1. DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks
- Author
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Keqin Liu, Jingkang Shen, Hualiang Jiang, David L. Burk, Bing Xiong, and Jie Wu
- Subjects
Statistics and Probability ,Databases, Factual ,Proteome ,Computer science ,Systems biology ,computer.software_genre ,Biochemistry ,Interactome ,User-Computer Interface ,chemistry.chemical_compound ,Metabolomics ,Computer Graphics ,Chemogenomics ,Computer Simulation ,Databases, Protein ,Cluster analysis ,Molecular Biology ,Fingerprint (computing) ,Small molecule ,Computer Science Applications ,Visualization ,Computational Mathematics ,Pharmaceutical Preparations ,Computational Theory and Mathematics ,chemistry ,Drug Design ,Data mining ,computer ,Software ,Biological network - Abstract
Summary: DrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome. DrugViz can import drug–target network information in an extended SIF file format to Cytoscape and display the two-dimensional (2D) structures of small molecule nodes in a unified visualization environment. It also can identify small molecule nodes by means of three different 2D structure searching methods, namely isomorphism, substructure and fingerprint-based similarity searches. After selections, users can furthermore conduct a two-side clustering analysis on drugs and targets, which allows for a detailed analysis of the active compounds in the network, and elucidate relationships between these drugs and targets. DrugViz represents a new tool for the analysis of data from chemogenomics, metabolomics and systems biology. Availability: DrugViz and data set used in Application are freely available for download at http://202.127.30.184:8080/software.html Contact: jkshen@mail.shcnc.ac.cn
- Published
- 2008