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Volumn 264, Issue 1, 1996, Pages 121-136

Deviations from standard atomic volumes as a quality measure for protein crystal structures

Author keywords

Protein structures; Quality assessment; Voronoi volumes

Indexed keywords

ARTICLE; CALCULATION; COMPUTER PROGRAM; COMPUTER SYSTEM; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; R FACTOR; STEREOCHEMISTRY;

EID: 0030598343     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0628     Document Type: Article
Times cited : (565)

References (33)
  • 4
    • 0023140814 scopus 로고
    • Crystallographic R-factor refinement by molecular dynamics
    • Brünger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Brünger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 5
    • 0016606973 scopus 로고
    • Structural invariants in protein folding
    • Chothia, C. (1975). Structural invariants in protein folding. Nature, 254, 304-308.
    • (1975) Nature , vol.254 , pp. 304-308
    • Chothia, C.1
  • 6
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly, M. L. (1983). Analytical molecular surface calculation. J. Appl. Crystallog. 16, 548-558.
    • (1983) J. Appl. Crystallog. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 7
    • 33845377446 scopus 로고
    • Computation of molecular volume
    • Connolly, M. L. (1985). Computation of molecular volume. J. Am. Chem. Soc. 107, 1118-1124.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 1118-1124
    • Connolly, M.L.1
  • 9
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structures refinement
    • Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structures refinement. Acta Crystallog. sect. A, 47, 392-400.
    • (1991) Acta Crystallog. Sect. A , vol.47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 10
    • 0016816308 scopus 로고
    • Volume occupation, environment and accessibility in proteins. The problem of the protein surface
    • Finney, J. L. (1975). Volume occupation, environment and accessibility in proteins. The problem of the protein surface. J. Mol. Biol. 96, 721-732.
    • (1975) J. Mol. Biol. , vol.96 , pp. 721-732
    • Finney, J.L.1
  • 11
    • 0020491206 scopus 로고
    • Calculation of protein volumes: An alternative to the Voronoi procedure
    • Gellatly, B. J. & Finney, J. L. (1982). Calculation of protein volumes: an alternative to the Voronoi procedure. J. Mol. Biol. 161, 305-322.
    • (1982) J. Mol. Biol. , vol.161 , pp. 305-322
    • Gellatly, B.J.1    Finney, J.L.2
  • 13
    • 0029004611 scopus 로고
    • The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra
    • Gerstein, M., Tsai, J. & Levitt, M. (1995). The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249, 955-966.
    • (1995) J. Mol. Biol. , vol.249 , pp. 955-966
    • Gerstein, M.1    Tsai, J.2    Levitt, M.3
  • 14
    • 0028773889 scopus 로고
    • Volume changes on protein folding
    • Harpaz, Y., Gerstein, M. & Chothia, C. (1994). Volume changes on protein folding. Structure, 2, 611-649.
    • (1994) Structure , vol.2 , pp. 611-649
    • Harpaz, Y.1    Gerstein, M.2    Chothia, C.3
  • 15
    • 85030282168 scopus 로고
    • (Diamond, R., Ramaseshan S. & Venkatesan K., eds). Indian Acad. Sci., Bangalore
    • Hendrickson, W. A. & Konnert, J. H. (1980). In Computing in Crystallography (Diamond, R., Ramaseshan S. & Venkatesan K., eds), pp. 1301, Indian Acad. Sci., Bangalore.
    • (1980) Computing in Crystallography , vol.1301
    • Hendrickson, W.A.1    Konnert, J.H.2
  • 16
    • 0026505184 scopus 로고
    • Evaluation of protein models by atomic solvation preference
    • Holm, L. & Sander, C. (1992). Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225, 93-105.
    • (1992) J. Mol. Biol. , vol.225 , pp. 93-105
    • Holm, L.1    Sander, C.2
  • 17
    • 0014842661 scopus 로고
    • Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969)
    • IUPAC-IUB Commission on Biochemical Nomenclature. (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969). Biochemisty, 9, 3471-3479.
    • (1970) Biochemisty , vol.9 , pp. 3471-3479
  • 18
    • 84918314491 scopus 로고
    • Refinement of large structures by simultaneous minimization of energy and R-factor
    • Jack, A. & Levitt, M. (1978). Refinement of large structures by simultaneous minimization of energy and R-factor. Acta Crystallog. sect A, 34, 931-935.
    • (1978) Acta Crystallog. Sect A , vol.34 , pp. 931-935
