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Molecular surfaces: calculations, uses and representations
International Tables for Crystallography (2012). Vol. F, ch. 22.2, pp. 713-720 [ doi:10.1107/97809553602060000886 ]
... Programs that are currently distributed use more sophisticated methods. 22.2.2.3. Connolly dot surface algorithm | | A molecular dot surface is a smooth ... be calculated exactly by analytic and differential geometry (Richmond, 1984; Connolly, 1983). An advantage of analytical expressions over the prior ... atoms to give a dense impression of a surface. 22.2.4.1.2. `Connolly' and solid polyhedral surfaces | | In one of the earliest ...
Schematic and two-dimensional representations such as `roadmap'
International Tables for Crystallography (2012). Vol. F, Section 22.2.4.2, p. 719 [ doi:10.1107/97809553602060000886 ]
... Reprinted with the permission of Cambridge University Press. References Chapman, M. S. (1993). Mapping the surface properties of macromolecules. Protein ... mutants of the poliovirus receptor. Virology, 214, 559-570. Rossmann, M. G. & Palmenberg, A. C. (1988). Conservation of the putative ...
[more results from section 22.2.4 in volume F]
Other non-graphical interpretive methods using surface area
International Tables for Crystallography (2012). Vol. F, Section 22.2.3.3, pp. 716-717 [ doi:10.1107/97809553602060000886 ]
... of the hypervariable regions of known antibody structures. References Gerstein, M. (1992). A resolution-sensitive procedure for comparing surfaces and ... sites. Acta Cryst. A48, 271-276. Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400. Lewis, M. & Rees, D. C. (1985). Fractal surfaces of proteins. ...
[more results from section 22.2.3 in volume F]
Extended atoms account for missing hydrogen atoms
International Tables for Crystallography (2012). Vol. F, Section 22.2.2.8, p. 715 [ doi:10.1107/97809553602060000886 ]
Extended atoms account for missing hydrogen atoms 22.2.2.8. Extended atoms account for missing hydrogen atoms Structures of macromolecules determined by X-ray crystallography rarely reveal the positions of the hydrogen atoms. It is, of course, possible to add explicit hydrogen atoms at the stereochemically most likely positions, but this is rarely ...
[more results from section 22.2.2 in volume F]
Hydrophobicity
International Tables for Crystallography (2012). Vol. F, Section 22.2.1.4, p. 714 [ doi:10.1107/97809553602060000886 ]
... protein denaturation. Adv. Protein Chem. 14, 1-63. Richards, F. M. (1985). Calculation of molecular volumes and areas for structures ...
[more results from section 22.2.1 in volume F]
Conclusion
International Tables for Crystallography (2012). Vol. F, Section 22.2.5, p. 719 [ doi:10.1107/97809553602060000886 ]
... synthesis at 2 Å resolution. Nature (London), 206, 757-761. Chapman, M. S. (1993). Mapping the surface properties of macromolecules. Protein Sci. 2, 459-469. Chapman, M. S. (1994). Sequence similarity scores and the inference of ... Kelly, J. A., Sielecki, A. R., Sykes, B. D., James, M. N. & Phillips, D. C. (1979). X-ray crystallography ...
International Tables for Crystallography (2012). Vol. F, ch. 22.2, pp. 713-720 [ doi:10.1107/97809553602060000886 ]
... Programs that are currently distributed use more sophisticated methods. 22.2.2.3. Connolly dot surface algorithm | | A molecular dot surface is a smooth ... be calculated exactly by analytic and differential geometry (Richmond, 1984; Connolly, 1983). An advantage of analytical expressions over the prior ... atoms to give a dense impression of a surface. 22.2.4.1.2. `Connolly' and solid polyhedral surfaces | | In one of the earliest ...
Schematic and two-dimensional representations such as `roadmap'
International Tables for Crystallography (2012). Vol. F, Section 22.2.4.2, p. 719 [ doi:10.1107/97809553602060000886 ]
... Reprinted with the permission of Cambridge University Press. References Chapman, M. S. (1993). Mapping the surface properties of macromolecules. Protein ... mutants of the poliovirus receptor. Virology, 214, 559-570. Rossmann, M. G. & Palmenberg, A. C. (1988). Conservation of the putative ...
[more results from section 22.2.4 in volume F]
Other non-graphical interpretive methods using surface area
International Tables for Crystallography (2012). Vol. F, Section 22.2.3.3, pp. 716-717 [ doi:10.1107/97809553602060000886 ]
... of the hypervariable regions of known antibody structures. References Gerstein, M. (1992). A resolution-sensitive procedure for comparing surfaces and ... sites. Acta Cryst. A48, 271-276. Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400. Lewis, M. & Rees, D. C. (1985). Fractal surfaces of proteins. ...
[more results from section 22.2.3 in volume F]
Extended atoms account for missing hydrogen atoms
International Tables for Crystallography (2012). Vol. F, Section 22.2.2.8, p. 715 [ doi:10.1107/97809553602060000886 ]
Extended atoms account for missing hydrogen atoms 22.2.2.8. Extended atoms account for missing hydrogen atoms Structures of macromolecules determined by X-ray crystallography rarely reveal the positions of the hydrogen atoms. It is, of course, possible to add explicit hydrogen atoms at the stereochemically most likely positions, but this is rarely ...
[more results from section 22.2.2 in volume F]
Hydrophobicity
International Tables for Crystallography (2012). Vol. F, Section 22.2.1.4, p. 714 [ doi:10.1107/97809553602060000886 ]
... protein denaturation. Adv. Protein Chem. 14, 1-63. Richards, F. M. (1985). Calculation of molecular volumes and areas for structures ...
[more results from section 22.2.1 in volume F]
Conclusion
International Tables for Crystallography (2012). Vol. F, Section 22.2.5, p. 719 [ doi:10.1107/97809553602060000886 ]
... synthesis at 2 Å resolution. Nature (London), 206, 757-761. Chapman, M. S. (1993). Mapping the surface properties of macromolecules. Protein Sci. 2, 459-469. Chapman, M. S. (1994). Sequence similarity scores and the inference of ... Kelly, J. A., Sielecki, A. R., Sykes, B. D., James, M. N. & Phillips, D. C. (1979). X-ray crystallography ...
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