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Volumn 31, Issue 2, 1998, Pages 139-149

Influence of protein structure databases on the predictive power of statistical pair potentials

Author keywords

Assessing protein models; Protein structure; Protein structure database; Statistical potentials

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; DATA BASE; ENERGY TRANSFER; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; RELIABILITY; STATISTICAL ANALYSIS;

EID: 0032080720     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980501)31:2<139::AID-PROT4>3.0.CO;2-H     Document Type: Article
Times cited : (34)

References (43)
  • 1
    • 0028929556 scopus 로고
    • Principles of protein folding: A perspective from simple exact models
    • Dill, K.A., Bromberg, S., Yue, K.Z., et al. Principles of protein folding: A perspective from simple exact models. Protein Sci. 4:561-602, 1995.
    • (1995) Protein Sci. , vol.4 , pp. 561-602
    • Dill, K.A.1    Bromberg, S.2    Yue, K.Z.3
  • 2
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • Jernigan, R.L., Bahar, I. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6:195-209, 1996.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 4
    • 0029869187 scopus 로고    scopus 로고
    • Mean-field minimization methods for biological macromolecules
    • Koehl, P., Delarue, M. Mean-field minimization methods for biological macromolecules. Curr. Opinion Struct. Biol. 6:222-226, 1996.
    • (1996) Curr. Opinion Struct. Biol. , vol.6 , pp. 222-226
    • Koehl, P.1    Delarue, M.2
  • 6
    • 0030904524 scopus 로고    scopus 로고
    • Novel methods of sampling phase space in the simulation of biological systems
    • Berne, B.J., Straub, J.E. Novel methods of sampling phase space in the simulation of biological systems. Curr. Opin. Struct. Biol. 7:181-189, 1997.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 181-189
    • Berne, B.J.1    Straub, J.E.2
  • 8
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl, M.J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:229-235, 1995.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 9
    • 0031566950 scopus 로고    scopus 로고
    • Interresidue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar, I., Jernigan, R.L. Interresidue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:195-214, 1997.
    • (1997) J. Mol. Biol. , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 10
    • 0026785519 scopus 로고
    • Contact potential that recognises the correct folding of globular proteins
    • Maiorov, V.N., Crippen, G.M. Contact potential that recognises the correct folding of globular proteins. J. Mol. Biol. 227:876-888, 1992.
    • (1992) J. Mol. Biol. , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 12
    • 0029114646 scopus 로고
    • Conformation, energy, and folding ability of selected amino acid sequences
    • Sasai, M. Conformation, energy, and folding ability of selected amino acid sequences. Proc. Natl. Acad. Sci. U.S.A. 92:8438-8442, 1995.
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 8438-8442
    • Sasai, M.1
  • 13
    • 0029895539 scopus 로고    scopus 로고
    • Self-consistently optimized statistical mechanical energy functions for sequence structure alignment
    • Koretke, K.K., Luthey-Schulten, Z., Wolynes, P.G. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Sci. 5:1043-1059, 1996.
    • (1996) Protein Sci. , vol.5 , pp. 1043-1059
    • Koretke, K.K.1    Luthey-Schulten, Z.2    Wolynes, P.G.3
  • 14
    • 0000829596 scopus 로고    scopus 로고
    • Optimizing potential functions for protein folding
    • Hao, M.H., Scheraga, H.A. Optimizing potential functions for protein folding. J. Phys. Chem. 100:14540-14548, 1996.
    • (1996) J. Phys. Chem. , vol.100 , pp. 14540-14548
    • Hao, M.H.1    Scheraga, H.A.2
  • 15
    • 0029909384 scopus 로고    scopus 로고
    • An iterative method for extracting energy-like quantities from protein structures
    • Thomas, P.D., Dill, K.A. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. U.S.A. 93:11628-11633, 1996.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 11628-11633
    • Thomas, P.D.1    Dill, K.A.2
  • 16
    • 0030593470 scopus 로고    scopus 로고
    • Easily searched protein folding potentials
    • Crippen, G.M. Easily searched protein folding potentials. J. Mol. Biol. 260:467-475, 1996.
