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Volumn 12, Issue 9, 2003, Pages 2032-2046

Discrete restraint-based protein modeling and the Cα-trace problem

Author keywords

Automated structure determination; C trace; Comparative modeling; Protein modeling; RAPPER

Indexed keywords

PROTEIN;

EID: 0042010163     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0386903     Document Type: Article
Times cited : (23)

References (45)
  • 1
    • 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
  • 2
    • 0026439783 scopus 로고
    • Application of a directed conformational search for generating 3-D coordinates for protein structures from α-carbon coordinates
    • Bassolino-Klimas, D. and Bruccoleri, R.E. 1992. Application of a directed conformational search for generating 3-D coordinates for protein structures from α-carbon coordinates. Proteins 14: 465-474.
    • (1992) Proteins , vol.14 , pp. 465-474
    • Bassolino-Klimas, D.1    Bruccoleri, R.E.2
  • 4
    • 0023305986 scopus 로고
    • Knowledge-based prediction of protein structures and the design of novel molecules
    • Blundell, T.L., Sibanda, B.L., Sternberg, M.J., and Thornton, J.M. 1987. Knowledge-based prediction of protein structures and the design of novel molecules. Nature 326: 347-352.
    • (1987) Nature , vol.326 , pp. 347-352
    • Blundell, T.L.1    Sibanda, B.L.2    Sternberg, M.J.3    Thornton, J.M.4
  • 5
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
    • Bower, M.J., Cohen, F.E., and Dunbrack Jr., R.L. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J. Mol. Biol. 267: 1268-1282.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack R.L., Jr.3
  • 6
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C. and Lesk, A.M. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5: 823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 8
    • 0025288651 scopus 로고
    • The building ofprotein structures from α-carbon coordinates
    • Correa, P.E. 1990. The building ofprotein structures from α-carbon coordinates. Proteins 7: 366-377.
    • (1990) Proteins , vol.7 , pp. 366-377
    • Correa, P.E.1
  • 10
    • 0037375615 scopus 로고    scopus 로고
    • Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model
    • de Bakker, P.I.W., DePristo, M.A., Burke, D.F., and Blundell, T.L. 2003. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model. Proteins 51: 21-40.
    • (2003) Proteins , vol.51 , pp. 21-40
    • De Bakker, P.I.W.1    DePristo, M.A.2    Burke, D.F.3    Blundell, T.L.4
  • 11
    • 0037375742 scopus 로고    scopus 로고
    • Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles
    • DePristo, M.A., de Bakker, P.I.W., Lovell, S.C., and Blundell, T.L. 2003. Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles. Proteins 51: 41-55.
    • (2003) Proteins , vol.51 , pp. 41-55
    • DePristo, M.A.1    De Bakker, P.I.W.2    Lovell, S.C.3    Blundell, T.L.4
  • 12
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for x-ray protein structure refinement
    • Engh, R.A. and Huber, R. 1991. Accurate bond and angle parameters for x-ray protein structure refinement. Acta Crystallgr. A 47: 392-400.
    • (1991) Acta Crystallgr. A , vol.47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 13
    • 0028066936 scopus 로고
    • Comparison of systematic search and database methods for constructing segments of protein structure
    • Fidelis, K., Stern, P.S., Bacon, D.J., and Moult, J. 1994. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7: 953-960.
    • (1994) Protein Eng. , vol.7 , pp. 953-960
    • Fidelis, K.1    Stern, P.S.2    Bacon, D.J.3    Moult, J.4
  • 14
    • 0022307513 scopus 로고
    • Computer skeletonization and automatic electron density map analysis
    • Greer, J. 1985. Computer skeletonization and automatic electron density map analysis. Methods Enzymol. 115: 206-224.
    • (1985) Methods Enzymol. , vol.115 , pp. 206-224
    • Greer, J.1
  • 15
    • 0025978283 scopus 로고
