메뉴 건너뛰기




Volumn 30, Issue 6, 2014, Pages 784-791

Fast protein fragment similarity scoring using a Binet-Cauchy kernel

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE FRAGMENT; PROTEIN;

EID: 84897831849     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt618     Document Type: Article
Times cited : (15)

References (32)
  • 1
    • 0001072998 scopus 로고
    • Residual life time at great age
    • Balkema, A. and de Haan, L. (1974) Residual life time at great age. Ann. Probab., 2, 792-804.
    • (1974) Ann. Probab. , vol.2 , pp. 792-804
    • Balkema, A.1    De Haan, L.2
  • 2
    • 0035888284 scopus 로고    scopus 로고
    • Universal similarity measure for comparing protein structures
    • Betancourt, M.R. and Skolnick, J. (2001) Universal similarity measure for comparing protein structures. Biopolymers, 59, 305-309.
    • (2001) Biopolymers , vol.59 , pp. 305-309
    • Betancourt, M.R.1    Skolnick, J.2
  • 3
    • 0030221244 scopus 로고    scopus 로고
    • Local sequence-structure correlations in proteins
    • Bystroff, C. et al. (1996) Local sequence-structure correlations in proteins. Curr. Opin. Biotechnol., 7, 417-421.
    • (1996) Curr. Opin. Biotechnol. , vol.7 , pp. 417-421
    • Bystroff, C.1
  • 4
    • 0034977013 scopus 로고    scopus 로고
    • A normalized root-mean-square distance for comparing protein three-dimensional structures
    • Carugo, O. and Pongor, S. (2001) A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci., 10, 1470-1473.
    • (2001) Protein Sci. , vol.10 , pp. 1470-1473
    • Carugo, O.1    Pongor, S.2
  • 5
    • 0032728082 scopus 로고    scopus 로고
    • Fast detection of common geometric substructure in proteins
    • Chew, L. et al. (1999) Fast detection of common geometric substructure in proteins. J. Comput. Biol., 6, 313-325.
    • (1999) J. Comput. Biol. , vol.6 , pp. 313-325
    • Chew, L.1
  • 6
    • 8344246968 scopus 로고    scopus 로고
    • Using quaternions to calculate RMSD
    • Coutsias, E. et al. (2004) Using quaternions to calculate RMSD. J. Comput. Chem., 25, 1849-1857.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1849-1857
    • Coutsias, E.1
  • 8
    • 23444459516 scopus 로고    scopus 로고
    • Connecting the protein structure universe by using sparse recurring fragments
    • Friedberg, I. and Godzik, A. (2005) Connecting the protein structure universe by using sparse recurring fragments. Structure, 13, 1213-1224.
    • (2005) Structure , vol.13 , pp. 1213-1224
    • Friedberg, I.1    Godzik, A.2
  • 9
    • 84894304707 scopus 로고    scopus 로고
    • Assessing 3D scores for protein structure fragment mining
    • Guyon, F. and Tuffery, P. (2010) Assessing 3D scores for protein structure fragment mining. Open Access Bioinformatics, 2, 67-77.
    • (2010) Open Access Bioinformatics , vol.2 , pp. 67-77
    • Guyon, F.1    Tuffery, P.2
  • 10
    • 0028871926 scopus 로고
    • Dali: A network tool for protein structure comparison
    • Holm, L. and Sander, C. (1995) Dali: a network tool for protein structure comparison. Trends Biochem. Sci., 20, 478-480.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 478-480
    • Holm, L.1    Sander, C.2
  • 11
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A, 32, 922-923.
    • (1976) Acta Crystallogr. A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 12
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch, W. (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystall. A, 34, 827-828.
    • (1978) Acta Crystall. A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 13
    • 0032749097 scopus 로고    scopus 로고
    • Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories
    • Kedem, K. et al. (1999) Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. Proteins, 37, 554-564.
    • (1999) Proteins , vol.37 , pp. 554-564
    • Kedem, K.1
  • 14
    • 0029057126 scopus 로고
    • Size-independent comparison of protein three-dimensional structures
    • Maiorov, V.N. and Crippen, G.M. (1995) Size-independent comparison of protein three-dimensional structures. Proteins, 22, 273-283.
    • (1995) Proteins , vol.22 , pp. 273-283
    • Maiorov, V.N.1    Crippen, G.M.2
  • 15
    • 45549109966 scopus 로고    scopus 로고
    • Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments
    • Manikandan, K. et al. (2008) Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. Genome Biol., 9, R52.
