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Volumn 61, Issue 4, 2005, Pages 748-762

Protein loop structure prediction with flexible stem geometries

Author keywords

Loop structure; Optimization; Structure prediction

Indexed keywords

ACCURACY; ARTICLE; COMPARATIVE STUDY; DENSITY; ENERGY; GEOMETRY; HYBRID; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

EID: 28644441632     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20669     Document Type: Article
Times cited : (31)

References (27)
  • 1
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A, Do RKG, Sali A. Modeling of loops in protein structures. Protein Sci 2000;9:1753-1773.
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.G.2    Sali, A.3
  • 2
    • 0037188507 scopus 로고    scopus 로고
    • Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
    • Xiang Z, Soto C, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci USA 2002;99:7432-7437.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 7432-7437
    • Xiang, Z.1    Soto, C.2    Honig, B.3
  • 3
    • 0027448801 scopus 로고
    • Origins of structural diversity within sequentially identical hexapeptides
    • Cohen BI, Presnell SR, Cohen FE. Origins of structural diversity within sequentially identical hexapeptides. Protein Sci 1993;2:2134-2145.
    • (1993) Protein Sci , vol.2 , pp. 2134-2145
    • Cohen, B.I.1    Presnell, S.R.2    Cohen, F.E.3
  • 5
    • 1842584571 scopus 로고    scopus 로고
    • High-resolution prediction of protein helix positions and orientations
    • Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins 2004;55:368-382.
    • (2004) Proteins , vol.55 , pp. 368-382
    • Li, X.1    Jacobson, M.P.2    Friesner, R.A.3
  • 6
    • 0037375742 scopus 로고    scopus 로고
    • Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles
    • DePristo MA, de Bakker PIW, Lovell SC, Blundell TL. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins 2003;51:41-55.
    • (2003) Proteins , vol.51 , pp. 41-55
    • DePristo, M.A.1    De Bakker, P.I.W.2    Lovell, S.C.3    Blundell, T.L.4
  • 7
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with Rosetta
    • Rohl CA, Strauss CEM, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 2004;55:656-677.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.M.2    Chivian, D.3    Baker, D.4
  • 8
    • 0023173201 scopus 로고
    • Prediction of the folding of short polypeptide segments by uniform conformational sampling
    • Bruccoleri RE, Karplus M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987;26:137-168.
    • (1987) Biopolymers , vol.26 , pp. 137-168
    • Bruccoleri, R.E.1    Karplus, M.2
  • 9
    • 0032530578 scopus 로고    scopus 로고
    • Clustering of low-energy conformations near the native structures of small proteins
    • Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 1998;95:11158-11162.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 11158-11162
    • Shortle, D.1    Simons, K.T.2    Baker, D.3
  • 10
    • 0037375615 scopus 로고    scopus 로고
    • Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized Born solvation model
    • de Bakker PIW, DePristo MA, Burke DF, Blundell TL. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized Born solvation model. Proteins 2003;51:21-40.
    • (2003) Proteins , vol.51 , pp. 21-40
    • De Bakker, P.I.W.1    DePristo, M.A.2    Burke, D.F.3    Blundell, T.L.4
  • 11
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side chain rotamers from a backbone dependent rotamer library: A new homology modeling tool
    • Bower MJ, Cohen FE, Dunbrack RL. Prediction of protein side chain rotamers from a backbone dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack, R.L.3
  • 13
    • 0001138328 scopus 로고
    • Algorithm AS 136: A K-means clustering algorithm
    • Hartigan JA, Wong MA. Algorithm AS 136: a K-means clustering algorithm. Appl Stat 1979;28:100-108.
    • (1979) Appl Stat , vol.28 , pp. 100-108
