메뉴 건너뛰기




Volumn 7, Issue 3, 2012, Pages

Β-sheet topology prediction with high precision and recall for β and mixed α/β proteins

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 8; CASPASE 9; PROTEIN;

EID: 84857980124     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032461     Document Type: Article
Times cited : (23)

References (62)
  • 1
    • 62849107262 scopus 로고    scopus 로고
    • Protein structure prediction and model quality assessment
    • Kryshtafovych A, Fidelis K, (2009) Protein structure prediction and model quality assessment. Drug Disc Today 14: 386-393.
    • (2009) Drug Disc Today , vol.14 , pp. 386-393
    • Kryshtafovych, A.1    Fidelis, K.2
  • 2
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • Zhang Y, (2008) Progress and challenges in protein structure prediction. Current Opinion in Structural Biology 18: 342-348.
    • (2008) Current Opinion in Structural Biology , vol.18 , pp. 342-348
    • Zhang, Y.1
  • 4
    • 34249824268 scopus 로고    scopus 로고
    • Computational methods in protein structure prediction
    • Floudas CA, (2007) Computational methods in protein structure prediction. Biotech Bioeng 97: 207-213.
    • (2007) Biotech Bioeng , vol.97 , pp. 207-213
    • Floudas, C.A.1
  • 5
    • 0018782641 scopus 로고
    • Hierarchic organization of domains in globular proteins
    • Rose GD, (1979) Hierarchic organization of domains in globular proteins. J Mol Bio 134: 447-470.
    • (1979) J Mol Bio , vol.134 , pp. 447-470
    • Rose, G.D.1
  • 6
    • 0019588920 scopus 로고
    • Folding units in globular proteins
    • Lesk AM, Rose GD, (1981) Folding units in globular proteins. Proc Nat Acad Sci USA 78: 4304-4308.
    • (1981) Proc Nat Acad Sci USA , vol.78 , pp. 4304-4308
    • Lesk, A.M.1    Rose, G.D.2
  • 7
    • 0032972986 scopus 로고    scopus 로고
    • Is protein folding hierarchic? i. local structure and peptide folding
    • Baldwin RL, Rose GD, (1999) Is protein folding hierarchic? i. local structure and peptide folding. Trends Biochem Sci 134: 26-33.
    • (1999) Trends Biochem Sci , vol.134 , pp. 26-33
    • Baldwin, R.L.1    Rose, G.D.2
  • 8
    • 0033080081 scopus 로고    scopus 로고
    • Is protein folding hierarchic? ii. folding intermediates and transition states
    • Baldwin RL, Rose GD, (1999) Is protein folding hierarchic? ii. folding intermediates and transition states. Trends Biochem Sci 24: 77-83.
    • (1999) Trends Biochem Sci , vol.24 , pp. 77-83
    • Baldwin, R.L.1    Rose, G.D.2
  • 9
    • 0032744232 scopus 로고    scopus 로고
    • Protein folding: from the levinthal paradox to structure prediction
    • Kryshtafovych A, Venclovas C, Fidelis K, Moult J, (1999) Protein folding: from the levinthal paradox to structure prediction. J Mol Bio 293: 283-293.
    • (1999) J Mol Bio , vol.293 , pp. 283-293
    • Kryshtafovych, A.1    Venclovas, C.2    Fidelis, K.3    Moult, J.4
  • 10
    • 84857946670 scopus 로고    scopus 로고
    • Astro-fold 2.0: An enhanced framework for protein structure prediction
    • doi: 10.1002/aic.12669
    • Subramani A, Wei Y, Floudas CA, (2011) Astro-fold 2.0: An enhanced framework for protein structure prediction. AIChE J doi:10.1002/aic.12669.
    • (2011) AIChE J
    • Subramani, A.1    Wei, Y.2    Floudas, C.A.3
  • 11
    • 77950519334 scopus 로고    scopus 로고
    • An improved hybrid global optimization method for protein tertiary structure prediction
    • McAllister SR, Floudas CA, (2010) An improved hybrid global optimization method for protein tertiary structure prediction. Comput Optim Appl 45: 377-413.
