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Volumn 16, Issue 7, 2007, Pages 1410-1421

Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models

Author keywords

Comparative modeling; Knowledge based potentials; Protein structure assessment; Protein structure prediction; Statistical potentials

Indexed keywords

PROTEIN;

EID: 34250886494     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062735907     Document Type: Article
Times cited : (11)

References (56)
  • 1
    • 0032126517 scopus 로고    scopus 로고
    • Generalized affine gap costs for protein sequence alignment
    • Altschul, S. 1998. Generalized affine gap costs for protein sequence alignment. Proteins 32: 88-96.
    • (1998) Proteins , vol.32 , pp. 88-96
    • Altschul, S.1
  • 2
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker, D. and Sali, A. 2001. Protein structure prediction and structural genomics. Science 294: 93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 4
    • 0034284122 scopus 로고    scopus 로고
    • Recent changes to RasMol, recombining the variants
    • Bernstein, H.J. 2000. Recent changes to RasMol, recombining the variants. Trends Biochem. Sci. 25: 453-455.
    • (2000) Trends Biochem. Sci , vol.25 , pp. 453-455
    • Bernstein, H.J.1
  • 9
    • 0029844461 scopus 로고    scopus 로고
    • Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise nonbonded interactions
    • DeBolt, S.E. and Skolnick, J. 1996. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise nonbonded interactions. Protein Eng. 9: 637-655.
    • (1996) Protein Eng , vol.9 , pp. 637-655
    • DeBolt, S.E.1    Skolnick, J.2
  • 10
    • 0031022887 scopus 로고    scopus 로고
    • Additivity principles in biochemistry
    • Dill, K.A. 1997. Additivity principles in biochemistry. J. Biol. Chem. 272: 701-704.
    • (1997) J. Biol. Chem , vol.272 , pp. 701-704
    • Dill, K.A.1
  • 13
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser, A., Do, R.K., and Sali, A. 2000. Modeling of loops in protein structures. Protein Sci. 9: 1753-1773.
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 14
    • 14844299756 scopus 로고    scopus 로고
    • BMP-1/Tolloid-like metalloproteases process endorepellin, the angiostatic C-terminal fragment of perlecan
    • Gonzalez, E.M., Reed, C., Bix, G., Fu, J., Zhang, Y., Gopalakrishnan, B., Greenspan, D.S., and Iozzo, R.V. 2004. BMP-1/Tolloid-like metalloproteases process endorepellin, the angiostatic C-terminal fragment of perlecan. J. Biol. Chem. 280: 7080-7087.
    • (2004) J. Biol. Chem , vol.280 , pp. 7080-7087
    • Gonzalez, E.M.1    Reed, C.2    Bix, G.3    Fu, J.4    Zhang, Y.5    Gopalakrishnan, B.6    Greenspan, D.S.7    Iozzo, R.V.8
  • 15
    • 0016399124 scopus 로고
    • Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals
    • Hagler, A.T., Huler, E., and Lifson, S. 1974. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. Chem. Soc. 96: 5319-5327.
    • (1974) J. Am. Chem. Soc , vol.96 , pp. 5319-5327
    • Hagler, A.T.1    Huler, E.2    Lifson, S.3
  • 16
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones, D.T. 1999. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287: 797-815.
    • (1999) J. Mol. Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 17
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. A new approach to protein fold recognition. Nature 358: 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 18
    • 0348062818 scopus 로고    scopus 로고
    • The SWISS-MODEL repository of annotated three-dimensional protein structure homology models
    • Kopp, J. and Schwede, T. 2004. The SWISS-MODEL repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res. 32: D230-D234.
    • (2004) Nucleic Acids Res , vol.32
    • Kopp, J.1    Schwede, T.2
  • 19
  • 20
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • Lazaridis, T. and Karplus, M. 1998. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288: 477-487.
    • (1998) J. Mol. Biol , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 21
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • Lu, H. and Skolnick, J. 2001. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44: 223-232.
    • (2001) Proteins , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 22
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field,M.J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102: 3586-3616.
    • MacKerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field,M.J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102: 3586-3616.
  • 24
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic level
    • Melo, F. and Feytmans, E. 1997. Novel knowledge-based mean force potential at atomic level. J. Mol. Biol. 267: 207-222.
    • (1997) J. Mol. Biol , vol.267 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 25
    • 0032540222 scopus 로고    scopus 로고
    • Assessing protein structures with a non-local atomic interaction energy
    • Melo, F. and Feytmans, E. 1998. Assessing protein structures with a non-local atomic interaction energy. J. Mol. Biol. 277: 1141-1152.
    • (1998) J. Mol. Biol , vol.277 , pp. 1141-1152
    • Melo, F.1    Feytmans, E.2
  • 26
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • Melo, F., Sanchez, R., and Sali, A. 2002. Statistical potentials for fold assessment. Protein Sci. 11: 430-448.
    • (2002) Protein Sci , vol.11 , pp. 430-448
    • Melo, F.1    Sanchez, R.2    Sali, A.3
  • 27
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S. and Jernigan, R.L. 1985. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18: 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 28
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • Park, B.H. and Levitt, M. 1996. Energy functions that discriminate X-ray and near-native folds 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
  • 29
    • 0031557390 scopus 로고    scopus 로고
    • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    • Park, B.H., Huang, E.S., and Levitt, M. 1997. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 266: 831-846.
    • (1997) J. Mol. Biol , vol.266 , pp. 831-846
    • Park, B.H.1    Huang, E.S.2    Levitt, M.3
  • 33
    • 0031844330 scopus 로고    scopus 로고
    • Function and fold predictions for Mycoplasma genitalium proteins