    • Jack, A.1    Levitt, M.2
  • 19
    • 0027169515 scopus 로고
    • Main-chain bond lengths and bond angles in protein structures
    • Laskowski, R. A., Moss, D. S. & Thornton, J. (1993a). Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231, 1049-1067.
    • (1993) J. Mol. Biol. , vol.231 , pp. 1049-1067
    • Laskowski, R.A.1    Moss, D.S.2    Thornton, J.3
  • 20
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993b). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26, 283-291.
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 21
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 22
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Luthy, R., Bowie, J. U. & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
    • (1992) Nature , vol.356 , pp. 83-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 23
    • 0027999315 scopus 로고
    • Knowledge based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy
    • MacArthur, M. W., Laskowski, R. A. & Thornton, J. M. (1994). Knowledge based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr Opin. Struct. Biol. 4, 731-737.
    • (1994) Curr Opin. Struct. Biol. , vol.4 , pp. 731-737
    • MacArthur, M.W.1    Laskowski, R.A.2    Thornton, J.M.3
  • 25
    • 0027220647 scopus 로고
    • Identification and classification of protein fold families
    • Orengo, C. A., Flores, T. P., Taylor, W. R. & Thornton, J. M. (1993). Identification and classification of protein fold families. Protein Eng. 6, 485-500.
    • (1993) Protein Eng. , vol.6 , pp. 485-500
    • Orengo, C.A.1    Flores, T.P.2    Taylor, W.R.3    Thornton, J.M.4
  • 26
    • 0015977588 scopus 로고
    • The interpretation of protein structures: Total volume, group volume distributions and packing density
    • Richards, F. M. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14.
    • (1974) J. Mol. Biol. , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 27
    • 0022328790 scopus 로고
    • Calculation of molecular volumes and areas for structures of known geometry
    • Richards, F. M. (1985). Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 115, 440-464.
    • (1985) Methods Enzymol. , vol.115 , pp. 440-464
    • Richards, F.M.1
  • 28
    • 0026704815 scopus 로고
    • Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known conformations
    • Sippl, M. J. & Weitckus, S. (1992). Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known conformations. Proteins: Struct. Funct. Genet. 13, 258-271.
    • (1992) Proteins: Struct. Funct. Genet. , vol.13 , pp. 258-271
    • Sippl, M.J.1    Weitckus, S.2
  • 29
    • 0025299887 scopus 로고
    • Occurrence and role of cis peptide bonds in protein structures
    • Stewart, D. E., Sarkar, A. & Wampler, J. E. (1990). Occurrence and role of cis peptide bonds in protein structures. J. Mol. Biol. 214, 253-260.
    • (1990) J. Mol. Biol. , vol.214 , pp. 253-260
    • Stewart, D.E.1    Sarkar, A.2    Wampler, J.E.3
  • 30
    • 0028883878 scopus 로고
    • Significance of structural changes in proteins: Expected errors in refined protein structures
    • Stroud, R. M. & Fauman, E. B. (1995). Significance of structural changes in proteins: expected errors in refined protein structures. Protein Sci. 4, 2392-2404.
    • (1995) Protein Sci. , vol.4 , pp. 2392-2404
    • Stroud, R.M.1    Fauman, E.B.2
  • 31
    • 0022298619 scopus 로고
    • (Wyckoff, H. W. et al., eds). Academic Press, Florida
    • Sussman, J. L. (1985). In Methods in Enzymology (Wyckoff, H. W. et al., eds), vol. 115, pp. 271-303, Academic Press, Florida.
    • (1985) Methods in Enzymology , vol.115 , pp. 271-303
    • Sussman, J.L.1
  • 32
    • 84913050729 scopus 로고
    • An efficient general-purpose least-squares refinement program for macromolecular structures
    • Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallog. sect. A, 43, 489-501.
    • (1987) Acta Crystallog. Sect. A , vol.43 , pp. 489-501
    • Tronrud, D.E.1    Ten Eyck, L.F.2    Matthews, B.W.3
  • 33
    • 84927514013 scopus 로고
    • Nouvelles applications des paramètres continus à la théorie des formes quadratiques
    • Voronoi, G. F. (1908). Nouvelles applications des paramètres continus à la théorie des formes quadratiques. J. Reine Angew. Math. 134, 198-287.
    • (1908) J. Reine Angew. Math. , vol.134 , pp. 198-287
    • Voronoi, G.F.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.