    • (2010) Comput Optim Appl , vol.45 , pp. 377-413
    • McAllister, S.R.1    Floudas, C.A.2
  • 12
    • 0029055313 scopus 로고
    • Linus: A hierarchic procedure to predict the fold of a protein
    • Srinivasan R, Rose GD, (1995) Linus: A hierarchic procedure to predict the fold of a protein. Proteins 22: 81-89.
    • (1995) Proteins , vol.22 , pp. 81-89
    • Srinivasan, R.1    Rose, G.D.2
  • 14
    • 77950477912 scopus 로고    scopus 로고
    • Investigation of protein folding by coarse-grained molecular dynamics with the unres force field
    • Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA, (2010) Investigation of protein folding by coarse-grained molecular dynamics with the unres force field. J Phys Chem A 114: 4471-4485.
    • (2010) J Phys Chem A , vol.114 , pp. 4471-4485
    • Maisuradze, G.G.1    Senet, P.2    Czaplewski, C.3    Liwo, A.4    Scheraga, H.A.5
  • 16
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS, (1981) The anatomy and taxonomy of protein structure. Adv Prot Chem 34: 167-339.
    • (1981) Adv Prot Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 17
    • 0025277191 scopus 로고
    • The classification and origins of protein folding patterns
    • Chothia C, Finkelstein AV, (1990) The classification and origins of protein folding patterns. Annu Rev Biochem 59: 1007-1039.
    • (1990) Annu Rev Biochem , vol.59 , pp. 1007-1039
    • Chothia, C.1    Finkelstein, A.V.2
  • 18
    • 0027057526 scopus 로고
    • A database of protein structure families with common folding motifs
    • Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G, (1992) A database of protein structure families with common folding motifs. Prot Sci 1: 1691-1698.
    • (1992) Prot Sci , vol.1 , pp. 1691-1698
    • Holm, L.1    Ouzounis, C.2    Sander, C.3    Tuparev, G.4    Vriend, G.5
  • 19
    • 0027220647 scopus 로고
    • Identification and classification of protein fold families
    • Orengo CA, Flores TP, Taylor WR, Thornton JM, (1993) Identification and classification of protein fold families. Prot Eng 6: 485-500.
    • (1993) Prot Eng , vol.6 , pp. 485-500
    • Orengo, C.A.1    Flores, T.P.2    Taylor, W.R.3    Thornton, J.M.4
  • 20
    • 0028319318 scopus 로고
    • Classification of protein folds
    • Orengo CA, (1994) Classification of protein folds. Curr Opin Struct Biol 4: 429-440.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 429-440
    • Orengo, C.A.1
  • 21
    • 0028961335 scopus 로고
    • SCOP - a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP- a structural classification of proteins database for the investigation of sequences and structures. J Mol Bio 247: 536-540.
    • (1995) J Mol Bio , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 22
    • 0027918137 scopus 로고
    • Alpha plus beta folds revisited: some favoured motifs
    • Orengo CA, Thornton JM, (1993) Alpha plus beta folds revisited: some favoured motifs. Structure 1: 105-120.
    • (1993) Structure , vol.1 , pp. 105-120
    • Orengo, C.A.1    Thornton, J.M.2
  • 23
    • 0027251341 scopus 로고
    • The greek key motif: extraction, classification and analysis
    • Hutchinson EG, Thornton JM, (1993) The greek key motif: extraction, classification and analysis. Prot Eng 6: 233-245.
    • (1993) Prot Eng , vol.6 , pp. 233-245
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 24
    • 0344037144 scopus 로고
    • Handedness of crossover connections in β-sheets
    • Richardson JS, (1976) Handedness of crossover connections in β-sheets. Proc Nat Acad Sci USA 73: 2619-2623.
