The Partial Visibility Representation Extension Problem

For a graph $G$, a function $\psi$ is called a \emph{bar visibility representation} of $G$ when for each vertex $v \in V(G)$, $\psi(v)$ is a horizontal line segment (\emph{bar}) and $uv \in E(G)$ iff there is an unobstructed, vertical, $\varepsilon$-wide line of sight between $\psi(u)$ and $\psi(v)$. Graphs admitting such representations are well understood (via simple characterizations) and recognizable in linear time. For a directed graph $G$, a bar visibility representation $\psi$ of $G$, additionally, puts the bar $\psi(u)$ strictly below the bar $\psi(v)$ for each directed edge $(u,v)$ of $G$. We study a generalization of the recognition problem where a function $\psi'$ defined on a subset $V'$ of $V(G)$ is given and the question is whether there is a bar visibility representation $\psi$ of $G$ with $\psi(v) = \psi'(v)$ for every $v \in V'$. We show that for undirected graphs this problem together with closely related problems are \NP-complete, but for certain cases involving directed graphs it is solvable in polynomial time.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Microstructural and morphological properties of homoepitaxial (001)ZnTe layers investigated by x-ray diffuse scattering

The microstructural and morphological properties of homoepitaxial (001)ZnTe layers are investigated by x-ray diffuse scattering. High resolution reciprocal space maps recorded close to the ZnTe (004) Bragg peak show different diffuse scattering features. One kind of cross-shaped diffuse scattering streaks along directions can be attributed to stacking faults within the epilayers. Another kind of cross-shaped streaks inclined at an angle of about 80deg with respect to the in-plane direction arises from the morphology of the epilayers. (abridged version

A quality metric for homology modeling: the H-factor

<p>Abstract</p> <p>Background</p> <p>The analysis of protein structures provides fundamental insight into most biochemical functions and consequently into the cause and possible treatment of diseases. As the structures of most known proteins cannot be solved experimentally for technical or sometimes simply for time constraints, <it>in silico </it>protein structure prediction is expected to step in and generate a more complete picture of the protein structure universe. Molecular modeling of protein structures is a fast growing field and tremendous works have been done since the publication of the very first model. The growth of modeling techniques and more specifically of those that rely on the existing experimental knowledge of protein structures is intimately linked to the developments of high resolution, experimental techniques such as NMR, X-ray crystallography and electron microscopy. This strong connection between experimental and <it>in silico </it>methods is however not devoid of criticisms and concerns among modelers as well as among experimentalists.</p> <p>Results</p> <p>In this paper, we focus on homology-modeling and more specifically, we review how it is perceived by the structural biology community and what can be done to impress on the experimentalists that it can be a valuable resource to them. We review the common practices and provide a set of guidelines for building better models. For that purpose, we introduce the H-factor, a new indicator for assessing the quality of homology models, mimicking the R-factor in X-ray crystallography. The methods for computing the H-factor is fully described and validated on a series of test cases.</p> <p>Conclusions</p> <p>We have developed a web service for computing the H-factor for models of a protein structure. This service is freely accessible at <url>http://koehllab.genomecenter.ucdavis.edu/toolkit/h-factor</url>.</p

PRIMO: an interactive homology modeling pipeline

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling

Cryo-Electron Microscopy Analysis of a 105 kDa Protein Particle: The Xylulose Kinase from E. Coli

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 200