    • (1996) J. Mol. Biol. , vol.260 , pp. 467-475
    • Crippen, G.M.1
  • 17
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential: A new approach to an old problem
    • Mirny, L.A., Shakhnovich, E.I. How to derive a protein folding potential: A new approach to an old problem. J. Mol. Biol. 264:1164-1179, 1996.
    • (1996) J. Mol. Biol. , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 18
    • 0017021957 scopus 로고    scopus 로고
    • Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka, S., Scheraga, H.A. Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9:1976.
    • Macromolecules , vol.9 , pp. 1976
    • Tanaka, S.1    Scheraga, H.A.2
  • 19
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasichemical approximation
    • Miyazawa, S., Jernigan, R.L. Estimation of effective interresidue contact energies from protein crystal structures: Quasichemical approximation. Macromolecules 18:534-552, 1985.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 20
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M.J. Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 1990:859-883, 1990.
    • (1990) J. Mol. Biol. , vol.1990 , pp. 859-883
    • Sippl, M.J.1
  • 21
    • 0025008445 scopus 로고
    • Identification of native protein folds amongst a large number of incorrect models
    • Hendlich, M., Lackner, P., Weitckus, S., et al. Identification of native protein folds amongst a large number of incorrect models. J. Mol. Biol. 216:167-180, 1990.
    • (1990) J. Mol. Biol. , vol.216 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3
  • 22
    • 0026655922 scopus 로고
    • Protein tertiary structure recognition using optimized hamiltonians with local interactions
    • Goldstein, R.A., Luthey-Schulten, Z.A., Wolynes, P.G. Protein tertiary structure recognition using optimized hamiltonians with local interactions. Proc. Natl. Acad. Sci. U.S.A. 89:9029-9033, 1992.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 9029-9033
    • Goldstein, R.A.1    Luthey-Schulten, Z.A.2    Wolynes, P.G.3
  • 23
    • 0000778903 scopus 로고
    • A general method for the prediction of the three-dimensional structure and folding pathway of globular proteins: Application to designed helical proteins
    • Kolinski, A., Godzik, A., Skolnick, J. A general method for the prediction of the three-dimensional structure and folding pathway of globular proteins: Application to designed helical proteins. J. Chem. Phys. 98:7420-7433, 1993.
    • (1993) J. Chem. Phys. , vol.98 , pp. 7420-7433
    • Kolinski, A.1    Godzik, A.2    Skolnick, J.3
  • 25
    • 0029044472 scopus 로고
    • Atomic environment energies in proteins denned from statistics of accessible and contact surface areas
    • Delarue, M., Koehl, P. Atomic environment energies in proteins denned from statistics of accessible and contact surface areas. J. Mol. Biol. 249:675-690, 1995.
    • (1995) J. Mol. Biol. , vol.249 , pp. 675-690
    • Delarue, M.1    Koehl, P.2
  • 26
    • 0030056418 scopus 로고    scopus 로고
    • Hydrophobic regions on protein surfaces: Derivation of the solvation energy from their area distribution in crystallographic protein structures
    • Eisenhaber, F. Hydrophobic regions on protein surfaces: Derivation of the solvation energy from their area distribution in crystallographic protein structures. Protein Sci. 5:1676-1686, 1996.
    • (1996) Protein Sci. , vol.5 , pp. 1676-1686
    • Eisenhaber, F.1
  • 28
    • 0028072364 scopus 로고
    • Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy
    • DeWitte, R.S., Shakhnovich, E.I. Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy. Prot. Sci. 3:1570-1581, 1994.
    • (1994) Prot. Sci. , vol.3 , pp. 1570-1581
    • DeWitte, R.S.1    Shakhnovich, E.I.2
  • 29
    • 0026016378 scopus 로고
    • The frequency of ion pair substructures is quantitatively related to the electrostatic potential: A statistical model for nonbonded interactions
    • Bryant, S.H., Lawrence, C.E. The frequency of ion pair substructures is quantitatively related to the electrostatic potential: A statistical model for nonbonded interactions. Proteins 9:108-119, 1991.
    • (1991) Proteins , vol.9 , pp. 108-119
    • Bryant, S.H.1    Lawrence, C.E.2
  • 30
    • 0030564892 scopus 로고    scopus 로고
    • Helmholtz free energy of peptide hydrogen bonds in proteins
