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Volumn 25, Issue 21, 2009, Pages 2757-2763

CCHMM_PROF: A HMM-based coiled-coil predictor with evolutionary information

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; FALSE POSITIVE RESULT; GENETIC ANALYSIS; GENETIC CONSERVATION; HIDDEN MARKOV MODEL; INTERNET; MACHINE LEARNING; MATHEMATICAL ANALYSIS; MOLECULAR BIOLOGY; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT;

EID: 70350683807     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp539     Document Type: Article
Times cited : (39)

References (32)
  • 1
    • 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
  • 2
    • 0029145638 scopus 로고
    • Predicting coiled coils by use of pairwise residue correlations
    • Berger,B. et al. (1995) Predicting coiled coils by use of pairwise residue correlations. Proc. Natl Acad. Sci. USA, 92, 8259-8263.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 8259-8263
    • Berger, B.1
  • 3
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 4
    • 0032541424 scopus 로고    scopus 로고
    • Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41
    • Caffrey,M. et al. (1998) Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41. EMBO J., 17, 4572-4584.
    • (1998) EMBO J , vol.17 , pp. 4572-4584
    • Caffrey, M.1
  • 5
    • 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
  • 6
    • 0025130161 scopus 로고
    • Structural features in the heptad substructure and longer range repeats of two-stranded alpha-fibrous proteins
    • Conway,J.F. and Parry,D.A. (1990) Structural features in the heptad substructure and longer range repeats of two-stranded alpha-fibrous proteins. Int. J. Biol. Macromol., 12, 328-334.
    • (1990) Int. J. Biol. Macromol , vol.12 , pp. 328-334
    • Conway, J.F.1    Parry, D.A.2
  • 7
    • 0035999986 scopus 로고    scopus 로고
    • An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
    • Delorenzi,M. and Speed,T. (2002) An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics, 18, 617-625.
    • (2002) Bioinformatics , vol.18 , pp. 617-625
    • Delorenzi, M.1    Speed, T.2
  • 8
    • 70350649716 scopus 로고    scopus 로고
    • Durbin,R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, The Edinburgh Building, Cambridge, UK.
    • Durbin,R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, The Edinburgh Building, Cambridge, UK.
  • 9
    • 33947417295 scopus 로고    scopus 로고
    • Anew decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins
    • Fariselli,P. et al. (2005)Anew decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics, 6(Suppl. 4), S12.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 4
    • Fariselli, P.1
  • 10
    • 34548075339 scopus 로고    scopus 로고
    • Prediction of structurally-determined coiled-coil domains with Hidden Markov Models
    • Fariselli,P. et al. (2007) Prediction of structurally-determined coiled-coil domains with Hidden Markov Models. Lecture Notes in Computer Science, 4414, 292-302.
    • (2007) Lecture Notes in Computer Science , vol.4414 , pp. 292-302
    • Fariselli, P.1
  • 11
    • 0344628627 scopus 로고    scopus 로고
    • Historical review: Another 50th anniversary-new periodicities in coiled coils
    • Gruber,M. and Lupas,A.N. (2003) Historical review: Another 50th anniversary-new periodicities in coiled coils. Trends Biochem. Sci. 28, 679-685.
    • (2003) Trends Biochem. Sci , vol.28 , pp. 679-685
    • Gruber, M.1    Lupas, A.N.2
  • 12
    • 23144450570 scopus 로고    scopus 로고
    • REPPER-repeats and their periodicities in fibrous proteins
    • Gruber,M. et al. (2005) REPPER-repeats and their periodicities in fibrous proteins. Nucleic Acids Res., 33, 239-243.
    • (2005) Nucleic Acids Res , vol.33 , pp. 239-243
    • Gruber, M.1
  • 13
    • 33747788700 scopus 로고    scopus 로고
    • Comparative analysis of coiled-coil prediction methods
    • Gruber,M. et al. (2006) Comparative analysis of coiled-coil prediction methods. J. Struct. Biol., 155, 140-145.
    • (2006) J. Struct. Biol , vol.155 , pp. 140-145
    • Gruber, M.1
  • 14
    • 0028834461 scopus 로고
    • A trimeric structural domain of the HIV-1 transmembrane glycoprotein
    • Lu,M. et al. (1995) A trimeric structural domain of the HIV-1 transmembrane glycoprotein. Nat. Struct. Biol., 2, 1075-1082.
    • (1995) Nat. Struct. Biol , vol.2 , pp. 1075-1082
    • Lu, M.1
  • 15
    • 0030004228 scopus 로고    scopus 로고
    • Prediction and analysis of coiled-coil structures
    • Lupas,A. (1996) Prediction and analysis of coiled-coil structures. Methods Enzymol., 266, L513-L525.
    • (1996) Methods Enzymol , vol.266
    • Lupas, A.1
  • 16
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas,A. et al. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1
  • 17
    • 17444424974 scopus 로고    scopus 로고
    • The structure of alpha-helical coiled coils
    • Lupas,A.N. and Gruber,M. (2005) The structure of alpha-helical coiled coils. Adv. Protein Chem., 70, 37-78.
