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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 PyMine data integration panel with functional tabs. b PyMOL window showing receptor in green, ligand in yellow, binding site in red, and SAVs in ball and stick style. On right hand side, an expandable list of binding sites selections. c Output directory and files
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Fig2: a PyMine data integration panel with functional tabs. b PyMOL window showing receptor in green, ligand in yellow, binding site in red, and SAVs in ball and stick style. On right hand side, an expandable list of binding sites selections. c Output directory and files

Mentions: In the current version, the only user input required is the PDB ID of the wild-type sequence of the protein of interest. A user is also allowed to input his own protein structure file, along with the UniProt ID. Using the PDB ID of 4E26 as input (Fig. 2a), the PDB structure file of the BRAF protein was fetched from the PDB database [14] and loaded in PyMOL’s graphic visualizer. Since this structure also contains an inhibitor, the available structural information of the inhibitor was also automatically imported. The binding site data of this BRAF protein was obtained from the IBIS database [18]. The binding site information was annotated either from experimental data or based on the binding site information of homologous proteins [18]. The RESTful web services are used to map the PDB ID to the UniProt ID using the pdbtosp.txt file at www.uniport.org/docs/ [13] in order to import the UniProt file of this protein sequence. The UniProt ID is also used to import SAV information from the HUMSAVAR database [17], the approved drug and compound activity data from the CHEMBL database [15], and the pathway information from the KEGG pathway database [16]. All these information can be accessed through the corresponding buttons in the Data Panel (Fig. 2a).Fig. 2


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

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

a PyMine data integration panel with functional tabs. b PyMOL window showing receptor in green, ligand in yellow, binding site in red, and SAVs in ball and stick style. On right hand side, an expandable list of binding sites selections. c Output directory and files
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: a PyMine data integration panel with functional tabs. b PyMOL window showing receptor in green, ligand in yellow, binding site in red, and SAVs in ball and stick style. On right hand side, an expandable list of binding sites selections. c Output directory and files
Mentions: In the current version, the only user input required is the PDB ID of the wild-type sequence of the protein of interest. A user is also allowed to input his own protein structure file, along with the UniProt ID. Using the PDB ID of 4E26 as input (Fig. 2a), the PDB structure file of the BRAF protein was fetched from the PDB database [14] and loaded in PyMOL’s graphic visualizer. Since this structure also contains an inhibitor, the available structural information of the inhibitor was also automatically imported. The binding site data of this BRAF protein was obtained from the IBIS database [18]. The binding site information was annotated either from experimental data or based on the binding site information of homologous proteins [18]. The RESTful web services are used to map the PDB ID to the UniProt ID using the pdbtosp.txt file at www.uniport.org/docs/ [13] in order to import the UniProt file of this protein sequence. The UniProt ID is also used to import SAV information from the HUMSAVAR database [17], the approved drug and compound activity data from the CHEMBL database [15], and the pathway information from the KEGG pathway database [16]. All these information can be accessed through the corresponding buttons in the Data Panel (Fig. 2a).Fig. 2

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.