메뉴 건너뛰기




Volumn 56, Issue 4, 2004, Pages 704-714

Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing

Author keywords

Ab initio prediction; Fragment assembly; Global optimization; Protein folding; Tertiary structure prediction

Indexed keywords

PEPTIDE FRAGMENT; PEPTIDE LIBRARY; PROTEIN;

EID: 4043058565     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20150     Document Type: Article
Times cited : (87)

References (61)
  • 1
    • 0032606039 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): Round III
    • Moult J, Hubbard T, Fidelis K, Pedersen JT. Critical assessment of methods of protein structure prediction (CASP): round III. Proteins 1999;(Suppl)3:2-6.
    • (1999) Proteins , vol.3 , Issue.SUPPL. , pp. 2-6
    • Moult, J.1    Hubbard, T.2    Fidelis, K.3    Pedersen, J.T.4
  • 2
    • 0035702809 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): Round IV
    • Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins 2001;(Suppl)5:2-7.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 2-7
    • Moult, J.1    Fidelis, K.2    Zemla, A.3    Hubbard, T.4
  • 3
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 5
    • 0014693695 scopus 로고
    • A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme
    • Browne WJ, North ACT, Phillips DC, Brew K, Vanaman TC, Hill RL. A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. J Mol Biol 1969:42;65-86.
    • (1969) J Mol Biol , vol.42 , pp. 65-86
    • Browne, W.J.1    North, A.C.T.2    Phillips, D.C.3    Brew, K.4    Vanaman, T.C.5    Hill, R.L.6
  • 6
    • 0019888748 scopus 로고
    • Comparative model building of the mammalian serine proteases
    • Greer J. Comparative model building of the mammalian serine proteases. J Mol Biol 1981;153:1027-1042.
    • (1981) J Mol Biol , vol.153 , pp. 1027-1042
    • Greer, J.1
  • 7
    • 0023305986 scopus 로고
    • Knowledge-based prediction of protein structures and the design of novel molecules
    • Blundell TL, Sibanda BL, Sternberg MJE, Thornton JM. Knowledge-based prediction of protein structures and the design of novel molecules. Nature 1987;326:347-352.
    • (1987) Nature , vol.326 , pp. 347-352
    • Blundell, T.L.1    Sibanda, B.L.2    Sternberg, M.J.E.3    Thornton, J.M.4
  • 8
    • 0026018780 scopus 로고
    • A new method for building protein conformations from sequence alignments with homologues of known structure
    • Havel TF, Snow ME. A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 1991;217:1-7.
    • (1991) J Mol Biol , vol.217 , pp. 1-7
    • Havel, T.F.1    Snow, M.E.2
  • 9
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt M. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992;226:507-533.
    • (1992) J Mol Biol , vol.226 , pp. 507-533
    • Levitt, M.1
  • 10
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 11
    • 0031576989 scopus 로고    scopus 로고
    • Sidechain prediction from a backbonedependent rotamer library: A new tool for homology modeling
    • Bower M, Cohen FE, Dunbrack RL. Sidechain prediction from a backbonedependent rotamer library: a new tool for homology modeling. J Mol Biol 1997;267:1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.1    Cohen, F.E.2    Dunbrack, R.L.3
  • 12
    • 0032606105 scopus 로고    scopus 로고
    • Sequence to structure alignment in comparative modeling using PrISM
    • Yang AS, Honig B. Sequence to structure alignment in comparative modeling using PrISM. Proteins 1999;(Suppl)3:66-72.
    • (1999) Proteins , vol.3 , Issue.SUPPL. , pp. 66-72
    • Yang, A.S.1    Honig, B.2
  • 13
    • 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
  • 14
    • 0035427225 scopus 로고    scopus 로고
    • Generalized Comparative Modeling (GENECOMP): A combination of sequence comparison, threading, lattice and off lattice modeling for protein structure prediction and refinement
    • Kolinski A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. Generalized Comparative Modeling (GENECOMP): a combination of sequence comparison, threading, lattice and off lattice modeling for protein structure prediction and refinement. Proteins 2001;44:133-149.
