectors
    • Kabsch W. A solution of the best rotation to relate two sets of vectors. Acta Crystallographica A 1976, 32:922-923.
    • (1976) Acta Crystallographica A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 52
    • 8344246968 scopus 로고    scopus 로고
    • Using quaternions to calculate RMSD
    • Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. J Comp Chemistry 2004, 25(15):1849-1849.
    • (2004) J Comp Chemistry , vol.25 , Issue.15 , pp. 1849-1849
    • Coutsias, E.A.1    Seok, C.2    Dill, K.A.3
  • 53
    • 77950876974 scopus 로고    scopus 로고
    • Fast determination of the optimal rotational matrix for macromolecular superpositions
    • Liu P, Agrafiotis DK, Theobald DL. Fast determination of the optimal rotational matrix for macromolecular superpositions. J Comput Chem 2010, 31(7):1561-3.
    • (2010) J Comput Chem , vol.31 , Issue.7 , pp. 1561-1563
    • Liu, P.1    Agrafiotis, D.K.2    Theobald, D.L.3
  • 54
    • 29844457403 scopus 로고    scopus 로고
    • Rapid calculation of RMSDs using a quaternion-based characteristic polynomial
    • Theobald DL. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallogr A 2005, 61(Pt 4):478-480.
    • (2005) Acta Crystallogr A , vol.61 , Issue.PART 4 , pp. 478-480
    • Theobald, D.L.1
  • 57
    • 0035175679 scopus 로고    scopus 로고
    • PDBsum: summaries and analyses of PDB structures
    • Laskowski RA. PDBsum: summaries and analyses of PDB structures. Nucleic Acids Research 2001, 29:221-222.
    • (2001) Nucleic Acids Research , vol.29 , pp. 221-222
    • Laskowski, R.A.1
  • 58
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.
    • (1995) J Mol Biol , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 59
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    • Porter CT, Bartlett GJ, Thornton JM. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004, (32 Database):D129-33.
    • (2004) Nucleic Acids Res , Issue.32 DATABASE
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 61
    • 2542555845 scopus 로고    scopus 로고
    • Superfamily active site templates
    • Meng EC, Polacco BJ, Babbitt PC. Superfamily active site templates. Proteins 2004, 55(4):962-976.
    • (2004) Proteins , vol.55 , Issue.4 , pp. 962-976
    • Meng, E.C.1    Polacco, B.J.2    Babbitt, P.C.3
  • 62
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • Kleywegt GJ. Recognition of spatial motifs in protein structures. Journal of Molecular Biology 1999, 285(4):1887-1897.
    • (1999) Journal of Molecular Biology , vol.285 , Issue.4 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 64
    • 14744305761 scopus 로고    scopus 로고
    • Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families
    • Torrance JW, Bartlett GJ, Porter CT, Thornton JM. Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 2005, 347(3):565-81.
    • (2005) J Mol Biol , vol.347 , Issue.3 , pp. 565-581
    • Torrance, J.W.1    Bartlett, G.J.2    Porter, C.T.3    Thornton, J.M.4
  • 65
    • 77951971437 scopus 로고    scopus 로고
    • Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
    • Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE. Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics 2010, 11(242).
    • (2010) BMC Bioinformatics , vol.11 , Issue.242
    • Bryant, D.H.1    Moll, M.2    Chen, B.Y.3    Fofanov, V.Y.4    Kavraki, L.E.5
  • 66
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 2003, 19:163-164.
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 67
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: an efficient way to compute molecular surfaces
    • Sanner MF, Olson AJ, Spehner JC. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996, 38(3):305-320.
    • (1996) Biopolymers , vol.38 , Issue.3 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 68
    • 0028285219 scopus 로고
    • Catalytic metal ion binding in enolase: the crystal structure of an enolase-Mn2+-phosphonoacetohydroxamate complex at 2.4-A resolution
    • Zhang E, Hatada M, Brewer JM, Lebioda L. Catalytic metal ion binding in enolase: the crystal structure of an enolase-Mn2+-phosphonoacetohydroxamate complex at 2.4-A resolution. Biochemistry 1994, 33(20):6295-6300.
    • (1994) Biochemistry , vol.33 , Issue.20 , pp. 6295-6300
    • Zhang, E.1    Hatada, M.2    Brewer, J.M.3    Lebioda, L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.