Adepth: new representation and its implications for atomic depths of macromolecules

作者：Chen Shu wen W; Pellequer Jean Luc^*

来源：Nucleic Acids Research, 2013, 41(W1): W412-W416.

DOI：10.1093/nar/gkt299

We applied the signed distance SDF) for representing the depths of atoms in a macromolecule. The calculations of SDF values were performed on grid points in a rectangular box that accommodates the macromolecule. The depth for an atom inside the molecule was then obtained as a result of tri-linear interpolation of SDF values at the nearest grid points surrounding the atom. For testing the performance of present program Adepth, we have constructed an artificial molecule whose atomic depths are known as the gold standard for accuracy assessments. On average, our results showed that Adepth reached an accuracy of 1.6% at 0.5 angstrom of grid spacing, whereas the current reference server DEPTH reached 7.5%. The Adepth program provides both depth and height representations; it is capable of computing isosurfaces for atomic depths and presenting graphical view of macromolecular shape at some distance away from the surface. Web interface is available at http://biodev.cea.fr/adepth.

• 出版日期2013-7
• 单位中国地震局