Cavity detection of protein 2ptn.

<p>Left panel is the outer molecular surface and cavities of the protein; right panel shows the atoms around the cavities.</p

Average relative errors of area and volume of molecular surface at two different resolutions calculated by EDTSurf, LSMS [20] and MSMS [10].

<p>Average relative errors of area and volume of molecular surface at two different resolutions calculated by EDTSurf, LSMS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008140#pone.0008140-Can1" target="_blank">[20]</a> and MSMS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008140#pone.0008140-Sanner1" target="_blank">[10]</a>.</p

Molecular surfaces of three atoms at the resolution 128³.

<p>(A) generated by EDTSurf-MC; (B) generated by EDTSurf-VCMC.</p

Illustration of three macromolecular surfaces from EDT in a 2D plane.

<p>(A) EDT with the minimal macromolecular surface (yellow) as the boundary. The isosurface with isovalue equaling the negative of the minimal van der Waals radius is the van der Waals surface (blue). (B) EDT with van der Waals surface (blue) as the boundary. The isosurface with isovalue equaling the negative of the probe radius is the solvent-accessible surface (red). (C) EDT with solvent-accessible surface (red) as the boundary. The isosurface with isovalue equaling the probe radius is the molecular surface which contains the surface (green) and reentrant surface (pink).</p

Illustration of three macromolecular surfaces in a 2D plane.

<p>(A) van der Waals surface (blue); (B) solvent-accessible surface (red); (C) molecular surface which includes contact surface (green) and reentrant surface (pink).</p

CPU time and memory use for molecular surface generation by EDTSurf, LSMS [20] and MSMS [10].

<p>CPU time and memory use for molecular surface generation by EDTSurf, LSMS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008140#pone.0008140-Can1" target="_blank">[20]</a> and MSMS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008140#pone.0008140-Sanner1" target="_blank">[10]</a>.</p

Three macromolecular surfaces of protein 1eca.

<p>(A) van der Waals surface (B) solvent-accessible surface (C) molecular surface.</p

Comparison of sequence profiles between cancer and non-cancer groups and selected features (residues marked with arrows) based on entropy calculation in the R3'/R3 region.

<p>Comparison of sequence profiles between cancer and non-cancer groups and selected features (residues marked with arrows) based on entropy calculation in the R3'/R3 region.</p

Residues around the seven cavities of protein 2ptn calculated by EDTSurf.

<p>Residues around the seven cavities of protein 2ptn calculated by EDTSurf.</p

Detected residues by calculating entropy difference for each intervening region between Western and East Asian subtypes.

<p>Detected residues by calculating entropy difference for each intervening region between Western and East Asian subtypes.</p