    • (2005) Adv. Protein Chem , vol.70 , pp. 37-78
    • Lupas, A.N.1    Gruber, M.2
  • 18
    • 0032483021 scopus 로고    scopus 로고
    • Crystal structure of the simian immunodeficiency virus (SIV) gp41 core: Conserved helical interactions underlie the broad inhibitory activity of gp41 peptides
    • Malashkevich,V.N. et al. (1998) Crystal structure of the simian immunodeficiency virus (SIV) gp41 core: Conserved helical interactions underlie the broad inhibitory activity of gp41 peptides. Proc. Natl Acad. Sci. USA, 95, 9134-9139.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 9134-9139
    • Malashkevich, V.N.1
  • 19
    • 0033020204 scopus 로고    scopus 로고
    • Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-Å resolution
    • Malashkevich,V.N. et al. (1999) Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-Å resolution. PNAS, 96, 2662-2267.
    • (1999) PNAS , vol.96 , pp. 2662-2267
    • Malashkevich, V.N.1
  • 20
    • 4243671284 scopus 로고    scopus 로고
    • A sequence-profile-based HMM for predicting and discriminating b-barrel membrane proteins
    • Martelli,P.L. et al. (2002) A sequence-profile-based HMM for predicting and discriminating b-barrel membrane proteins. Bioinformatics, 18, S46-S53.
    • (2002) Bioinformatics , vol.18
    • Martelli, P.L.1
  • 21
    • 0034086980 scopus 로고    scopus 로고
    • The core of the respiratory syncytial virus fusion protein is a trimeric coiled coil
    • Matthews,J.M. et al. (2000) The core of the respiratory syncytial virus fusion protein is a trimeric coiled coil. J. Virol., 74 5911-5920.
    • (2000) J. Virol , vol.74 , pp. 5911-5920
    • Matthews, J.M.1
  • 22
    • 32144456009 scopus 로고    scopus 로고
    • Paircoil2: Improved prediction of coiled coils from sequence
    • McDonnell,A.V. et al. (2006) Paircoil2: Improved prediction of coiled coils from sequence. Bioinformatics, 22, 356-358.
    • (2006) Bioinformatics , vol.22 , pp. 356-358
    • McDonnell, A.V.1
  • 23
    • 58149119313 scopus 로고    scopus 로고
    • A periodic table of coiled-coil protein structures
    • Moutevelis,E. and Woolfson,D.N. (2008) A periodic table of coiled-coil protein structures. J. Mol. Biol., 385, 726-732.
    • (2008) J. Mol. Biol , vol.385 , pp. 726-732
    • Moutevelis, E.1    Woolfson, D.N.2
  • 24
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1
  • 25
    • 51349107479 scopus 로고    scopus 로고
    • Fifty years of coiled-coils and alpha-helical bundles: A close relationship between sequence and structure
    • Parry,D.A. et al. (2008) Fifty years of coiled-coils and alpha-helical bundles: A close relationship between sequence and structure. J. Struct. Biol., 163, 258-269.
    • (2008) J. Struct. Biol , vol.163 , pp. 258-269
    • Parry, D.A.1
  • 26
    • 0027169638 scopus 로고
    • Improved prediction of protein secondary structure by use of sequence profiles and neural networks
    • Rost,B. and Sander,C. (1993) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl Acad. Sci. USA, 90, 7558-7562.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 7558-7562
    • Rost, B.1    Sander, C.2
  • 27
    • 0033618320 scopus 로고    scopus 로고
    • LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins
    • Singh,M. et al. (1999) LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins. J. Mol. Biol, 290, 1031-1041.
    • (1999) J. Mol. Biol , vol.290 , pp. 1031-1041
    • Singh, M.1
  • 28
    • 58149185130 scopus 로고    scopus 로고
    • CC+: A relational database of coiled-coil structures
    • Testa,O.D. et al. (2009) CC+: A relational database of coiled-coil structures. Nucleic Acids Res., 37, D315-D322.
    • (2009) Nucleic Acids Res , vol.37
    • Testa, O.D.1
  • 29
    • 38549097071 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • The UniProt Consortium
    • The UniProt Consortium (2008) The Universal Protein Resource (UniProt). Nucleic Acids Res., 36, D190-D195.
    • (2008) Nucleic Acids Res , vol.36
  • 30
    • 0035853291 scopus 로고    scopus 로고
    • Socket: A program for identifying and analysing coiled-coil motifs within protein structures
    • Walshaw,J. and Woolfson,D.N. (2001) Socket: A program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol., 307, 1427-1450.
    • (2001) J. Mol. Biol , vol.307 , pp. 1427-1450
    • Walshaw, J.1    Woolfson, D.N.2
  • 31
    • 0030987407 scopus 로고    scopus 로고
    • MultiCoil: A program for predicting two- and three-stranded coiled coils
    • Wolf,E. et al. (1997) MultiCoil: A program for predicting two- and three-stranded coiled coils. Protein Sci., 6, 1179-1189.
    • (1997) Protein Sci , vol.6 , pp. 1179-1189
    • Wolf, E.1
  • 32
    • 0033081846 scopus 로고    scopus 로고
    • A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment
    • Zemla,A et al. (1999) A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment. Proteins, 34, 220-223.
    • (1999) Proteins , vol.34 , pp. 220-223
    • Zemla, A.1


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