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Volumn 30, Issue 1, 2001, Pages 1-10

Physicochemical evaluation of protein folds predicted by threading

Author keywords

Molecular mechanics force field; Protein structure prediction; Side chain packing; Solvent effects

Indexed keywords

BACTERIAL PROTEIN; BACTERIOPHAGE LAMBDA REPRESSOR PROTEIN; CYSTEINE; DISULFIDE; DNA BINDING PROTEIN; HEMERYTHRIN; ISOENZYME; MEMBRANE PROTEIN; METHYL ACCEPTING CHEMOTAXIS PROTEINS; METHYL-ACCEPTING CHEMOTAXIS PROTEINS; MONELLIN PROTEIN, DIOSCOREOPHYLLUM CUMMINSII; PLASTOCYANIN; PROTEIN; REPRESSOR PROTEIN; RIBONUCLEASE; RIBONUCLEASE SA3; THIOREDOXIN; VEGETABLE PROTEIN; VIRUS PROTEIN;

EID: 0035231317     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490000111     Document Type: Article
Times cited : (11)

References (36)
  • 1
    • 0009130599 scopus 로고    scopus 로고
    • A structural explanation for the twilight zone of protein sequence homology
    • Chung SY and Subbiah S (1996) A structural explanation for the twilight zone of protein sequence homology. Structure 4: 1123-1127
    • (1996) Structure , vol.4 , pp. 1123-1127
    • Chung, S.Y.1    Subbiah, S.2
  • 2
    • 0026012258 scopus 로고
    • The DNA binding arm of lambda represser: Critical contacts from a flexible region
    • Clarke ND, Beamer LJ, Goldberg HR, Berkower C, Pabo CO (1991) The DNA binding arm of lambda represser: critical contacts from a flexible region. Science 254: 267-270
    • (1991) Science , vol.254 , pp. 267-270
    • Clarke, N.D.1    Beamer, L.J.2    Goldberg, H.R.3    Berkower, C.4    Pabo, C.O.5
  • 3
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA (1990) Dominant forces in protein folding. Biochemistry 29: 7133-7155
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 4
    • 0000580222 scopus 로고
    • Accuracy and precision in protein crystal structure analysis: Restrained leastsquares refinement of the crystal structure of poplar plastocyanin at 1.33 angstroms resolution
    • Guss JM, Bartunik HD, Freeman HC (1992) Accuracy and precision in protein crystal structure analysis: restrained leastsquares refinement of the crystal structure of poplar plastocyanin at 1.33 angstroms resolution. Acta Crystallogr Sect B 48: 790-811
    • (1992) Acta Crystallogr Sect B , vol.48 , pp. 790-811
    • Guss, J.M.1    Bartunik, H.D.2    Freeman, H.C.3
  • 5
    • 0025932859 scopus 로고
    • An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance
    • Havel TF (1991) An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog Biophys Mol Biol 56: 43-78
    • (1991) Prog Biophys Mol Biol , vol.56 , pp. 43-78
    • Havel, T.F.1
  • 6
    • 0025879206 scopus 로고
    • Structures of met and azidomet hemerythrin at 1.66 a resolution
    • Holmes MA, Stenkamp RE (1991) Structures of met and azidomet hemerythrin at 1.66 A resolution. J Mol Biol 220: 723-737
    • (1991) J Mol Biol , vol.220 , pp. 723-737
    • Holmes, M.A.1    Stenkamp, R.E.2
  • 7
    • 0032461411 scopus 로고    scopus 로고
    • Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms
    • Janardhan A, Vajda S (1998) Selecting near-native conformations in homology modeling: the role of molecular mechanics and solvation terms. Protein Sci 7: 1772-1780
    • (1998) Protein Sci , vol.7 , pp. 1772-1780
    • Janardhan, A.1    Vajda, S.2
  • 8
  • 9
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • Lazaridis T, Karplus M (1999a) Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 288: 477-487
    • (1999) J Mol Biol , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 10
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M (1999b) Effective energy function for proteins in solution. Proteins 35: 133-152
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 12
    • 0030956593 scopus 로고    scopus 로고
    • Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three-dimensional structure of murine homeodomain Msx-1
    • Li H, Tejero R, Monleon D, Bassolino Klimas D, Abate Shen C, Bruccoleri RE, Montelione GT (1997) Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1. Protein Sci 6: 956-970
    • (1997) Protein Sci , vol.6 , pp. 956-970
    • Li, H.1    Tejero, R.2    Monleon, D.3    Bassolino Klimas, D.4    Abate Shen, C.5    Bruccoleri, R.E.6    Montelione, G.T.7
  • 14
    • 0029083544 scopus 로고
    • Detection of protein 3D-ID compatibility characterized by the evaluation of sidechain packing and electrostatic interactions
    • Tokyo
    • Matsuo Y, Nakamura H, Nishikawa K (1995) Detection of protein 3D-ID compatibility characterized by the evaluation of sidechain packing and electrostatic interactions. J Biochem (Tokyo) 118: 137-148
    • (1995) J Biochem , vol.118 , pp. 137-148
    • Matsuo, Y.1    Nakamura, H.2    Nishikawa, K.3
  • 15
    • 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 Biol 247: 536-540
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 16
    • 0027347355 scopus 로고
    • Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties
    • Nakai T, Kidera A, Nakamura H (1993) Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties. J Biomol NMR 3: 19-40
    • (1993) J Biomol NMR , vol.3 , pp. 19-40
    • Nakai, T.1    Kidera, A.2    Nakamura, H.3
  • 17
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides
