International Tables for Crystallography (2012). Vol. F. ch. 22.2, pp. 713-720   | 1 | 2 |
https://doi.org/10.1107/97809553602060000886

Chapter 22.2. Molecular surfaces: calculations, uses and representations

Contents

  • 22.2. Molecular surfaces: calculations, uses and representations  (pp. 713-720) | html | pdf | chapter contents |
    M. S. Chapman and M. L. Connolly
    • 22.2.1. Introduction  (pp. 713-714) | html | pdf |
      • 22.2.1.1. Uses of surface-area calculations  (p. 713) | html | pdf |
      • 22.2.1.2. Molecular, solvent-accessible and occluded surface areas  (pp. 713-714) | html | pdf |
      • 22.2.1.3. Hydration surface  (p. 714) | html | pdf |
      • 22.2.1.4. Hydrophobicity  (p. 714) | html | pdf |
    • 22.2.2. Calculation of surface area and energies of interaction  (pp. 714-715) | html | pdf |
      • 22.2.2.1. Introduction  (p. 714) | html | pdf |
      • 22.2.2.2. Lee & Richards planar slices  (p. 714) | html | pdf |
      • 22.2.2.3. Connolly dot surface algorithm  (p. 714) | html | pdf |
      • 22.2.2.4. Marching-cube algorithm  (p. 714) | html | pdf |
      • 22.2.2.5. Complete and connected rolling algorithms  (pp. 714-715) | html | pdf |
      • 22.2.2.6. Analytic surface calculations and the Gauss–Bonnet theorem  (p. 715) | html | pdf |
      • 22.2.2.7. Approximations to the surface  (p. 715) | html | pdf |
      • 22.2.2.8. Extended atoms account for missing hydrogen atoms  (p. 715) | html | pdf |
    • 22.2.3. Estimation of binding energies  (pp. 715-717) | html | pdf |
      • 22.2.3.1. Hydrophobicity  (pp. 715-716) | html | pdf |
      • 22.2.3.2. Estimates of binding energies  (p. 716) | html | pdf |
      • 22.2.3.3. Other non-graphical interpretive methods using surface area  (pp. 716-717) | html | pdf |
    • 22.2.4. Graphical representations of shape and properties  (pp. 717-719) | html | pdf |
      • 22.2.4.1. Realistic  (pp. 717-718) | html | pdf |
        • 22.2.4.1.1. Shaded backbone  (p. 717) | html | pdf |
        • 22.2.4.1.2. `Connolly' and solid polyhedral surfaces  (p. 717) | html | pdf |
        • 22.2.4.1.3. Photorealistic rendering  (pp. 717-718) | html | pdf |
        • 22.2.4.1.4. GRASP surfaces  (p. 718) | html | pdf |
        • 22.2.4.1.5. Implementations in popular packages  (p. 718) | html | pdf |
      • 22.2.4.2. Schematic and two-dimensional representations such as `roadmap'  (p. 719) | html | pdf |
    • 22.2.5. Conclusion  (p. 719) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 22.2.1.1. Surfaces in a plane cut through a hypothetical molecule  (p. 713) | html | pdf |
      • Fig. 22.2.4.1. GRASP example  (p. 716) | html | pdf |
      • Fig. 22.2.4.2. (a) Solvent-accessible surface topology of a rhinovirus 14–drug complex (Kim et al., 1993)  (p. 717) | html | pdf |
      • Fig. 22.2.4.3. Different projections illustrated with lysozyme  (p. 718) | html | pdf |
    • Tables
      • Table 22.2.3.1. The atomic solvation parameters of Eisenberg & McLachlan (1986)  (p. 715) | html | pdf |