Dataset Information

Tools for 3D Interactome Visualization.

ABSTRACT: In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable the detection of both intra- and intermolecular protein interactions in organelles, cells, tissues, and organs. Quantitative XL-MS enables the detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. We have developed new informatics capabilities, the first to enable 3D visualization of multiple quantitative interactome data sets, acquired over time or with varied perturbation levels, to reveal relevant dynamic interactome changes. These new tools are integrated within release 3.0 of our online cross-linked peptide database and analysis tool suite XLinkDB. With the recent rapid expansion in XL-MS for protein structural studies and the extension to quantitative XL-MS measurements, 3D interactome visualization tools are of critical need.

SUBMITTER: Keller A

PROVIDER: S-EPMC6519740 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Tools for 3D Interactome Visualization.

Keller Andrew A Chavez Juan D JD Eng Jimmy K JK Thornton Zorian Z Bruce James E JE

Journal of proteome research 20181218 2

In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable the detection of both intra- and intermolecular protein interactions in organelles, cells, tissues, and organs. Quantitative XL-MS enables the detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbation ...[more]

PMID: 30520642

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Project description:Photoacoustic (PA) imaging (or optoacoustic imaging) is a novel biomedical imaging method in biological and medical research. This modality performs morphological, functional, and molecular imaging with and without labels in both microscopic and deep tissue imaging domains. A variety of innovations have enhanced 3D PA imaging performance and thus has opened new opportunities in preclinical and clinical imaging. However, the 3D visualization tools for PA images remains a challenge. There are several commercially available software packages to visualize the generated 3D PA images. They are generally expensive, and their features are not optimized for 3D visualization of PA images. Here, we demonstrate a specialized 3D visualization software package, namely 3D Photoacoustic Visualization Studio (3D PHOVIS), specifically targeting photoacoustic data, image, and visualization processes. To support the research environment for visualization and fast processing, we incorporated 3D PHOVIS onto the MATLAB with graphical user interface and developed multi-core graphics processing unit modules for fast processing. The 3D PHOVIS includes following modules: (1) a mosaic volume generator, (2) a scan converter for optical scanning photoacoustic microscopy, (3) a skin profile estimator and depth encoder, (4) a multiplanar viewer with a navigation map, and (5) a volume renderer with a movie maker. This paper discusses the algorithms present in the software package and demonstrates their functions. In addition, the applicability of this software to ultrasound imaging and optical coherence tomography is also investigated. User manuals and application files for 3D PHOVIS are available for free on the website (www.boa-lab.com). Core functions of 3D PHOVIS are developed as a result of a summer class at POSTECH, "High-Performance Algorithm in CPU/GPU/DSP, and Computer Architecture." We believe our 3D PHOVIS provides a unique tool to PA imaging researchers, expedites its growth, and attracts broad interests in a wide range of studies.

Dataset Information

Tools for 3D Interactome Visualization.

Publications

Tools for 3D Interactome Visualization.

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