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Protein geometry: volumes, areas and distances
International Tables for Crystallography (2012). Vol. F, ch. 22.1, pp. 703-712 [ doi:10.1107/97809553602060000885 ]
... does not amount to more than 1 part in 500 (Gerstein et al., 1995). 22.1.2.3.3. `Chopping-down' method of finding ... resolution protein crystal structures, which have many solvent atoms positioned (Gerstein & Chothia, 1996). Alternatively, one can make up the positions ... to the results of molecular simulation (Finney et al., 1980; Gerstein et al., 1995; Richards, 1974). 22.1.3.2. Definitions of ...
The tight packing of the protein core
International Tables for Crystallography (2012). Vol. F, Section 22.1.5.2, pp. 710-711 [ doi:10.1107/97809553602060000885 ]
... to be a strong constraint on protein flexibility and motions (Gerstein et al., 1993; Gerstein, Lesk & Chothia, 1994). However, there are exceptions, and some ... getting the overall volume of the core right rather easily (Gerstein, Sonnhammer & Chothia, 1994; Kapp et al., 1995; Lim & Ptitsyn, ...
[more results from section 22.1.5 in volume F]
The probe radius
International Tables for Crystallography (2012). Vol. F, Section 22.1.4.2, p. 709 [ doi:10.1107/97809553602060000885 ]
... to be about 1.4 Å. References Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static ...
[more results from section 22.1.4 in volume F]
Further points
International Tables for Crystallography (2012). Vol. F, Section 22.1.3.3.4, p. 708 [ doi:10.1107/97809553602060000885 ]
... surface more closely linked to the behaviour of real water (Gerstein & Lynden-Bell, 1993c). The definitions of accessible surface and ... Leicester et al., 1988; Pattabiraman et al., 1995). References Gerstein, M. & Lynden-Bell, R. M. (1993c). What is the ...
[more results from section 22.1.3 in volume F]
Delaunay triangulation
International Tables for Crystallography (2012). Vol. F, Section 22.1.2.4, pp. 705-706 [ doi:10.1107/97809553602060000885 ]
... 1994; Peters et al., 1996). References Edelsbrunner, H., Facello, M. & Liang, J. (1996). On the Definition and Construction of ... Macromolecules, pp. 272-287. Singapore: World Scientific. Edelsbrunner, H., Facello, M., Ping, F. & Jie, L. (1995). Measuring proteins and voids ... acid residues. J. Comput. Biol. 3, 213-222. Tsai, J., Gerstein, M. & Levitt, M. (1996). Keeping the shape but ...
[more results from section 22.1.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 22.1.1, p. 703 [ doi:10.1107/97809553602060000885 ]
Introduction 22.1.1. Introduction For geometric analysis, a protein consists of a set of points in three dimensions. This information corresponds to the actual data provided by the experiment, which are fundamentally of a geometric rather than chemical nature. That is, crystallography primarily tells one about the positions of atoms and perhaps ...
International Tables for Crystallography (2012). Vol. F, ch. 22.1, pp. 703-712 [ doi:10.1107/97809553602060000885 ]
... does not amount to more than 1 part in 500 (Gerstein et al., 1995). 22.1.2.3.3. `Chopping-down' method of finding ... resolution protein crystal structures, which have many solvent atoms positioned (Gerstein & Chothia, 1996). Alternatively, one can make up the positions ... to the results of molecular simulation (Finney et al., 1980; Gerstein et al., 1995; Richards, 1974). 22.1.3.2. Definitions of ...
The tight packing of the protein core
International Tables for Crystallography (2012). Vol. F, Section 22.1.5.2, pp. 710-711 [ doi:10.1107/97809553602060000885 ]
... to be a strong constraint on protein flexibility and motions (Gerstein et al., 1993; Gerstein, Lesk & Chothia, 1994). However, there are exceptions, and some ... getting the overall volume of the core right rather easily (Gerstein, Sonnhammer & Chothia, 1994; Kapp et al., 1995; Lim & Ptitsyn, ...
[more results from section 22.1.5 in volume F]
The probe radius
International Tables for Crystallography (2012). Vol. F, Section 22.1.4.2, p. 709 [ doi:10.1107/97809553602060000885 ]
... to be about 1.4 Å. References Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static ...
[more results from section 22.1.4 in volume F]
Further points
International Tables for Crystallography (2012). Vol. F, Section 22.1.3.3.4, p. 708 [ doi:10.1107/97809553602060000885 ]
... surface more closely linked to the behaviour of real water (Gerstein & Lynden-Bell, 1993c). The definitions of accessible surface and ... Leicester et al., 1988; Pattabiraman et al., 1995). References Gerstein, M. & Lynden-Bell, R. M. (1993c). What is the ...
[more results from section 22.1.3 in volume F]
Delaunay triangulation
International Tables for Crystallography (2012). Vol. F, Section 22.1.2.4, pp. 705-706 [ doi:10.1107/97809553602060000885 ]
... 1994; Peters et al., 1996). References Edelsbrunner, H., Facello, M. & Liang, J. (1996). On the Definition and Construction of ... Macromolecules, pp. 272-287. Singapore: World Scientific. Edelsbrunner, H., Facello, M., Ping, F. & Jie, L. (1995). Measuring proteins and voids ... acid residues. J. Comput. Biol. 3, 213-222. Tsai, J., Gerstein, M. & Levitt, M. (1996). Keeping the shape but ...
[more results from section 22.1.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 22.1.1, p. 703 [ doi:10.1107/97809553602060000885 ]
Introduction 22.1.1. Introduction For geometric analysis, a protein consists of a set of points in three dimensions. This information corresponds to the actual data provided by the experiment, which are fundamentally of a geometric rather than chemical nature. That is, crystallography primarily tells one about the positions of atoms and perhaps ...
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