메뉴 건너뛰기




Volumn 25, Issue 14, 2009, Pages 1761-1767

pGenTHREADER and pDomTHREADER: New methods for improved protein fold recognition and superfamily discrimination

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; INTERMETHOD COMPARISON; LEARNING ALGORITHM; PREDICTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SUPPORT VECTOR MACHINE;

EID: 67649887151     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp302     Document Type: Article
Times cited : (247)

References (45)
  • 1
    • 0031576355 scopus 로고    scopus 로고
    • Do aligned sequences share the same fold?
    • Abagyan,R.A. and Batalov,S. (1997) Do aligned sequences share the same fold? J. Mol. Biol., 273, 355-368.
    • (1997) J. Mol. Biol , vol.273 , pp. 355-368
    • Abagyan, R.A.1    Batalov, S.2
  • 2
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 3
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 4
    • 33846059668 scopus 로고    scopus 로고
    • The generation of new protein functions by the combination of domains
    • Bashton,M. and Chothia,C. (2003) The generation of new protein functions by the combination of domains. Structure, 15, 85-89.
    • (2003) Structure , vol.15 , pp. 85-89
    • Bashton, M.1    Chothia, C.2
  • 5
    • 34347388470 scopus 로고    scopus 로고
    • UniRef: Comprehensive and non-redundant UniProt reference clusters
    • Baris,E. et al. (2007) UniRef: Comprehensive and non-redundant UniProt reference clusters Bioinformatics, 23, 1282-1288
    • (2007) Bioinformatics , vol.23 , pp. 1282-1288
    • Baris, E.1
  • 6
    • 0348129526 scopus 로고    scopus 로고
    • The ASTRAL compendium in 2004
    • Chandonia,J.M. et al. (2004) The ASTRAL compendium in 2004. Nucleic Acids Res., 32, D189-D192.
    • (2004) Nucleic Acids Res , vol.32
    • Chandonia, J.M.1
  • 7
    • 40849133659 scopus 로고    scopus 로고
    • Discrimination between distant homologs and structural analogs: Lessons from manually constructed, reliable data sets
    • Cheng,H. et al. (2008) Discrimination between distant homologs and structural analogs: Lessons from manually constructed, reliable data sets. J. Mol. Biol., 377, 1265-1278.
    • (2008) J. Mol. Biol , vol.377 , pp. 1265-1278
    • Cheng, H.1
  • 8
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin,N.V (2001) Fold change in evolution of protein structures. J. Struct. Biol., 134, 167-185.
    • (2001) J. Struct. Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 9
    • 0036428739 scopus 로고    scopus 로고
    • Quantifying the similarities wtihin fold space
    • Harrison,A. et al. (2002) Quantifying the similarities wtihin fold space. J. Mol. Biol., 323, 909-926.
    • (2002) J. Mol. Biol , vol.323 , pp. 909-926
    • Harrison, A.1
  • 10
    • 0034767547 scopus 로고    scopus 로고
    • Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins
    • Heygi,H. and Gerstein,M. (2001) Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res. 11, 1632-1640.
    • (2001) Genome Res , vol.11 , pp. 1632-1640
    • Heygi, H.1    Gerstein, M.2
  • 11
    • 0036081436 scopus 로고    scopus 로고
    • In search for more accurate alignments in the twilight zone
    • Jaroszewski,L. et al. (2002) In search for more accurate alignments in the twilight zone. Protein Sci., 11, 1702-13.
    • (2002) Protein Sci , vol.11 , pp. 1702-1713
    • Jaroszewski, L.1
  • 12
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones,D.T. (1999a) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol., 287 797-815.
    • (1999) J. Mol. Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 13
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones,D.T. (1999b) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 14
    • 0035698619 scopus 로고    scopus 로고
    • Predicting novel protein folds by using FRAGFOLD
    • Jones,D.T. (2001) Predicting novel protein folds by using FRAGFOLD. Proteins Struct. Func. Bioinf., 45, 127-132.
    • (2001) Proteins Struct. Func. Bioinf , vol.45 , pp. 127-132
    • Jones, D.T.1
  • 16