    • Nakajima N, Nakamura H, Kidera A (1997) Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides. J Phys Chem B 101: 817-824
    • (1997) J Phys Chem B , vol.101 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 18
    • 84962439356 scopus 로고    scopus 로고
    • Roles of electrostatic interaction in proteins
    • Nakamura H (1996) Roles of electrostatic interaction in proteins. Q Rev Biophys 29: 1-90
    • (1996) Q Rev Biophys , vol.29 , pp. 1-90
    • Nakamura, H.1
  • 19
    • 0021691918 scopus 로고
    • An analysis of incorrectly folded protein models - Implications for structure predictions
    • Novotny J, Bruccoleri R, Karplus M (1984) An analysis of incorrectly folded protein models - implications for structure predictions. J Mol Biol 177: 787-818
    • (1984) J Mol Biol , vol.177 , pp. 787-818
    • Novotny, J.1    Bruccoleri, R.2    Karplus, M.3
  • 20
    • 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 (1987) Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA 84: 3086-3090
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Nemethy, G.3    Scheraga, H.A.4
  • 22
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native fold from well-constructed decoys
    • Park BH, Levitt M (1996) Energy functions that discriminate X-ray and near-native fold from well-constructed decoys. J Mol Biol 258: 367-392
    • (1996) J Mol Biol , vol.258 , pp. 367-392
    • Park, B.H.1    Levitt, M.2
  • 23
    • 0027815614 scopus 로고
    • An analysis of packing in the protein folding problem
    • Richards FM, Lim WA (1993) An analysis of packing in the protein folding problem. Q Rev Biophys 26: 423-498
    • (1993) Q Rev Biophys , vol.26 , pp. 423-498
    • Richards, F.M.1    Lim, W.A.2
  • 24
    • 0021755764 scopus 로고
    • Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect
    • Richmond TJ (1984) Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. J Mol Biol 178: 63-89
    • (1984) J Mol Biol , vol.178 , pp. 63-89
    • Richmond, T.J.1
  • 25
    • 0029645581 scopus 로고
    • Crystal structure of thioredoxin-2 from anabaena
    • Saarinen M, Gleason FK, Eklund H (1995) Crystal structure of thioredoxin-2 from anabaena. Structure 3: 1097-1108
    • (1995) Structure , vol.3 , pp. 1097-1108
    • Saarinen, M.1    Gleason, F.K.2    Eklund, H.3
  • 26
    • 0032396395 scopus 로고    scopus 로고
    • Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments
    • Sahasrabudhe PV, Tejero R, Kitao S, Furuichi Y, Montelione GT (1998) Homology modeling of an RNP domain from a human RNA-binding protein: homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments. Proteins 33: 558-566
    • (1998) Proteins , vol.33 , pp. 558-566
    • Sahasrabudhe, P.V.1    Tejero, R.2    Kitao, S.3    Furuichi, Y.4    Montelione, G.T.5
  • 27
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R, Moult J (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275: 895-916
    • (1998) J Mol Biol , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 28
    • 0027293405 scopus 로고
    • Complex of ribonuclease Sa with a cyclic nucleotide and a proposed model for the reaction intermediate
    • Sevcik J, Zegers I, Wyns L, Dauter Z, Wilson KS (1993) Complex of ribonuclease Sa with a cyclic nucleotide and a proposed model for the reaction intermediate. Eur J Biochem 216: 301-305
    • (1993) Eur J Biochem , vol.216 , pp. 301-305
    • Sevcik, J.1    Zegers, I.2    Wyns, L.3    Dauter, Z.4    Wilson, K.S.5
  • 29
    • 0029000696 scopus 로고
    • Knowledge-based potential for proteins
    • Sippl MJ (1995) Knowledge-based potential for proteins. Curr Opin Struct Biol 5: 229-235
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 30
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314: 141-151
    • (1999) Chem Phys Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 32
    • 0025741662 scopus 로고
    • Crystal structure of Escherichia coli CheY refined at 1.7-Å resolution
    • Volz K, Matsumura P (1991) Crystal structure of Escherichia coli CheY refined at 1.7-Å resolution. J Biol Chem 266: 15511-15519
    • (1991) J Biol Chem , vol.266 , pp. 15511-15519
    • Volz, K.1    Matsumura, P.2
  • 33
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • Vorobjev YN, Almagro JC, Hermans J (1998) Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins 32: 399-413
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 34
    • 0024893329 scopus 로고
    • Monte Carlo simulations of a protein molecule with and without hydration energy calculated by the hydrationshell model
    • Wako H (1989) Monte Carlo simulations of a protein molecule with and without hydration energy calculated by the hydrationshell model. J Protein Chem 8: 733-747
    • (1989) J Protein Chem , vol.8 , pp. 733-747
    • Wako, H.1
  • 35
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner SJ, Kollman PA, Nguyen DT, Case DA (1986) An all atom force field for simulations of proteins and nucleic acids. J Comput Chem 7: 230-252
    • (1986) J Comput Chem , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 36
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to molecular dynamics of proteins in solution
    • Wesson L, Eisenberg D (1992) Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1: 227-235
    • (1992) Protein Sci , vol.1 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2


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