ArticleNucleic acids research2013
Adepth: New Representation and its implications for atomic depths of macromolecules.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome.Applied microbiology and biotechnology · 2021Article
- Structural and Functional Characterization of the Type Three Secretion System (T3SS) Needle ofFrontiers in microbiology · 2019Article
- Safety, Stability and Pharmacokinetic Properties of (super)Factor Va, a Novel Engineered Coagulation Factor V for Treatment of Severe Bleeding.Pharmaceutical research · 2016Article
- Measuring the shapes of macromolecules - and why it matters.Computational and structural biotechnology journal · 2013Review
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Authors and funding
2 authors.
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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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