    • (2001) Proteins , vol.44 , pp. 133-149
    • Kolinski, A.1    Betancourt, M.R.2    Kihara, D.3    Rotkiewicz, P.4    Skolnick, J.5
  • 15
    • 0035747672 scopus 로고    scopus 로고
    • Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
    • Bates PA, Kelley LA, MacCallum RM, Sternberg MJE. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins 2001; (Suppl)5:39-46.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 39-46
    • Bates, P.A.1    Kelley, L.A.2    MacCallum, R.M.3    Sternberg, M.J.E.4
  • 16
    • 0035748717 scopus 로고    scopus 로고
    • Comparative modeling of CASP4 target proteins: Combining results of sequence search with three-dimensional structure assessment
    • Venclovas C. Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment. Proteins 2001;(Suppl)5:47-54.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 47-54
    • Venclovas, C.1
  • 17
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 18
    • 0029000696 scopus 로고
    • Knowledge-based potentials for preteins
    • Sippl MJ. Knowledge-based potentials for preteins. Curr Opin Struct Biol 1995;5;229-235.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 19
  • 20
    • 0029643801 scopus 로고    scopus 로고
    • Threading thrills and threats
    • Sippl MJ, Flockner H. Threading thrills and threats. Structure 1996;4;15-19.
    • (1996) Structure , vol.4 , pp. 15-19
    • Sippl, M.J.1    Flockner, H.2
  • 21
    • 0041905968 scopus 로고    scopus 로고
    • New approaches in molecular structure prediction
    • Bohm G. New approaches in molecular structure prediction. Biophys Chem 1996;59:1-32.
    • (1996) Biophys Chem , vol.59 , pp. 1-32
    • Bohm, G.1
  • 22
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996;6:195-209.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 23
    • 0030967586 scopus 로고    scopus 로고
    • Perspectives in protein-fold recognition
    • Torda AE. Perspectives in protein-fold recognition. Curr Opin Struct Biol 1997;7:200-205.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 200-205
    • Torda, A.E.1
  • 24
    • 0035703313 scopus 로고    scopus 로고
    • Fold recognition from sequence comparisons
    • Koretke KK, Russell RB, Lupas AN. Fold recognition from sequence comparisons. Proteins 2001;(Suppl)5:68-75.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 68-75
    • Koretke, K.K.1    Russell, R.B.2    Lupas, A.N.3
  • 25
    • 0035747811 scopus 로고    scopus 로고
    • CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4
    • Murzin AG, Bateman A. CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4. Proteins 2001;(Suppl)5:76-85.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 76-85
    • Murzin, A.G.1    Bateman, A.2
  • 28
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in CASP4: Predictions of three-dimensional structures, secondary structures, and interresidue contacts
    • Lesk AM, Conte LL, Hubbard TJP. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins 2001; (Suppl)5:98-118.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 98-118
    • Lesk, A.M.1    Conte, L.L.2    Hubbard, T.J.P.3
  • 29
    • 0033514939 scopus 로고    scopus 로고
    • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
    • Lee J, Liwo A, Scheraga HA. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc Natl Acad Sci 1999;96:2025-2030.
    • (1999) Proc Natl Acad Sci , vol.96 , pp. 2025-2030
    • Lee, J.1    Liwo, A.2    Scheraga, H.A.3
  • 30
    • 0032605909 scopus 로고    scopus 로고
    • Calculation of protein conformation by global optimization of a potential energy function
    • Lee J, Liwo A, Ripoll DR, Pillardy J, Scheraga HA. Calculation of protein conformation by global optimization of a potential energy function. Proteins 1999;(Suppl)3:204-208.
    • (1999) Proteins , vol.3 , Issue.SUPPL. , pp. 204-208
    • Lee, J.1    Liwo, A.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 32
    • 0033545962 scopus 로고    scopus 로고
