RiboVision suite for visualization and analysis of ribosomes

2014 ◽  
Vol 169 ◽  
pp. 195-207 ◽  
Author(s):  
Chad R. Bernier ◽  
Anton S. Petrov ◽  
Chris C. Waterbury ◽  
James Jett ◽  
Fengbo Li ◽  
...  
Keyword(s):  
Molecular Interactions ◽  
Ribosomal Proteins ◽  
Secondary Structures ◽  
Macromolecular Complex ◽  
Analysis Tool ◽  
Complex Data ◽  
Helical Structures ◽  
Haloarcula Marismortui ◽  
3D Structures ◽  
2D And 3D

RiboVision is a visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex containing ribosomal RNA and ribosomal proteins and is a key component of life responsible for the synthesis of proteins in all living organisms. RiboVision is intended for rapid retrieval, analysis, filtering, and display of a variety of ribosomal data. Preloaded information includes 1D, 2D, and 3D structures augmented by base-pairing, base-stacking, and other molecular interactions. RiboVision is preloaded with rRNA secondary structures, rRNA domains and helical structures, phylogeny, crystallographic thermal factors,etc.RiboVision contains structures of ribosomal proteins and a database of their molecular interactions with rRNA. RiboVision contains preloaded structures and data for two bacterial ribosomes (Thermus thermophilusandEscherichia coli), one archaeal ribosome (Haloarcula marismortui), and three eukaryotic ribosomes (Saccharomyces cerevisiae,Drosophila melanogaster, andHomo sapiens). RiboVision revealed several major discrepancies between the 2D and 3D structures of the rRNAs of the small and large subunits (SSU and LSU). Revised structures mapped with a variety of data are available in RiboVision as well as in a public gallery (http://apollo.chemistry.gatech.edu/RibosomeGallery). RiboVision is designed to allow users to distill complex data quickly and to easily generate publication-quality images of data mapped onto secondary structures. Users can readily import and analyze their own data in the context of other work. This package allows users to import and map data from CSV files directly onto 1D, 2D, and 3D levels of structure. RiboVision has features in rough analogy with web-based map services capable of seamlessly switching the type of data displayed and the resolution or magnification of the display. RiboVision is available at http://apollo.chemistry.gatech.edu/RiboVision.

scholarly journals DESIGNING A DATA VISUALISATION AND ANALYSIS TOOL FOR SUPPORTING DECISION-MAKING WITH PUBLIC TRANSPORTATION NETWORK

2021 ◽  
Vol 1 ◽  
pp. 1093-1102
Author(s):  
Flore Vallet ◽  
Mostepha Khouadjia ◽  
Ahmed Amrani ◽  
Juliette Pouzet
Keyword(s):  
Decision Making ◽  
Public Transportation ◽  
Transportation Network ◽  
Visual Exploration ◽  
Problem Solution ◽  
Analysis Tool ◽  
Complex Data ◽  
Data Visualisation ◽  
Ex Post ◽  
Passenger Flows

AbstractMassive data are surrounding us in our daily lives. Urban mobility generates a very high number of complex data reflecting the mobility of people, vehicles and objects. Transport operators are primary users who strive to discover the meaning of phenomena behind traffic data, aiming at regulation and transport planning. This paper tackles the question "How to design a supportive tool for visual exploration of digital mobility data to help a transport analyst in decision making?” The objective is to support an analyst to conduct an ex post analysis of train circulation and passenger flows, notably in disrupted situations. We propose a problem-solution process combined with data visualisation. It relies on the observation of operational agents, creativity sessions and the development of user scenarios. The process is illustrated for a case study on one of the commuter line of the Paris metropolitan area. Results encompass three different layers and multiple interlinked views to explore spatial patterns, spatio-temporal clusters and passenger flows. We join several transport network indicators whether are measured, forecasted, or estimated. A user scenario is developed to investigate disrupted situations in public transport.

Ecotoxicity prediction by adaptive fuzzy partitioning: comparing descriptors computed on 2D and 3D structures

2006 ◽  
Vol 17 (2) ◽  
pp. 225-251 ◽  
Author(s):  
N. Piclin ◽  
M. Pintore ◽  
C. Wechman ◽  
A. Roncaglioni ◽  
E. Benfenati ◽  
...  
Keyword(s):  
3D Structures ◽  
Adaptive Fuzzy ◽  
Fuzzy Partitioning ◽  
2D And 3D

scholarly journals On the structural stability and optical properties of germanium-based schwarzites: a density functional theory investigation

2020 ◽  
Vol 22 (28) ◽  
pp. 16286-16293
Author(s):  
Raphael M. Tromer ◽  
Levi C. Felix ◽  
Cristiano F. Woellner ◽  
Douglas S. Galvao
Keyword(s):  
Density Functional Theory ◽  
Optical Properties ◽  
Structural Stability ◽  
Density Functional ◽  
Functional Theory ◽  
3D Structures ◽  
Carbon Allotropes ◽  
2D And 3D

Since graphene was synthesized the interest in building new 2D and 3D structures based on carbon allotropes has been growing every day.

scholarly journals Detecting Protein-Protein Interactions in the Intact Cell of Bacillus subtilis (ATCC 6633)

2003 ◽  
Vol 185 (14) ◽  
pp. 4268-4275 ◽  
Author(s):  
Michael S. Winters ◽  
R. A. Day
Keyword(s):  
Bacillus Subtilis ◽  
Protein Interactions ◽  
Ribosomal Proteins ◽  
Intact Cell ◽  
Protein Biosynthesis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Protein Database ◽  
Haloarcula Marismortui ◽  
Associated Proteins ◽  
Covalently Linked

ABSTRACT The salt bridge, paired group-specific reagent cyanogen (ethanedinitrile; C2N2) converts naturally occurring pairs of functional groups into covalently linked products. Cyanogen readily permeates cell walls and membranes. When the paired groups are shared between associated proteins, isolation of the covalently linked proteins allows their identity to be assigned. Examination of organisms of known genome sequence permits identification of the linked proteins by mass spectrometric techniques applied to peptides derived from them. The cyanogen-linked proteins were isolated by polyacrylamide gel electrophoresis. Digestion of the isolated proteins with proteases of known specificity afforded sets of peptides that could be analyzed by mass spectrometry. These data were compared with those derived theoretically from the Swiss Protein Database by computer-based comparisons (Protein Prospector; http://prospector.ucsf.edu ). Identification of associated proteins in the ribosome of Bacillus subtilis strain ATCC 6633 showed that there is an association homology with the association patterns of the ribosomal proteins of Haloarcula marismortui and Thermus thermophilus. In addition, other proteins involved in protein biosynthesis were shown to be associated with ribosomal proteins.

A new family of 1D, 2D and 3D frameworks aggregated from Ni5, Ni4 and Ni7 building units: synthesis, structure, and magnetism

2016 ◽  
Vol 45 (22) ◽  
pp. 9267-9278 ◽  
Author(s):  
Ya-Hui Liu ◽  
Li-Ping Lu ◽  
Miao-Li Zhu ◽  
Si-Si Feng ◽  
Feng Su
Keyword(s):  
Tricarboxylic Acid ◽  
Ferromagnetic Coupling ◽  
Magnetic Studies ◽  
3D Structures ◽  
New Family ◽  
Magnetic Chain ◽  
2D And 3D

Three polynuclear nickel(ii) complexes with 1D, 2D and 3D structures are controlled by carboxylate bridges of biphenyl-3,4′,5-tricarboxylic acid. Magnetic studies reveal that the polymers have ferromagnetic coupling features for 1 and 2 and an alternating magnetic chain behavior for 3.

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