    • (2008) Genome Biol. , vol.9
    • Manikandan, K.1
  • 16
    • 14644390842 scopus 로고    scopus 로고
    • A survey of left-handed helices in protein structures
    • Novotny, M. and Kleywegt, G.J. (2005) A survey of left-handed helices in protein structures. J. Mol. Biol., 347, 231-241.
    • (2005) J. Mol. Biol. , vol.347 , pp. 231-241
    • Novotny, M.1    Kleywegt, G.J.2
  • 17
    • 0029948001 scopus 로고    scopus 로고
    • SSAP: Sequential structure alignment program for protein structure comparison
    • Orengo, C.A. and Taylor, W.R. (1996) SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol., 266, 617-635.
    • (1996) Methods Enzymol. , vol.266 , pp. 617-635
    • Orengo, C.A.1    Taylor, W.R.2
  • 18
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz, A.R. et al. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci., 11, 2606-2621.
    • (2002) Protein Sci. , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1
  • 20
    • 0001075431 scopus 로고
    • Statistical inference using extreme order statistics
    • Pickands, J. (1975) Statistical inference using extreme order statistics. Ann. Stat., 3, 119-131.
    • (1975) Ann. Stat. , vol.3 , pp. 119-131
    • Pickands, J.1
  • 21
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert, M. et al. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173-175.
    • (2012) Nat. Methods , vol.9 , pp. 173-175
    • Remmert, M.1
  • 22
    • 58149193244 scopus 로고    scopus 로고
    • Protein segment finder: An online search engine for segment motifs in the PDB
    • Samson, A.O. and Levitt, M. (2009) Protein segment finder: an online search engine for segment motifs in the PDB. Nucleic Acids Res., 37, D224-D228.
    • (2009) Nucleic Acids Res. , vol.37
    • Samson, A.O.1    Levitt, M.2
  • 23
    • 77951989828 scopus 로고    scopus 로고
    • Searching protein three-dimensional structures in faster than linear time
    • Shibuya, T. (2010) Searching protein three-dimensional structures in faster than linear time. J. Comput. Biol., 17, 593-602.
    • (2010) J. Comput. Biol. , vol.17 , pp. 593-602
    • Shibuya, T.1
  • 24
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension of the optimum path
    • Shindyalov, I.N. and Bourne, P.E. (1998) Protein structure alignment by incremental combinatorial extension of the optimum path. Protein Eng., 11, 739-747.
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 25
    • 0034674709 scopus 로고    scopus 로고
    • Chitin-binding proteins in invertebrates and plants comprise a common chitin-binding structural motif
    • Suetake, T. et al. (2000) Chitin-binding proteins in invertebrates and plants comprise a common chitin-binding structural motif. J. Biol. Chem., 275, 17929-17932.
    • (2000) J. Biol. Chem. , vol.275 , pp. 17929-17932
    • Suetake, T.1
  • 26
    • 79952118761 scopus 로고    scopus 로고
    • FragKB: Structural and literature annotation resource of conserved peptide fragments and residues
    • Tendulkar, A.V. et al. (2010) FragKB: structural and literature annotation resource of conserved peptide fragments and residues. PLoS One, 5, e9679.
    • (2010) PLoS One , vol.5
    • Tendulkar, A.V.1
  • 27
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the universal protein resource (uniprot)
    • TheUniProtConsortium. (2012) Reorganizing the protein space at the universal protein resource (uniprot). Nucleic Acids Res., 40, D71-D75.
    • (2012) Nucleic Acids Res. , vol.40
    • Theuniprotconsortium1
  • 28
    • 0024395940 scopus 로고
    • A 3D building blocks approach to analyzing and predicting structure of proteins
    • Unger, R. et al. (1989) A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins, 5, 355-373.
    • (1989) Proteins , vol.5 , pp. 355-373
    • Unger, R.1
  • 30
    • 4644322072 scopus 로고    scopus 로고
    • Learning over sets using kernel principal angles
    • Wolf, L. and Shashua, A. (2003) Learning over sets using kernel principal angles. J. Mach. Learn. Res., 4, 913-931.
    • (2003) J. Mach. Learn. Res. , vol.4 , pp. 913-931
    • Wolf, L.1    Shashua, A.2
  • 31
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang, Y. and Skolnick, J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 32
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang, Y. and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.