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PyMine – A PyMol Plugin to Integrate and Visualize Chemical and Biological Data for Drug Discovery

PyMine is an innovative PyMol plugin that integrates data from chemical and biological databases to aid in drug discovery. It automates cheminformatics workflows and prioritizes data-driven hypotheses, enhancing research efficiency. Visit https://github.com/rrchaudhari/PyMine for more information.

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PyMine – A PyMol Plugin to Integrate and Visualize Chemical and Biological Data for Drug Discovery

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  1. PyMine – A PyMol Plugin to Integrate and Visualize Chemical and Biological Data for Drug Discovery Zhijun Li, Ph.D. Departments of Chemistry & Biochemistry University of the Sciences in Philadelphia USA

  2. Drug discovery is a costly process http://www.chemistry-blog.com/2012/01/04/tedtalk-medicine-for-the-99-hes-about-99-wrong/.

  3. Cheminformatics and bioinformatics can facilitate drug discovery • Target identification • Target modeling • In silico screening and design Krasky et al., Genomics, 2007, 89: 36-43.

  4. Data integration remains a challenge www.ncbi.nlm.nih.gov

  5. Service-oriented web approach Data warehousing approach Other approaches Current Approaches for Bioinformatics Data Integration

  6. PyMine Development

  7. PyMol • Molecular visualization system • Open source • Leading software package http://ww.pymol.org

  8. UniProt PDB ChEMBL Databases • IBIS • HUMSAVAR • KEGG

  9. Integration

  10. Interface and Output Panel Interface PyMol 3D visualization Output Directory Chaudhari and Li., BMC Research Notes, 2015, submitted.

  11. Case Study

  12. Major enzymes in the production of NADPH Also closely associated with the TCA cycle, a central metabolic hub In mammalian cells, two major malic enzyme isoforms (ME1 and ME2) have been identified Human Malic Acid Enzymes

  13. Malic enzymes reciprocally module p53 Jiang et al., Nature, 2013, 493: 689-695.

  14. ME1 structure Catalytic site Known inhibitors PyMine Study and CADD Approach • Ligand-based approach using ShapeSignature • Structure-based approach using Glide • Assay testing

  15. CADD Results

  16. Developed an innovative and automated tool to integrate and visualize chemical and biological data for drug discovery. PyMine integrates data from six high-quality chemical and biological databases and maps imported structural information onto receptor 3D structure. PyMine imports and/or generates files that can be used directly for drug discovery projects. Summary https://github.com/rrchaudhari/PyMine

  17. To include support for additional chemical/biological databases. To apply inductive logic programming in order to generate and prioritize data driven hypotheses. To automate cheminformatics workflows based on imported structural data to test generated hypothesis. Future Development

  18. Acknowledgement Univ. of Pennsylvinia Dr. Wenchao Song; Dr. Xiaolu Yang CHOP Dr. Hakon Hakonarson, Duke University Dr. Chin-Ho Chen; Dr. Li Huang Wistar Institute Dr. Jose Conejo-Garcia University of Sydney, Australia Dr. John Christodoulou Meharry Medical College Dr. Hua Xie Univ. of Missouri Dr. Gerald L. Hazelbauer Usciences Dr. Zhiyu Li; Dr. Preston Moore Dr. Jun Gao Dr. Vagmita Pabuwal Dr. Jhenny Galan Dr. Andrew Heim Usha K. Muppirala Rajan Chaudhari Daoyuan Dong Tejashree Redij David Cho PhRMA Foundation NSF NIH UPenn- ITMAT

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