    • Protein structure prediction by global optimization of a potential energy function
    • Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA. Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci 1999;96:5482-5485.
    • (1999) Proc Natl Acad Sci , vol.96 , pp. 5482-5485
    • Liwo, A.1    Lee, J.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 33
    • 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
  • 34
    • 0035830958 scopus 로고    scopus 로고
    • Prospects for ab initio protein structural genomics
    • Simons KT, Strauss C, Baker D. Prospects for ab initio protein structural genomics. J Mol Biol 2001;306:1191-1199.
    • (2001) J Mol Biol , vol.306 , pp. 1191-1199
    • Simons, K.T.1    Strauss, C.2    Baker, D.3
  • 36
    • 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 , vol.5 , Issue.SUPPL. , pp. 127-132
    • Jones, D.T.1
  • 37
    • 0035748356 scopus 로고    scopus 로고
    • Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment
    • Standley DM, Eyrich VA, An Y, Pincus DL, Gunn JR, Friesner RA. Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment. Proteins 2001;(Suppl)5:133-139.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 133-139
    • Standley, D.M.1    Eyrich, V.A.2    An, Y.3    Pincus, D.L.4    Gunn, J.R.5    Friesner, R.A.6
  • 38
    • 0035703315 scopus 로고    scopus 로고
    • Application of PROSPECT in CASP4: Characterizing protein structures with new folds
    • Xu D, Crawford OH, LoCascio PF, Xu Y. Application of PROSPECT in CASP4: characterizing protein structures with new folds. Proteins 2001;(Suppl)5:140- 148.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 140-148
    • Xu, D.1    Crawford, O.H.2    LoCascio, P.F.3    Xu, Y.4
  • 39
    • 0035749546 scopus 로고    scopus 로고
    • Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement
    • Skolnick J, Kolinski A, Kihara D, Betancourt M, Rotkiewicz P, Boniecki M. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins 2001;(Suppl)5:149-156.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 149-156
    • Skolnick, J.1    Kolinski, A.2    Kihara, D.3    Betancourt, M.4    Rotkiewicz, P.5    Boniecki, M.6
  • 40
    • 0035964191 scopus 로고    scopus 로고
    • Touchstone: An ab initio protein structure prediction method that uses threading based tertiary restraints
    • Kihara D, Lu H, Kolinski A, Skolnick J. Touchstone: an ab initio protein structure prediction method that uses threading based tertiary restraints. Proc Natl Acad Sci 2001;98:10125-10130.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 10125-10130
    • Kihara, D.1    Lu, H.2    Kolinski, A.3    Skolnick, J.4
  • 41
    • 0015859467 scopus 로고
    • Studies on the principles that govern the folding of protein chains
    • Anfinsen CB. Studies on the principles that govern the folding of protein chains. Science 1973;181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 42
  • 43
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • Lee J, Scheraga HA, Rackovsky S. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J Comp Chem 1997;18:1222-1232.
    • (1997) J Comp Chem , vol.18 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 44
    • 0032146482 scopus 로고    scopus 로고
    • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
    • Lee J, Scheraga HA, Rackovsky S. Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers 1998;46:103-115.
    • (1998) Biopolymers , vol.46 , pp. 103-115
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 45
    • 0000542451 scopus 로고    scopus 로고
    • Conformational space annealing by parallel computations: Extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin
    • Lee J, Scheraga HA. Conformational space annealing by parallel computations: extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin. Int J Quant Chem 1999;75:255-265.
    • (1999) Int J Quant Chem , vol.75 , pp. 255-265
    • Lee, J.1    Scheraga, H.A.2
  • 46
    • 0344236093 scopus 로고    scopus 로고
    • Conformational space annealing and an off-lattice frustrated model protein