    • Hartigan, J.A.1    Wong, M.A.2
  • 14
    • 0035107308 scopus 로고    scopus 로고
    • CODA: A combined algorithm for predicting the structurally variable regions of protein models
    • Deane CM, Blundell TL. CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci 2001;10:599-612.
    • (2001) Protein Sci , vol.10 , pp. 599-612
    • Deane, C.M.1    Blundell, T.L.2
  • 15
    • 1642575364 scopus 로고    scopus 로고
    • Accurate and efficient loop selections by the DFIRE-based all atom statistical potential
    • Zhang C, Liu S, Zhou Y. Accurate and efficient loop selections by the DFIRE-based all atom statistical potential. Protein Sci 2003;13:391-399.
    • (2003) Protein Sci , vol.13 , pp. 391-399
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 16
    • 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
  • 17
    • 0000467663 scopus 로고    scopus 로고
    • Finding the needle in the haystack: Deducing native folds from ambiguous ab initio protein structure predictions
    • Betancourt M, Skolnick J. Finding the needle in the haystack: deducing native folds from ambiguous ab initio protein structure predictions. J Comput Chem 2001;22:339-353.
    • (2001) J Comput Chem , vol.22 , pp. 339-353
    • Betancourt, M.1    Skolnick, J.2
  • 18
    • 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
  • 19
    • 0037472756 scopus 로고    scopus 로고
    • Prediction of beta-sheet topology and disulfide bridges in polypeptides
    • Klepeis J, Floudas C. Prediction of beta-sheet topology and disulfide bridges in polypeptides. J Comput Chem 2003;24:191-208.
    • (2003) J Comput Chem , vol.24 , pp. 191-208
    • Klepeis, J.1    Floudas, C.2
  • 20
    • 15744373547 scopus 로고    scopus 로고
    • Analysis and prediction of loop segments in protein structure
    • Klepeis JL, Floudas CA. Analysis and prediction of loop segments in protein structure. Computers and Chemical Engineering 2005;29:423-436.
    • (2005) Computers and Chemical Engineering , vol.29 , pp. 423-436
    • Klepeis, J.L.1    Floudas, C.A.2
  • 21
    • 0037445044 scopus 로고    scopus 로고
    • A new class of hybrid global optimization algorithms for peptide structure prediction: Integrated hybrids
    • Klepeis JL, Pieja MT, Floudas CA. A new class of hybrid global optimization algorithms for peptide structure prediction: integrated hybrids. Comput Phys Commun 2003;151:121-140.
    • (2003) Comput Phys Commun , vol.151 , pp. 121-140
    • Klepeis, J.L.1    Pieja, M.T.2    Floudas, C.A.3
  • 22
    • 0037305932 scopus 로고    scopus 로고
    • Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids
    • Klepeis JL, Pieja MT, Floudas CA. Hybrid global optimization algorithms for protein structure prediction: alternating hybrids. Biophys J 2003;84:869-882.
    • (2003) Biophys J , vol.84 , pp. 869-882
    • Klepeis, J.L.1    Pieja, M.T.2    Floudas, C.A.3
  • 23
    • 0037196323 scopus 로고    scopus 로고
    • Ab initio prediction of helical segments in polypeptides
    • Klepeis JL, Floudas CA. Ab initio prediction of helical segments in polypeptides. J Comput Chem 2002;23:245-266.
    • (2002) J Comput Chem , vol.23 , pp. 245-266
    • Klepeis, J.L.1    Floudas, C.A.2
  • 24
    • 12944263648 scopus 로고    scopus 로고
    • Ab initio prediction of the 3-dimensional structure of a de novo designed protein: A double blind case study
    • Klepeis J, Wei Y, Hecht M, Floudas C. Ab initio prediction of the 3-dimensional structure of a de novo designed protein: a double blind case study. Proteins 2005;58:560-570.
    • (2005) Proteins , vol.58 , pp. 560-570
    • Klepeis, J.1    Wei, Y.2    Hecht, M.3    Floudas, C.4
  • 25
    • 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
  • 26
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Némethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 1992;96:6472-6484.
    • (1992) J Phys Chem , vol.96 , pp. 6472-6484
    • Némethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.