PDBFlex: exploring flexibility in protein structures.

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software

Using High-Rising Cities to Visualize Performance in Real-Time

For developers concerned with a performance drop or improvement in their software, a profiler allows a developer to quickly search and identify bottlenecks and leaks that consume much execution time. Non real-time profilers analyze the history of already executed stack traces, while a real-time profiler outputs the results concurrently with the execution of software, so users can know the results instantaneously. However, a real-time profiler risks providing overly large and complex outputs, which is difficult for developers to quickly analyze. In this paper, we visualize the performance data from a real-time profiler. We visualize program execution as a three-dimensional (3D) city, representing the structure of the program as artifacts in a city (i.e., classes and packages expressed as buildings and districts) and their program executions expressed as the fluctuating height of artifacts. Through two case studies and using a prototype of our proposed visualization, we demonstrate how our visualization can easily identify performance issues such as a memory leak and compare performance changes between versions of a program. A demonstration of the interactive features of our prototype is available at https://youtu.be/eleVo19Hp4k.Comment: 10 pages, VISSOFT 2017, Artifact: https://github.com/sefield/high-rising-city-artifac