CyToStruct: Augmenting the network visualization of CyToStruct with the power of molecular viewers

Sergey Nepomnyachiy; Nir Ben-Tal; Rachel Kolodny

doi:10.1016/j.str.2015.02.013

CyToStruct: Augmenting the network visualization of CyToStruct with the power of molecular viewers

Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

Abstract

It can be informative to view biological data, e.g., protein-protein interactions within a large complex, in a network representation coupled with three-dimensional structural visualizations of individual molecular entities. CyToStruct, introduced here, provides a transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular viewers from the network's edges and nodes. We provide demonstrations to analyze interactions among subunits in large protein/RNA/DNA complexes, and similarities among proteins. CyToStruct enriches the network tools of Cytoscape by adding a layer of structural analysis, offering all capabilities implemented in molecular viewers. CyToStruct is available at https://bitbucket.org/sergeyn/cytostruct/wiki/Home and in the Cytoscape App Store. Given the coordinates of a molecular complex, our web server (http://trachel-srv.cs.haifa.ac.il/rachel/ppi/) automatically generates all files needed to visualize the complex as a Cytoscape network with CyToStruct bridging to PyMOL, UCSF Chimera, VMD, and Jmol.

Original language	English
Pages (from-to)	941-948
Number of pages	8
Journal	Structure
Volume	23
Issue number	5
DOIs	https://doi.org/10.1016/j.str.2015.02.013
State	Published - 5 May 2015

Bibliographical note

Funding Information:
We thank Dr. Alexey Amunts for sharing the 3J7Y structure with us prior to publication, and Aya Narunsky and Gal Masrati for their helpful suggestions concerning visualization. N.B.-T. acknowledges the financial support of grant No. 1775/12 of the I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation.

Publisher Copyright:
© 2015 Elsevier Ltd.

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1016/j.str.2015.02.013

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title = "CyToStruct: Augmenting the network visualization of CyToStruct with the power of molecular viewers",

abstract = "It can be informative to view biological data, e.g., protein-protein interactions within a large complex, in a network representation coupled with three-dimensional structural visualizations of individual molecular entities. CyToStruct, introduced here, provides a transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular viewers from the network's edges and nodes. We provide demonstrations to analyze interactions among subunits in large protein/RNA/DNA complexes, and similarities among proteins. CyToStruct enriches the network tools of Cytoscape by adding a layer of structural analysis, offering all capabilities implemented in molecular viewers. CyToStruct is available at https://bitbucket.org/sergeyn/cytostruct/wiki/Home and in the Cytoscape App Store. Given the coordinates of a molecular complex, our web server (http://trachel-srv.cs.haifa.ac.il/rachel/ppi/) automatically generates all files needed to visualize the complex as a Cytoscape network with CyToStruct bridging to PyMOL, UCSF Chimera, VMD, and Jmol.",

author = "Sergey Nepomnyachiy and Nir Ben-Tal and Rachel Kolodny",

note = "Funding Information: We thank Dr. Alexey Amunts for sharing the 3J7Y structure with us prior to publication, and Aya Narunsky and Gal Masrati for their helpful suggestions concerning visualization. N.B.-T. acknowledges the financial support of grant No. 1775/12 of the I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation. Publisher Copyright: {\textcopyright} 2015 Elsevier Ltd.",

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doi = "10.1016/j.str.2015.02.013",

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CyToStruct: Augmenting the network visualization of CyToStruct with the power of molecular viewers

Abstract

Bibliographical note

ASJC Scopus subject areas

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