    • α trace: Application to model building and detection of coordinate errors
    • α trace: Application to model building and detection of coordinate errors. J. Mol. Biol. 218: 183-194.
    • (1991) J. Mol. Biol. , vol.218 , pp. 183-194
    • Holm, L.1    Sander, C.2
  • 16
    • 0000338489 scopus 로고
    • Comparison of solvent-inaccessible cores of homologous proteins: Definitions useful for protein modelling
    • Hubbard, T.J. and Blundell, T.L. 1987. Comparison of solvent-inaccessible cores of homologous proteins: Definitions useful for protein modelling. Protein Eng. 1: 159-171.
    • (1987) Protein Eng. , vol.1 , pp. 159-171
    • Hubbard, T.J.1    Blundell, T.L.2
  • 17
    • 0036775566 scopus 로고    scopus 로고
    • An efficient method for reconstructing protein backbones from α-carbon coordinates
    • Iwata, Y., Kasuya, A., and Miyamoto, S. 2002. An efficient method for reconstructing protein backbones from α-carbon coordinates. J. Mol. Graph. Model. 21: 119-128.
    • (2002) J. Mol. Graph. Model. , vol.21 , pp. 119-128
    • Iwata, Y.1    Kasuya, A.2    Miyamoto, S.3
  • 18
    • 0033548058 scopus 로고    scopus 로고
    • Nonproline cis peptide bonds in proteins
    • Jabs, A., Weiss, M.S., and Hilgenfeld, R. 1999. Nonproline cis peptide bonds in proteins. J. Mol. Biol. 286: 291-304.
    • (1999) J. Mol. Biol. , vol.286 , pp. 291-304
    • Jabs, A.1    Weiss, M.S.2    Hilgenfeld, R.3
  • 19
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones, T.A. and Thirup, S. 1986. Using known substructures in protein model building and crystallography. EMBO J. 5: 819-922.
    • (1986) EMBO J. , vol.5 , pp. 819-922
    • Jones, T.A.1    Thirup, S.2
  • 20
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and 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
  • 21
    • 0036558224 scopus 로고    scopus 로고
    • Energy-based reconstruction of a protein backbone from its α-carbon trace by a Monte-Carlo method
    • Kazmierkiewicz, R., Liwo, A., and Scheraga, H.A, 2002. Energy-based reconstruction of a protein backbone from its α-carbon trace by a Monte-Carlo method. J. Comp. Chem. 23: 715-723.
    • (2002) J. Comp. Chem. , vol.23 , pp. 715-723
    • Kazmierkiewicz, R.1    Liwo, A.2    Scheraga, H.A.3
  • 22
    • 0017157584 scopus 로고
    • A simplified representation of protein conformations for rapid simulation of protein folding
    • Levitt, M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104: 59-107.
    • (1976) J. Mol. Biol. , vol.104 , pp. 59-107
    • Levitt, M.1
  • 23
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • -. 1992. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226: 507-533.
    • (1992) J. Mol. Biol , vol.226 , pp. 507-533
  • 24
    • 0027524668 scopus 로고
    • Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment
    • Liwo, A., Pincus, M.R., Wawak, R.J., Rackovsky, S., and Scheraga, H.A. 1993. Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment. Protein Sci. 2: 1697-1714.
    • (1993) Protein Sci. , vol.2 , pp. 1697-1714
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Scheraga, H.A.5
  • 27
    • 0027584727 scopus 로고
    • PROGEN: An automated modelling algorithm for the generation of complete protein structures from the α-carbon atomic coordinates
    • Mandal, C. and Linthicum, D.S. 1993. PROGEN: An automated modelling algorithm for the generation of complete protein structures from the α-carbon atomic coordinates. J. Comput. Aided Mol. Des. 7: 199-224.
    • (1993) J. Comput. Aided Mol. Des. , vol.7 , pp. 199-224
    • Mandal, C.1    Linthicum, D.S.2
  • 28
    • 0028980317 scopus 로고
    • α coordinates using the dihedral probability grid Monte Carlo method
    • α coordinates using the dihedral probability grid Monte Carlo method. Protein Sci. 4: 1217-1232.
    • (1995) Protein Sci. , vol.4 , pp. 1217-1232
    • Mathiowetz, A.M.1    Goddard W.A. III2
  • 29
    • 0002118275 scopus 로고    scopus 로고
    • Algorithm for rapid reconstruction of protein backbone from α carbon coordinates