    • Sippl, M.J. Helmholtz free energy of peptide hydrogen bonds in proteins. J. Mol. Biol. 260:644-648, 1996.
    • (1996) J. Mol. Biol. , vol.260 , pp. 644-648
    • Sippl, M.J.1
  • 31
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • Park, B.H., Levitt, M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258:367-392, 1996.
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.H.1    Levitt, M.2
  • 32
    • 0026704815 scopus 로고
    • Detection of native-like models for amino-acid sequences of unknown three-dimensional structure in a database of known protein conformation
    • Sippl, M., Weitckus, S. Detection of native-like models for amino-acid sequences of unknown three-dimensional structure in a database of known protein conformation. Proteins 13:258-271, 1992.
    • (1992) Proteins , vol.13 , pp. 258-271
    • Sippl, M.1    Weitckus, S.2
  • 33
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl, M.J. Recognition of errors in three-dimensional structures of proteins. Proteins 17:355-362, 1993.
    • (1993) Proteins , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 34
    • 0027181904 scopus 로고
    • Lattice neural network minimization: Application of neural network optimization for locating the global-minimum conformations of proteins
    • Rabow, A.A., Scheraga, H.A. Lattice neural network minimization: Application of neural network optimization for locating the global-minimum conformations of proteins. J. Mol. Biol. 232:1157-1168, 1993.
    • (1993) J. Mol. Biol. , vol.232 , pp. 1157-1168
    • Rabow, A.A.1    Scheraga, H.A.2
  • 35
    • 0027438090 scopus 로고
    • A new approach to the design of stable proteins
    • Shakhnovich, E.I., Gutin, A.M. A new approach to the design of stable proteins. Protein Eng. 6:793-800, 1993.
    • (1993) Protein Eng. , vol.6 , pp. 793-800
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 36
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • Thomas, P.D., Dill, K.A. Statistical potentials extracted from protein structures: How accurate are they? J. Mol. Biol. 257:457-469, 1996.
    • (1996) J. Mol. Biol. , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 37
    • 0029563695 scopus 로고
    • Are database-derived potentials valid for scoring both forward and inverted protein folding?
    • Rooman, M.J., Wodak, S.J. Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng. 8:849-858, 1995.
    • (1995) Protein Eng. , vol.8 , pp. 849-858
    • Rooman, M.J.1    Wodak, S.J.2
  • 38
    • 0027650879 scopus 로고
    • Boltzmann's principle, knowledge-based mean fields and protein folding: An approach to the computational determination of protein structures
    • Sippl, M.J. Boltzmann's principle, knowledge-based mean fields and protein folding: An approach to the computational determination of protein structures. J. Comput. Aided. Mol. Des. 7:473-501, 1993.
    • (1993) J. Comput. Aided. Mol. Des. , vol.7 , pp. 473-501
    • Sippl, M.J.1
  • 39
    • 0017411710 scopus 로고
    • The protein databank: A computer-based archival file for macro-molecular structures
    • Bernstein, F.C., Koetzle, T.F., Williams, G., et al. The protein databank: A computer-based archival file for macro-molecular structures. J. Mol. Biol. 112:535-542, 1977.
    • (1977) J. Mol. Biol. , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.3
  • 41
    • 0007894360 scopus 로고    scopus 로고
    • Predictive power of mean force pair potentials
    • Bohr, H., Brunak, S. (eds.). Amsterdam: IOS Press
    • Sippl, M.J., Jaritz, M. Predictive power of mean force pair potentials. In: 'Proteins Structure by Distance Analysis.' Bohr, H., Brunak, S. (eds.). Amsterdam: IOS Press, 1994: 113-134.
    • Proteins Structure by Distance Analysis , vol.1994 , pp. 113-134
    • Sippl, M.J.1    Jaritz, M.2
  • 42
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher, J.-P.A., Rooman, M.J., Wodak, S. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235:1598-1613, 1994.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1598-1613
    • Kocher, J.-P.A.1    Rooman, M.J.2    Wodak, S.3
  • 43
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa, S., Jernigan, R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:623-644, 1996.
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2


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