Adepth: New Representation and Its Implications for Atomic Depths of Macromolecules

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2013 Apr 24

PMID 23609539

Citations 4

Authors

Shu-Wen W Chen

Jean-Luc Pellequer

Affiliations

Soon will be listed here.

Abstract

We applied the signed distance function (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 Å 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 iso-surfaces 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.

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