    • 0036796379 scopus 로고    scopus 로고
    • A comparison of profile hidden Markov model procedures for remote homology detection
    • Madera,M. and Gough,J. (2002) A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res. 30, 4321-4328.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4321-4328
    • Madera, M.1    Gough, J.2
  • 18
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the GenTHREADER method for genomic fold recognition
    • McGuffin,L.J. and Jones,D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • McGuffin, L.J.1    Jones, D.T.2
  • 19
    • 33746358516 scopus 로고    scopus 로고
    • High throughput profile-profile based fold recognition for the entire Human proteome
    • McGuffin,L.J. et al. (2006) High throughput profile-profile based fold recognition for the entire Human proteome. BMC Bioinformatics 7, 288.
    • (2006) BMC Bioinformatics , vol.7 , pp. 288
    • McGuffin, L.J.1
  • 20
    • 0041886960 scopus 로고    scopus 로고
    • Porbabilistic scoring measures for profile-profile comparison yield more accuracte short seed alignments
    • Mittelman,D. et al. (2003) Porbabilistic scoring measures for profile-profile comparison yield more accuracte short seed alignments. Bioinformatics, 19, 1531-1539.
    • (2003) Bioinformatics , vol.19 , pp. 1531-1539
    • Mittelman, D.1
  • 21
    • 36749042541 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction-Round VII
    • Moult,J. et al. (2007) Critical assessment of methods of protein structure prediction-Round VII. Proteins, 69 (Suppl. 8), 3-9.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 3-9
    • Moult, J.1
  • 22
    • 0345504211 scopus 로고    scopus 로고
    • Benchmarking PSI-BLAST in genome annotation
    • Muller,A. et al. (1999) Benchmarking PSI-BLAST in genome annotation. J. Mol. Biol., 293, 1257-1271.
    • (1999) J. Mol. Biol , vol.293 , pp. 1257-1271
    • Muller, A.1
  • 23
    • 22244450719 scopus 로고    scopus 로고
    • Protein families and their evolution: A structural perspective
    • Orengo,C.A and Thornton,J.M. (2005) Protein families and their evolution: A structural perspective. Ann. Rev. Biochem., 74, 867-900.
    • (2005) Ann. Rev. Biochem , vol.74 , pp. 867-900
    • Orengo, C.A.1    Thornton, J.M.2
  • 24
    • 0037440190 scopus 로고    scopus 로고
    • Finding weak similarities between proteins by sequence profile comparison
    • Panchenko. (2003) Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res, 31, 683-689.
    • (2003) Nucleic Acids Res , vol.31 , pp. 683-689
    • Panchenko1
  • 25
    • 0003243224 scopus 로고    scopus 로고
    • Probabilistic outputs for support vector machines and comparisons to regularized likelihood methods
    • Platt,J.C, ed, MIT press, pp
    • Platt,J.C. (1999) Probabilistic outputs for support vector machines and comparisons to regularized likelihood methods. In Platt,J.C. (ed.) Advances in Large Margin Classifiers. MIT press, pp. 61-71.
    • (1999) Advances in Large Margin Classifiers , pp. 61-71
    • Platt, J.C.1
  • 26
    • 36749059956 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions in the high accuracy template-based modeling category
    • Read,R.J. and Chavali,G. (2007) Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins, 69 (Suppl. 8), 27-37.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 27-37
    • Read, R.J.1    Chavali, G.2
  • 27
    • 44949122425 scopus 로고    scopus 로고
    • Exploring the structure and function paradigm
    • Redfern,O. et al. (2008) Exploring the structure and function paradigm. Curr. Opin. Struct. Biol., 18, 394-402.
    • (2008) Curr. Opin. Struct. Biol , vol.18 , pp. 394-402
    • Redfern, O.1
  • 28
    • 33745727120 scopus 로고    scopus 로고
    • Structural diversity of domain superfamilies in the CATH Database
    • Reeves,G.A. et al. (2006) Structural diversity of domain superfamilies in the CATH Database. J. Mol. Biol. 360, 725-741.
    • (2006) J. Mol. Biol , vol.360 , pp. 725-741
    • Reeves, G.A.1
  • 29
