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PyMine: a PyMOL plugin to integrate and visualize data for drug discovery.

Chaudhari R, Li Z - BMC Res Notes (2015)

Bottom Line: However, lack of integration makes it very challenging for individual scientists to access and understand all the data related to a specific protein of interest.To overcome this challenge, we developed PyMine, a PyMOL plugin that retrieves chemical, structural, pathway and other related biological data of a receptor and small molecules from a variety of high-quality databases and presents them in a graphic and uniformed way.Developed as an interactive and user-friendly tool, PyMine can be used as a central data-hub for users to access and visualize multiple types of data and to generate new ideas intuitively for structure-based molecule design.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, 19104, USA. rchaudhari@mail.usciences.edu.

ABSTRACT

Background: Tremendous amount of chemical and biological data are being generated by various high-throughput biotechnologies that could facilitate modern drug discovery. However, lack of integration makes it very challenging for individual scientists to access and understand all the data related to a specific protein of interest.

Findings: To overcome this challenge, we developed PyMine, a PyMOL plugin that retrieves chemical, structural, pathway and other related biological data of a receptor and small molecules from a variety of high-quality databases and presents them in a graphic and uniformed way.

Conclusions: Developed as an interactive and user-friendly tool, PyMine can be used as a central data-hub for users to access and visualize multiple types of data and to generate new ideas intuitively for structure-based molecule design.

No MeSH data available.


A diagram illustrates database integration in PyMine
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Fig1: A diagram illustrates database integration in PyMine

Mentions: We implemented PyMine as a PyMOL plugin that integrates and visualizes chemical and biological data in the 3D visualizer of PyMOL. For data integration, large databases including UniProt [13], PDB [14], CHEMBL [15] and KEGG [16] databases were accessed using REST API (Fig. 1). RESTful web services were selected over traditional SOAP services to minimize the dependence on external libraries. SAV information from the HUMSAVAR database [17] was connected using the urllib2 library. IBIS data [18] were uploaded to our account at Dropbox (www.dropbox.com) and were also connected using the urllib2 library.Fig. 1


PyMine: a PyMOL plugin to integrate and visualize data for drug discovery.

Chaudhari R, Li Z - BMC Res Notes (2015)

A diagram illustrates database integration in PyMine
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4590260&req=5

Fig1: A diagram illustrates database integration in PyMine
Mentions: We implemented PyMine as a PyMOL plugin that integrates and visualizes chemical and biological data in the 3D visualizer of PyMOL. For data integration, large databases including UniProt [13], PDB [14], CHEMBL [15] and KEGG [16] databases were accessed using REST API (Fig. 1). RESTful web services were selected over traditional SOAP services to minimize the dependence on external libraries. SAV information from the HUMSAVAR database [17] was connected using the urllib2 library. IBIS data [18] were uploaded to our account at Dropbox (www.dropbox.com) and were also connected using the urllib2 library.Fig. 1

Bottom Line: However, lack of integration makes it very challenging for individual scientists to access and understand all the data related to a specific protein of interest.To overcome this challenge, we developed PyMine, a PyMOL plugin that retrieves chemical, structural, pathway and other related biological data of a receptor and small molecules from a variety of high-quality databases and presents them in a graphic and uniformed way.Developed as an interactive and user-friendly tool, PyMine can be used as a central data-hub for users to access and visualize multiple types of data and to generate new ideas intuitively for structure-based molecule design.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, 19104, USA. rchaudhari@mail.usciences.edu.

ABSTRACT

Background: Tremendous amount of chemical and biological data are being generated by various high-throughput biotechnologies that could facilitate modern drug discovery. However, lack of integration makes it very challenging for individual scientists to access and understand all the data related to a specific protein of interest.

Findings: To overcome this challenge, we developed PyMine, a PyMOL plugin that retrieves chemical, structural, pathway and other related biological data of a receptor and small molecules from a variety of high-quality databases and presents them in a graphic and uniformed way.

Conclusions: Developed as an interactive and user-friendly tool, PyMine can be used as a central data-hub for users to access and visualize multiple types of data and to generate new ideas intuitively for structure-based molecule design.

No MeSH data available.