International Tables for Crystallography (2006). Vol. F. ch. 22.1, pp. 531-545
https://doi.org/10.1107/97809553602060000710 |
Chapter 22.1. Protein surfaces and volumes: measurement and use
Contents
- 22.1. Protein surfaces and volumes: measurement and use (pp. 531-545) | html | pdf | chapter contents |
- 22.1.1. Protein geometry: volumes, areas and distances (pp. 531-539) | html | pdf |
- 22.1.1.1. Introduction (p. 531) | html | pdf |
- 22.1.1.2. Definitions of protein volume (pp. 531-533) | html | pdf |
- 22.1.1.3. Definitions of protein surface (pp. 534-536) | html | pdf |
- 22.1.1.3.1. The problem of the protein surface (p. 534) | html | pdf |
- 22.1.1.3.2. Definitions of surface in terms of Voronoi polyhedra (the convex hull) (p. 534) | html | pdf |
- 22.1.1.3.3. Definitions of surface in terms of a probe sphere (pp. 534-536) | html | pdf |
- 22.1.1.3.3.1. van der Waals surface (VDWS) (p. 535) | html | pdf |
- 22.1.1.3.3.2. Solvent-accessible surface (SAS) (p. 535) | html | pdf |
- 22.1.1.3.3.3. Molecular surface as the sum of the contact and re-entrant surfaces (MS = CS + RS) (p. 535) | html | pdf |
- 22.1.1.3.3.4. Further points (pp. 535-536) | html | pdf |
- 22.1.1.4. Definitions of atomic radii (pp. 536-537) | html | pdf |
- 22.1.1.5. Application of geometry calculations: the measurement of packing (pp. 537-539) | html | pdf |
- 22.1.2. Molecular surfaces: calculations, uses and representations (pp. 539-545) | html | pdf |
- 22.1.2.1. Introduction (pp. 539-540) | html | pdf |
- 22.1.2.2. Calculation of surface area and energies of interaction (pp. 540-541) | html | pdf |
- 22.1.2.2.1. Introduction (pp. 540-541) | html | pdf |
- 22.1.2.2.2. Lee & Richards planar slices (p. 541) | html | pdf |
- 22.1.2.2.3. Connolly dot surface algorithm (p. 541) | html | pdf |
- 22.1.2.2.4. Marching-cube algorithm (p. 541) | html | pdf |
- 22.1.2.2.5. Complete and connected rolling algorithms (p. 541) | html | pdf |
- 22.1.2.2.6. Analytic surface calculations and the Gauss–Bonnet theorem (p. 541) | html | pdf |
- 22.1.2.2.7. Approximations to the surface (p. 541) | html | pdf |
- 22.1.2.2.8. Extended atoms account for missing hydrogen atoms (p. 541) | html | pdf |
- 22.1.2.3. Estimation of binding energies (pp. 542-543) | html | pdf |
- 22.1.2.4. Graphical representations of shape and properties (pp. 543-545) | html | pdf |
- 22.1.2.4.1. Realistic (pp. 543-544) | html | pdf |
- 22.1.2.4.1.1. Shaded backbone (p. 543) | html | pdf |
- 22.1.2.4.1.2. `Connolly' and solid polyhedral surfaces (p. 543) | html | pdf |
- 22.1.2.4.1.3. Photorealistic rendering (p. 543) | html | pdf |
- 22.1.2.4.1.4. GRASP surfaces (pp. 543-544) | html | pdf |
- 22.1.2.4.1.5. Implementations in popular packages (p. 544) | html | pdf |
- 22.1.2.4.2. Schematic and two-dimensional representations such as `roadmap' (pp. 544-545) | html | pdf |
- 22.1.2.4.1. Realistic (pp. 543-544) | html | pdf |
- 22.1.2.5. Conclusion (p. 545) | html | pdf |
- References | html | pdf |
- Figures
- Fig. 22.1.1.1. The Voronoi construction in two and three dimensions (p. 531) | html | pdf |
- Fig. 22.1.1.2. Labelling parts of Voronoi polyhedra (p. 532) | html | pdf |
- Fig. 22.1.1.3. Positioning of the dividing plane (p. 532) | html | pdf |
- Fig. 22.1.1.4. The `chopping-down' method of polyhedra construction (p. 533) | html | pdf |
- Fig. 22.1.1.5. Delaunay triangulation and its relation to the Voronoi construction (p. 534) | html | pdf |
- Fig. 22.1.1.6. The problem of the protein surface (p. 534) | html | pdf |
- Fig. 22.1.1.7. Definitions of the protein surface (p. 535) | html | pdf |
- Fig. 22.1.1.8. Packing efficiency (p. 537) | html | pdf |
- Fig. 22.1.2.1. Surfaces in a plane cut through a hypothetical molecule (p. 540) | html | pdf |
- Fig. 22.1.2.2. GRASP example (p. 543) | html | pdf |
- Fig. 22.1.2.3. (a) Solvent-accessible surface topology of a rhinovirus 14–drug complex (Kim et al (p. 544) | html | pdf |
- Fig. 22.1.2.4. Different projections illustrated with lysozyme (p. 545) | html | pdf |
- Tables
- Table 22.1.1.1. Standard atomic radii (Å) (p. 536) | html | pdf |
- Table 22.1.1.2. Probe radii and their relation to surface definition (p. 537) | html | pdf |
- Table 22.1.1.3. Standard residue volumes (p. 538) | html | pdf |
- Table 22.1.1.4. Standard atomic volumes (p. 539) | html | pdf |
- Table 22.1.2.1. The atomic solvation parameters of Eisenberg & McLachlan (1986) (p. 542) | html | pdf |
- 22.1.1. Protein geometry: volumes, areas and distances (pp. 531-539) | html | pdf |