    • (1976) Proc Nat Acad Sci USA , vol.73 , pp. 2619-2623
    • Richardson, J.S.1
  • 25
    • 0017575608 scopus 로고
    • On the conformation of proteins: An analysis of β-pleated sheets
    • Sternberg MJE, Thornton JM, (1977) On the conformation of proteins: An analysis of β-pleated sheets. J Mol Bio 110: 285-296.
    • (1977) J Mol Bio , vol.110 , pp. 285-296
    • Sternberg, M.J.E.1    Thornton, J.M.2
  • 26
    • 0017387723 scopus 로고
    • β-sheet topology and the relatedness of proteins
    • Richardson J, (1977) β-sheet topology and the relatedness of proteins. Nature 268: 495-500.
    • (1977) Nature , vol.268 , pp. 495-500
    • Richardson, J.1
  • 27
    • 0036643499 scopus 로고    scopus 로고
    • Distribution of beta sheets in proteins with application to structure prediction
    • Ruczinksi I, Kooperberg C, Bonneau R, Baker D, (2002) Distribution of beta sheets in proteins with application to structure prediction. Proteins 48: 85-97.
    • (2002) Proteins , vol.48 , pp. 85-97
    • Ruczinksi, I.1    Kooperberg, C.2    Bonneau, R.3    Baker, D.4
  • 28
    • 0037472756 scopus 로고    scopus 로고
    • Prediction of β-sheet topology and disulfide bridges in polypeptides
    • Floudas CA, (2003) Prediction of β-sheet topology and disulfide bridges in polypeptides. J Comput Chem 24: 191-208.
    • (2003) J Comput Chem , vol.24 , pp. 191-208
    • Floudas, C.A.1
  • 30
    • 0033003903 scopus 로고    scopus 로고
    • Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins
    • Zhu H, Braun W, (1999) Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. Prot Sci 8: 326-342.
    • (1999) Prot Sci , vol.8 , pp. 326-342
    • Zhu, H.1    Braun, W.2
  • 31
    • 0036681397 scopus 로고    scopus 로고
    • Prediction of strand pairing in antiparallel and parallel β-sheets using information theory
    • Steward RE, Thornton JM, (2002) Prediction of strand pairing in antiparallel and parallel β-sheets using information theory. Proteins 48: 178-191.
    • (2002) Proteins , vol.48 , pp. 178-191
    • Steward, R.E.1    Thornton, J.M.2
  • 32
    • 84860507958 scopus 로고    scopus 로고
    • Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms
    • Cheng J, Baldi P, (2005) Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 21: 75-84.
    • (2005) Bioinformatics , vol.21 , pp. 75-84
    • Cheng, J.1    Baldi, P.2
  • 33
    • 0028874810 scopus 로고
    • Fold recognition and ab initio structure predictions using hidden markov models and β-strand pair potentials
    • Hubbard TJ, Park J, (1995) Fold recognition and ab initio structure predictions using hidden markov models and β-strand pair potentials. Proteins 23: 398-402.
    • (1995) Proteins , vol.23 , pp. 398-402
    • Hubbard, T.J.1    Park, J.2
  • 34
    • 0030629054 scopus 로고    scopus 로고
    • Beta-sheet prediction using inter-strand residue pairs and refinement with hopfield neural network
    • Asogawa M, (1997) Beta-sheet prediction using inter-strand residue pairs and refinement with hopfield neural network. Proc Int Conf Intell Syst Mol Biol 5: 48-51.
    • (1997) Proc Int Conf Intell Syst Mol Biol , vol.5 , pp. 48-51
    • Asogawa, M.1
  • 35
    • 0028685410 scopus 로고
    • Predicting location and structure of beta-sheet regions using stochastic tree grammars
    • Mamitsuka H, Abe N, (1994) Predicting location and structure of beta-sheet regions using stochastic tree grammars. Proc Int Conf Intell Syst Mol Biol 2: 276-284.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 276-284
    • Mamitsuka, H.1    Abe, N.2
  • 36
    • 55949084241 scopus 로고    scopus 로고
    • Improved strand pairing prediction through exploring folding cooperativity
    • Jeong J, Berman P, Przytycka TM, (2008) Improved strand pairing prediction through exploring folding cooperativity. IEEE/ACM Trans Comput Biol Bioinform 5: 484-491.