    • Kim SY, Lee SJ, Lee J. Conformational space annealing and an off-lattice frustrated model protein. J Chem Phys 2003;119:10274-10279.
    • (2003) J Chem Phys , vol.119 , pp. 10274-10279
    • Kim, S.Y.1    Lee, S.J.2    Lee, J.3
  • 47
    • 0141904480 scopus 로고    scopus 로고
    • Unbiased global optimization of Lennard-Jones clusters for N≤201 using conformational space annealing method
    • Lee J, Lee IH, Lee J. Unbiased global optimization of Lennard-Jones clusters for N≤201 using conformational space annealing method. Phys Rev Lett 2003;91:0802011-0802014.
    • (2003) Phys Rev Lett , vol.91 , pp. 0802011-0802014
    • Lee, J.1    Lee, I.H.2    Lee, J.3
  • 50
    • 0001151042 scopus 로고    scopus 로고
    • An efficient, differentiable hydration potential for peptides and proteins
    • Auspurger JD, Scheraga H. An efficient, differentiable hydration potential for peptides and proteins. J Comp Chem 1996;17:1549-1558.
    • (1996) J Comp Chem , vol.17 , pp. 1549-1558
    • Auspurger, J.D.1    Scheraga, H.2
  • 51
    • 2642670311 scopus 로고    scopus 로고
    • Design of a 20-amino acid, three-stranded β-sheet protein
    • Kortemme T, Ramirez-Alvardo M, Serrano L. Design of a 20-amino acid, three-stranded β-sheet protein. Science 1998;281:253-256.
    • (1998) Science , vol.281 , pp. 253-256
    • Kortemme, T.1    Ramirez-Alvardo, M.2    Serrano, L.3
  • 52
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science 1997;278:82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 53
    • 0026801084 scopus 로고
    • Three-dimensional solution structure of the B domain of staphylococcal protein A: Comparisons of the solution and crystal structures
    • Gouda H, Torigoe H, Saito A, Sato M, Arata Y, Shimada I. Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures. Biochemistry 1992;31:9665-9672.
    • (1992) Biochemistry , vol.31 , pp. 9665-9672
    • Gouda, H.1    Torigoe, H.2    Saito, A.3    Sato, M.4    Arata, Y.5    Shimada, I.6
  • 54
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez JC, Pisabarro MT, Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol 1998;5:721-729.
    • (1998) Nat Struct Biol , vol.5 , pp. 721-729
    • Martinez, J.C.1    Pisabarro, M.T.2    Serrano, L.3
  • 55
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • Ooi T, Oobatake M, Nemethy G, Scheraga HA. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci 1987;84:3086-3090.
    • (1987) Proc Natl Acad Sci , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Nemethy, G.3    Scheraga, H.A.4
  • 57
    • 0035797727 scopus 로고    scopus 로고
    • Optimization of parameters in macromolecular potential energy functions by conformational space annealing
    • Lee J, Ripoll DR, Czaplewski C, Pillardy J, Wedemeyer WJ, Scheraga HA. Optimization of parameters in macromolecular potential energy functions by conformational space annealing. J Phys Chem B 2001;105:7291-7298.
    • (2001) J Phys Chem B , vol.105 , pp. 7291-7298
    • Lee, J.1    Ripoll, D.R.2    Czaplewski, C.3    Pillardy, J.4    Wedemeyer, W.J.5    Scheraga, H.A.6
  • 59
    • 0037038520 scopus 로고    scopus 로고
    • Full optimization of linear parameters of a united residue protein potential
    • Lee J, Park K, Lee J. Full optimization of linear parameters of a united residue protein potential. J Phys Chem B 2002;106:11647-11657.
    • (2002) J Phys Chem B , vol.106 , pp. 11647-11657
    • Lee, J.1    Park, K.2    Lee, J.3
  • 60
    • 0037133165 scopus 로고    scopus 로고
    • A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field
    • Liwo A, Arlukowicz P, Czaplewski C, Oldziej S, Pillardy J, Scheraga HA. A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci 2002;99:1937-1942.
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 1937-1942
    • Liwo, A.1    Arlukowicz, P.2    Czaplewski, C.3    Oldziej, S.4    Pillardy, J.5    Scheraga, H.A.6
  • 61
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R, Billeter M, and Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.
    • (1996) J Mol Graph , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.