    • Milik, M., Kolinski, A., and Skolnick, J. 1997. Algorithm for rapid reconstruction of protein backbone from α carbon coordinates. J. Comp. Chem. 18: 80-85.
    • (1997) J. Comp. Chem. , vol.18 , pp. 80-85
    • Milik, M.1    Kolinski, A.2    Skolnick, J.3
  • 31
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park, B. 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.1    Levitt, M.2
  • 32
    • 0029063717 scopus 로고
    • The complexity and accuracy of discrete state models of protein structure
    • Park, B.H. and Levitt, M. 1995. The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol. 249: 493-507.
    • (1995) J. Mol. Biol. , vol.249 , pp. 493-507
    • Park, B.H.1    Levitt, M.2
  • 33
  • 34
    • 0036089481 scopus 로고    scopus 로고
    • MODBASE, a database of annotated comparative protein structure models
    • Pieper, U., Eswar, N., Stuart, A.C., Ilyin, V.A., and Sali, A. 2002. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 30: 255-259.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 255-259
    • Pieper, U.1    Eswar, N.2    Stuart, A.C.3    Ilyin, V.A.4    Sali, A.5
  • 35
    • 0021460399 scopus 로고
    • Conversion from a virtual-bond chain to a complete polypeptide backbone chain
    • Purisima, E.O. and Scheraga, H.A. 1984. Conversion from a virtual-bond chain to a complete polypeptide backbone chain. Biopolymers 23: 1207-1224.
    • (1984) Biopolymers , vol.23 , pp. 1207-1224
    • Purisima, E.O.1    Scheraga, H.A.2
  • 37
    • 0024570937 scopus 로고
    • Rebuilding flavodoxin from Cα coordinates: A test study
    • Reid, L.S. and Thornton, J.M. 1989. Rebuilding flavodoxin from Cα coordinates: A test study. Proteins 5: 170-182.
    • (1989) Proteins , vol.5 , pp. 170-182
    • Reid, L.S.1    Thornton, J.M.2
  • 38
    • 84986513586 scopus 로고
    • Efficient algorithm for the reconstruction of a protein backbone from the α-carbon coordinates
    • Rey, A. and Skolnick, J. 1992. Efficient algorithm for the reconstruction of a protein backbone from the α-carbon coordinates. J. Comp. Chem. 13: 443-456.
    • (1992) J. Comp. Chem. , vol.13 , pp. 443-456
    • Rey, A.1    Skolnick, J.2
  • 39
    • 0042176794 scopus 로고
    • Three-dimensional coordinates from stereodiagrams of molecular structures
    • Rossmann, M.G. and Argos, P. 1980. Three-dimensional coordinates from stereodiagrams of molecular structures. Acta Crystallogr. B 36: 819-823.
    • (1980) Acta Crystallogr. B , vol.36 , pp. 819-823
    • Rossmann, M.G.1    Argos, P.2
  • 40
    • 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
  • 41
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction
    • Samudrala, R. and Levitt, M. 2000. Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction. Protein Sci. 9: 1399-1401.
    • (2000) Protein Sci. , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 42
    • 0028012281 scopus 로고
    • A molecular dynamics approach for the generation of complete protein structures from limited coordinate data
    • van Gelder, C.W., Leusen, F.J., Leunissen, J.A., and Noordik, J.H. 1994. A molecular dynamics approach for the generation of complete protein structures from limited coordinate data. Proteins 18: 174-185.
    • (1994) Proteins , vol.18 , pp. 174-185
    • Van Gelder, C.W.1    Leusen, F.J.2    Leunissen, J.A.3    Noordik, J.H.4
  • 43
    • 0031933198 scopus 로고    scopus 로고
    • A new procedure for constructing peptides into a given Cα chain
    • Wang, Y., Huq, H.I., de la Cruz, X.F., and Lee, B. 1998. A new procedure for constructing peptides into a given Cα chain. Fold. Dev. 3: 1-10.
    • (1998) Fold. Dev. , vol.3 , pp. 1-10
    • Wang, Y.1    Huq, H.I.2    De la Cruz, X.F.3    Lee, B.4
  • 45
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word, J.M., Lovell, S.C., Richardson, J.S., and Richardson, D.C. 1999b. Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285: 1735-1747.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.