    • (2008) IEEE/ACM Trans Comput Biol Bioinform , vol.5 , pp. 484-491
    • Jeong, J.1    Berman, P.2    Przytycka, T.M.3
  • 38
    • 0028348081 scopus 로고
    • Principles determining the structure of beta barrels in proteins. i. a theoretical analysis
    • Murzin AG, Lesk AM, Chothia C, (1994) Principles determining the structure of beta barrels in proteins. i. a theoretical analysis. J Mol Bio 236: 1369-1381.
    • (1994) J Mol Bio , vol.236 , pp. 1369-1381
    • Murzin, A.G.1    Lesk, A.M.2    Chothia, C.3
  • 39
    • 0028330220 scopus 로고
    • Principles determining the structure of beta barrels in proteins. ii. the observed structures
    • Murzin AG, Lesk AM, Chothia C, (1994) Principles determining the structure of beta barrels in proteins. ii. the observed structures. J Mol Bio 236: 1382-1400.
    • (1994) J Mol Bio , vol.236 , pp. 1382-1400
    • Murzin, A.G.1    Lesk, A.M.2    Chothia, C.3
  • 40
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 41
    • 0030039296 scopus 로고    scopus 로고
    • Promotif - a program to identify and analyze structural motifs in proteins
    • Hutchinson EG, Thornton JM, (1996) Promotif- a program to identify and analyze structural motifs in proteins. Prot Sci 5: 212-220.
    • (1996) Prot Sci , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 42
    • 84863395869 scopus 로고    scopus 로고
    • Concord: A consensus method for protein secondary structure prediction via mixed integer linear optimization
    • doi: 10.1098/rspa.2011.0514
    • Wei Y, Thompson J, Floudas CA, (2012) Concord: A consensus method for protein secondary structure prediction via mixed integer linear optimization. Proc Royal Soc A doi:10.1098/rspa.2011.0514.
    • (2012) Proc Royal Soc A
    • Wei, Y.1    Thompson, J.2    Floudas, C.A.3
  • 45
    • 0017410112 scopus 로고
    • On the conformation of proteins: Towards the prediction of strand arrangements in β-pleated sheets
    • Sternberg MJE, Thornton JM, (1977) On the conformation of proteins: Towards the prediction of strand arrangements in β-pleated sheets. J Mol Bio 113: 401-418.
    • (1977) J Mol Bio , vol.113 , pp. 401-418
    • Sternberg, M.J.E.1    Thornton, J.M.2
  • 47
    • 34548787257 scopus 로고    scopus 로고
    • New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage
    • Chiang YS, Gelfand TI, Kister AE, Gelfand IM, (2007) New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage. Proteins 68: 915-921.
    • (2007) Proteins , vol.68 , pp. 915-921
    • Chiang, Y.S.1    Gelfand, T.I.2    Kister, A.E.3    Gelfand, I.M.4
  • 49
    • 0017760068 scopus 로고
    • On the conformation of proteins: Hydrophobic ordering of strands in β-pleated sheets
    • Sternberg MJE, Thornton JM, (1977) On the conformation of proteins: Hydrophobic ordering of strands in β-pleated sheets. J Mol Bio 115: 1-17.
    • (1977) J Mol Bio , vol.115 , pp. 1-17
    • Sternberg, M.J.E.1    Thornton, J.M.2
  • 51
    • 82455206265 scopus 로고    scopus 로고
    • Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins
    • Glyakina AV, Bogatyreva NS, Galzitskaya OV, (2011) Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. PLoS One 6: e28464.
    • (2011) PLoS One , vol.6
    • Glyakina, A.V.1    Bogatyreva, N.S.2    Galzitskaya, O.V.3
  • 52
    • 0019997016 scopus 로고
    • Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins
    • Cohen FE, Sternberg MJE, Taylor WR, (1982) Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins. J Mol Bio 156: 821-862.
