메뉴 건너뛰기




Volumn 81, Issue 2, 2013, Pages 229-239

Toward optimal fragment generations for ab initio protein structure assembly

Author keywords

ab initio folding; Contact prediction; Secondary structure prediction; Structural fragments

Indexed keywords

AB INITIO CALCULATION; ACCURACY; ARTICLE; MACHINE LEARNING; PRIORITY JOURNAL; PROTEIN STRUCTURE; RESTRICTION FRAGMENT; TORQUE;

EID: 84872600524     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24179     Document Type: Article
Times cited : (179)

References (49)
  • 1
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005; 21: 951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 2
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991; 253: 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 3
    • 0034663738 scopus 로고    scopus 로고
    • Protein threading using PROSPECT: design and evaluation
    • Xu Y, Xu D. Protein threading using PROSPECT: design and evaluation. Proteins 2000; 40: 343-354.
    • (2000) Proteins , vol.40 , pp. 343-354
    • Xu, Y.1    Xu, D.2
  • 4
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998; 14: 846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 8
    • 0027524668 scopus 로고
    • Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment
    • Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. Protein Sci 1993; 2: 1697-1714.
    • (1993) Protein Sci , vol.2 , pp. 1697-1714
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Scheraga, H.A.5
  • 9
    • 0141642142 scopus 로고    scopus 로고
    • ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
    • Klepeis JL, Floudas CA. ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J 2003; 85: 2119-2146.
    • (2003) Biophys J , vol.85 , pp. 2119-2146
    • Klepeis, J.L.1    Floudas, C.A.2
  • 10
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209-225.
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 11
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: a new approach to ab initio protein structure prediction
    • Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003; 85: 1145-1164.
    • (2003) Biophys J , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 12
    • 84862225232 scopus 로고    scopus 로고
    • Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
    • Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 2012; 80: 1715-1735.
    • (2012) Proteins , vol.80 , pp. 1715-1735
    • Xu, D.1    Zhang, Y.2
  • 14
    • 80051490632 scopus 로고    scopus 로고
    • Improving protein structure prediction using multiple sequence-based contact predictions
    • Wu S, Szilagyi A, Zhang Y. Improving protein structure prediction using multiple sequence-based contact predictions. Structure 2011; 19: 1182-1191.
    • (2011) Structure , vol.19 , pp. 1182-1191
    • Wu, S.1    Szilagyi, A.2    Zhang, Y.3
  • 16
    • 0028328263 scopus 로고
    • An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function
    • Bowie JU, Eisenberg D. An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 1994; 91: 4436-4440.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 4436-4440
    • Bowie, J.U.1    Eisenberg, D.2
  • 17
    • 0242267507 scopus 로고    scopus 로고
    • Assembling novel protein folds from super-secondary structural fragments
    • Jones DT, McGuffin LJ. Assembling novel protein folds from super-secondary structural fragments. Proteins 2003; 53 (Suppl 6): 480-485.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 480-485
    • Jones, D.T.1    McGuffin, L.J.2
  • 18
    • 80855147432 scopus 로고    scopus 로고
    • Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement
    • Xu D, Zhang J, Roy A, Zhang Y. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins 2011; 79 (Suppl 10): 147-160.
    • (2011) Proteins , vol.79 , Issue.SUPPL. 10 , pp. 147-160
    • Xu, D.1    Zhang, J.2    Roy, A.3    Zhang, Y.4
  • 19
    • 77954634881 scopus 로고    scopus 로고
    • Recognizing protein substructure similarity using segmental threading
    • Wu S, Zhang Y. Recognizing protein substructure similarity using segmental threading. Structure 2010; 18: 858-867.
    • (2010) Structure , vol.18 , pp. 858-867
    • Wu, S.1    Zhang, Y.2
  • 20
    • 34548608483 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using chunk-TASSER
    • Zhou H, Skolnick J. Ab initio protein structure prediction using chunk-TASSER. Biophys J 2007; 93: 1510-1518.
    • (2007) Biophys J , vol.93 , pp. 1510-1518
    • Zhou, H.1    Skolnick, J.2
  • 21
    • 0035698619 scopus 로고    scopus 로고
    • Predicting novel protein folds by using FRAGFOLD
    • Jones DT. Predicting novel protein folds by using FRAGFOLD. Proteins 2001;(Suppl 5): 127-132.
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 127-132
    • Jones, D.T.1
  • 22
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004; 101: 7594-7599.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 23
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007; 5: 17.
    • (2007) BMC Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 25
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein fragments model native protein structures accurately. J Mol Biol 2002; 323: 297-307.
    • (2002) J Mol Biol , vol.323 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 27
    • 84855651109 scopus 로고    scopus 로고
    • The dual role of fragments in fragment-assembly methods for de novo protein structure prediction