    • 34548806425 scopus 로고    scopus 로고
    • Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone
    • Reid,A.J. et al. (2007). Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics, 23, 2353-2360.
    • (2007) Bioinformatics , vol.23 , pp. 2353-2360
    • Reid, A.J.1
  • 30
    • 1642464839 scopus 로고    scopus 로고
    • Protein structure prediction using Rosetta
    • Rohl,C.A. et al. (2004) Protein structure prediction using Rosetta. Meth. Enzymol., 383, 66-93.
    • (2004) Meth. Enzymol , vol.383 , pp. 66-93
    • Rohl, C.A.1
  • 31
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski,L. et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
    • (2000) Protein Sci , vol.9 , pp. 232-241
    • Rychlewski, L.1
  • 32
    • 11144241105 scopus 로고    scopus 로고
    • LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
    • Rychlewski,L. and Fischer,D. (2005) LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction Protein. Sci., 14, 240-245
    • (2005) Protein. Sci , vol.14 , pp. 240-245
    • Rychlewski, L.1    Fischer, D.2
  • 33
    • 35448938488 scopus 로고    scopus 로고
    • Benchmarking template selection and model quality assessment for high-resolution comparative modeling
    • Sadowski,M.I. and Jones,D.T. (2007) Benchmarking template selection and model quality assessment for high-resolution comparative modeling. Proteins, 69, 476-485.
    • (2007) Proteins , vol.69 , pp. 476-485
    • Sadowski, M.I.1    Jones, D.T.2
  • 34
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Sali,A. and Blundell,T.L. (1993) Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815
    • (1993) J. Mol. Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 35
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede,T. et al. (2003) SWISS-MODEL: An automated protein homology-modeling server Nucleic Acids Res., 31, 3381-3385
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1
  • 37
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew,N. et al. (2000). MaxSub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics 16, 776-785.
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1
  • 38
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 39
    • 34347388470 scopus 로고    scopus 로고
    • UniRef: Comprehensive and non-redundant UniPort reference clusters
    • Suzek,B.E. et al. (2007) UniRef: Comprehensive and non-redundant UniPort reference clusters. Bioinformatics, 23, 1282-1288
    • (2007) Bioinformatics , vol.23 , pp. 1282-1288
    • Suzek, B.E.1
  • 40
    • 59849117778 scopus 로고    scopus 로고
    • Information theory provides a comprehensive framework for the evaluation of protein structure predictions
    • Swanson,R. et al. (2009) Information theory provides a comprehensive framework for the evaluation of protein structure predictions. Proteins, 74, 701-711.
    • (2009) Proteins , vol.74 , pp. 701-711
    • Swanson, R.1
  • 41
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona,G. and Levitt,M. (2002) Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275
    • (2002) J. Mol. Biol , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 42
    • 48449085801 scopus 로고    scopus 로고
    • 5: Improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model
    • 5: Improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. PLoS ONE, 3, e2325.
    • (2008) PLoS ONE , vol.3
    • Zhang, W.1
  • 43
    • 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
  • 44
    • 36749061828 scopus 로고    scopus 로고
    • Zhang,Y. (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins, S8, 108-117.
    • Zhang,Y. (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins, S8, 108-117.
  • 45
    • 36749095600 scopus 로고    scopus 로고
    • Zhou,H. et al. (2007) Analysis of TASSER-based CASP7 protein structure prediction results. Proteins, S8, 90-97
    • Zhou,H. et al. (2007) Analysis of TASSER-based CASP7 protein structure prediction results. Proteins, S8, 90-97


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.