    • Rychlewski, L., Zhang, B., and Godzik, A. 1998. Function and fold predictions for Mycoplasma genitalium proteins. Fold. Des. 3: 229-238.
    • (1998) Fold. Des , vol.3 , pp. 229-238
    • Rychlewski, L.1    Zhang, B.2    Godzik, A.3
  • 34
    • 0032983055 scopus 로고    scopus 로고
    • Insights from structural predictions: Analysis of Escherichia coli genome
    • Rychlewski, L., Zhang, B., and Godzik, A. 1999. Insights from structural predictions: Analysis of Escherichia coli genome. Protein Sci. 8: 614-624.
    • (1999) Protein Sci , vol.8 , pp. 614-624
    • Rychlewski, L.1    Zhang, B.2    Godzik, A.3
  • 35
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A. and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779-815.
    • (1993) J. Mol. Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 37
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala, R. and 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
  • 38
    • 0032506030 scopus 로고    scopus 로고
    • Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
    • Sanchez, R. and Sali, A. 1998. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. 95: 13597-13602.
    • (1998) Proc. Natl. Acad. Sci , vol.95 , pp. 13597-13602
    • Sanchez, R.1    Sali, A.2
  • 41
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede, T., Kopp, J., Guex, N., and Peitsch, M.C. 2003. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31: 3381-3385.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 42
    • 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. 1990. 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. 213: 859-883.
    • (1990) J. Mol. Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 43
    • 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. 1993a. 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) J. Comput. Aided Mol. Des , vol.7 , pp. 473-501
    • Sippl, M.J.1
  • 44
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl, M.J. 1993b. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
    • (1993) Proteins , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 45
    • 0026704815 scopus 로고
    • Detection of native like models for amino acid sequences of unknown three dimensional structure in a data base of known protein conformations
    • Sippl, M.J. and Weitckus, S. 1992. Detection of native like models for amino acid sequences of unknown three dimensional structure in a data base of known protein conformations. Proteins 13: 258-271.
    • (1992) Proteins , vol.13 , pp. 258-271
    • Sippl, M.J.1    Weitckus, S.2
  • 46
    • 33644842005 scopus 로고    scopus 로고
    • Improvement of statistical potentials and threading score functions using information maximization
    • Solis, A.D. and Rackovsky, S. 2006. Improvement of statistical potentials and threading score functions using information maximization. Proteins 62: 892-908.
    • (2006) Proteins , vol.62 , pp. 892-908
    • Solis, A.D.1    Rackovsky, S.2
  • 47
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems
    • Swets, J.A. 1988. Measuring the accuracy of diagnostic systems. Science 240: 1285-1293.
    • (1988) Science , vol.240 , pp. 1285-1293
    • Swets, J.A.1
  • 48
    • 0034294901 scopus 로고    scopus 로고
    • Better decisions through science
    • Swets, J.A., Dawes, R.M., and Monahan, J. 2000. Better decisions through science. Sci. Am. 283: 82-87.
    • (2000) Sci. Am , vol.283 , pp. 82-87
    • Swets, J.A.1    Dawes, R.M.2    Monahan, J.3
  • 49
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • Tsai, J., Bonneau, R., Morozov, A.V., Kuhlman, B., Rohl, C.A., and Baker, D. 2003. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 52: 76-87.
    • (2003) Proteins , vol.52 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Morozov, A.V.3    Kuhlman, B.4    Rohl, C.A.5    Baker, D.6
  • 50
    • 4544355522 scopus 로고    scopus 로고
    • Improved protein structure selection using decoy-dependent discriminatory functions
    • Wang, K., Fan, B., Levitt, M., and Samudrala, R. 2004. Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct. Biol. 4: 8.
    • (2004) BMC Struct. Biol , vol.4 , pp. 8
    • Wang, K.1    Fan, B.2    Levitt, M.3    Samudrala, R.4
  • 51
    • 84986518863 scopus 로고
    • AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
    • Weiner, P.K. and Kollman, P.A. 1981. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem. 2: 287-303.
    • (1981) J. Comput. Chem , vol.2 , pp. 287-303
    • Weiner, P.K.1    Kollman, P.A.2
  • 52
    • 0034733381 scopus 로고    scopus 로고
    • Ab initio construction of protein tertiary structures using a hierarchical approach
    • Xia, Y., Huang, E.S., Levitt, M., and Samudrala, R. 2000. Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol. 300: 171-185.
    • (2000) J. Mol. Biol , vol.300 , pp. 171-185
    • Xia, Y.1    Huang, E.S.2    Levitt, M.3    Samudrala, R.4
  • 53
    • 0032411227 scopus 로고    scopus 로고
    • Zhang, L., Godzik, A., Skolnick, J., and Fetrow, J.S. 1998. Functional analysis of the Escherichia coli genome for members of the αβ hydrolase family. Fold. Des. 3: 535-548.
    • Zhang, L., Godzik, A., Skolnick, J., and Fetrow, J.S. 1998. Functional analysis of the Escherichia coli genome for members of the αβ hydrolase family. Fold. Des. 3: 535-548.
  • 54
    • 0032932490 scopus 로고    scopus 로고
    • From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions
    • Zhang, B., Rychlewski, L., Pawlowski, K., Fetrow, J.S., Skolnick, J., and Godzik, A. 1999. From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions. Protein Sci. 8: 1104-1115.
    • (1999) Protein Sci , vol.8 , pp. 1104-1115
    • Zhang, B.1    Rychlewski, L.2    Pawlowski, K.3    Fetrow, J.S.4    Skolnick, J.5    Godzik, A.6
  • 55
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • Zhang, Y., Kolinski, A., and Skolnick, J. 2003. TOUCHSTONE II: A new approach to ab initio protein structure prediction. Biophys. J. 85: 1145-1164.
    • (2003) Biophys. J , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 56
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou, H. and Zhou, Y. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11: 2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2


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