    • Handl J, Knowles J, Vernon R, Baker D, Lovell SC. The dual role of fragments in fragment-assembly methods for de novo protein structure prediction. Proteins 2011; 80: 490-504.
    • (2011) Proteins , vol.80 , pp. 490-504
    • Handl, J.1    Knowles, J.2    Vernon, R.3    Baker, D.4    Lovell, S.C.5
  • 28
    • 80755169552 scopus 로고    scopus 로고
    • HHfrag: HMM-based fragment detection using HHpred
    • Kalev I, Habeck M. HHfrag: HMM-based fragment detection using HHpred. Bioinformatics 2011; 27: 3110-3116.
    • (2011) Bioinformatics , vol.27 , pp. 3110-3116
    • Kalev, I.1    Habeck, M.2
  • 30
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff S, Henikoff JG. Position-based sequence weights. J Mol Biol 1994; 243: 574-578.
    • (1994) J Mol Biol , vol.243 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 31
    • 0022471098 scopus 로고
    • Learning representations by back-propagating errors
    • Rumelhart DE, Hinton GE, Williams RJ. Learning representations by back-propagating errors. Nature 1986; 323: 533-536.
    • (1986) Nature , vol.323 , pp. 533-536
    • Rumelhart, D.E.1    Hinton, G.E.2    Williams, R.J.3
  • 32
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 33
    • 54849412811 scopus 로고    scopus 로고
    • ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction
    • Wu S, Zhang Y. ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction. PLoS One 2008; 3: e3400.
    • (2008) PLoS One , vol.3
    • Wu, S.1    Zhang, Y.2
  • 34
    • 77949504596 scopus 로고    scopus 로고
    • Generating triangulated macromolecular surfaces by Euclidean distance transform
    • Xu D, Zhang Y. Generating triangulated macromolecular surfaces by Euclidean distance transform. PLoS One 2009; 4: e8140.
    • (2009) PLoS One , vol.4
    • Xu, D.1    Zhang, Y.2
  • 35
    • 46449123146 scopus 로고    scopus 로고
    • MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information
    • Wu S, Zhang Y. MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 2008; 72: 547-556.
    • (2008) Proteins , vol.72 , pp. 547-556
    • Wu, S.1    Zhang, Y.2
  • 36
    • 11344292852 scopus 로고    scopus 로고
    • Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
    • Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2005; 58: 321-328.
    • (2005) Proteins , vol.58 , pp. 321-328
    • Zhou, H.1    Zhou, Y.2
  • 37
    • 0037440190 scopus 로고    scopus 로고
    • Finding weak similarities between proteins by sequence profile comparison
    • Panchenko AR. Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res 2003; 31: 683-689.
    • (2003) Nucleic Acids Res , vol.31 , pp. 683-689
    • Panchenko, A.R.1
  • 38
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 2006; 103: 5361-5366.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5361-5366
    • Misura, K.M.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 39
    • 41349114023 scopus 로고    scopus 로고
    • A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
    • Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 2008; 24: 924-931.
    • (2008) Bioinformatics , vol.24 , pp. 924-931
    • Wu, S.1    Zhang, Y.2
  • 40
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinform 2007; 8: 113.
    • (2007) BMC Bioinform , vol.8 , pp. 113
    • Cheng, J.1    Baldi, P.2
  • 41
    • 36749031067 scopus 로고    scopus 로고
    • Contact prediction using mutual information and neural nets
    • Shackelford G, Karplus K. Contact prediction using mutual information and neural nets. Proteins 2007; 69 (Suppl 8): 159-164.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 159-164
    • Shackelford, G.1    Karplus, K.2
  • 42
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: a clustering approach to identify near-native protein folds
    • Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004; 25: 865-871.
    • (2004) J Comput Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 44
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: a local meta-threading-server for protein structure prediction
    • Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 2007; 35: 3375-3382.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 45
    • 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 2005; 33: 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 46
    • 80855132587 scopus 로고    scopus 로고
    • Evaluation of residue-residue contact predictions in CASP9
    • Monastyrskyy B, Fidelis K, Tramontano A, Kryshtafovych A. Evaluation of residue-residue contact predictions in CASP9. Proteins 2011; 79 (Suppl 10): 119-125.
    • (2011) Proteins , vol.79 , Issue.SUPPL. 10 , pp. 119-125
    • Monastyrskyy, B.1    Fidelis, K.2    Tramontano, A.3    Kryshtafovych, A.4
  • 47
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. Twilight zone of protein sequence alignments. Protein Eng 1999; 12: 85-94.
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 48
    • 74249108517 scopus 로고    scopus 로고
    • Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8
    • Ezkurdia I, Grana O, Izarzugaza JM, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins 2009; 77 (Suppl 9): 196-209.
    • (2009) Proteins , vol.77 , Issue.SUPPL. 9 , pp. 196-209
    • Ezkurdia, I.1    Grana, O.2    Izarzugaza, J.M.3    Tress, M.L.4
  • 49
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999; 292: 195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.