    • (1982) J Mol Bio , vol.156 , pp. 821-862
    • Cohen, F.E.1    Sternberg, M.J.E.2    Taylor, W.R.3
  • 53
    • 77958044573 scopus 로고    scopus 로고
    • Re-evaluating the "rules" of protein topology
    • Grainger B, Sadowski MI, Taylor WR, (2010) Re-evaluating the "rules" of protein topology. J Comput Biol 17: 1371-1384.
    • (2010) J Comput Biol , vol.17 , pp. 1371-1384
    • Grainger, B.1    Sadowski, M.I.2    Taylor, W.R.3
  • 54
    • 0037195072 scopus 로고    scopus 로고
    • Common features in structures and sequences of sandwich-like proteins
    • Kister AE, Finkelstein AV, Gelfand IM, (2002) Common features in structures and sequences of sandwich-like proteins. Proc Nat Acad Sci USA 99: 14137-14141.
    • (2002) Proc Nat Acad Sci USA , vol.99 , pp. 14137-14141
    • Kister, A.E.1    Finkelstein, A.V.2    Gelfand, I.M.3
  • 55
    • 27644434290 scopus 로고    scopus 로고
    • A geometric construction determines all permissible strand arrangements of sandwich proteins
    • Fokas AS, Papatheodorou TS, Kister AE, Gelfand IM, (2005) A geometric construction determines all permissible strand arrangements of sandwich proteins. Proc Nat Acad Sci USA 102: 15851-15853.
    • (2005) Proc Nat Acad Sci USA , vol.102 , pp. 15851-15853
    • Fokas, A.S.1    Papatheodorou, T.S.2    Kister, A.E.3    Gelfand, I.M.4
  • 57
    • 0000935435 scopus 로고    scopus 로고
    • Distance geometry optimization for protein structures
    • Moré JJ, Wu Z, (1999) Distance geometry optimization for protein structures. J Glob Opt 15: 219-234.
    • (1999) J Glob Opt , vol.15 , pp. 219-234
    • Moré, J.J.1    Wu, Z.2
  • 58
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program dyana
    • Güntert P, Mumenthaler C, Wüthrich K, (1997) Torsion angle dynamics for NMR structure calculation with the new program dyana. J Mol Bio 273: 283-298.
    • (1997) J Mol Bio , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 59
    • 70350037671 scopus 로고    scopus 로고
    • Selecting high quality structures from diverse conformational ensembles
    • Subramani A, DiMaggio PA, Floudas CA, (2009) Selecting high quality structures from diverse conformational ensembles. Biophysical Journal 97: 1728-1736.
    • (2009) Biophysical Journal , vol.97 , pp. 1728-1736
    • Subramani, A.1    DiMaggio, P.A.2    Floudas, C.A.3
  • 60
    • 77958493840 scopus 로고    scopus 로고
    • A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression
    • DiMaggio PA, Subramani A, Judson RS, Floudas CA, (2010) A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression. Toxicol Sci 118: 251-265.
    • (2010) Toxicol Sci , vol.118 , pp. 251-265
    • DiMaggio, P.A.1    Subramani, A.2    Judson, R.S.3    Floudas, C.A.4
  • 61
    • 57949105676 scopus 로고    scopus 로고
    • Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
    • DiMaggio PA, McAllister SR, Floudas CA, Fend XJ, Rabinowitz JD, et al. (2008) Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformatics 97: 207-213.
    • (2008) BMC Bioinformatics , vol.97 , pp. 207-213
    • DiMaggio, P.A.1    McAllister, S.R.2    Floudas, C.A.3    Fend, X.J.4    Rabinowitz, J.D.5
  • 62
    • 68549123671 scopus 로고    scopus 로고
    • Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem
    • McAllister SR, DiMaggio PA, Floudas CA, (2009) Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem. J Glob Opt 45: 111-129.
    • (2009) J Glob Opt , vol.45 , pp. 111-129
    • McAllister, S.R.1    DiMaggio, P.A.2    Floudas, C.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.