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Illuminating the Druggable Genome Knowledge Management Center (IDG KMC)

  • Tudor Oprea, M.D., Ph.D.
    Overall Principal Investigator/Data Organizing Core
    Professor, Department of Internal Medicine

  • Larry A. Sklar, Ph.D.
    PI of the Administrative Core
    The Maralyn S. Budke and Robert E. Anderson Distinguished Endowed Chair in Cancer Drug Discovery
    Director, UNM Center for Molecular Discovery

  • Anton Simeonov, Ph.D.
    PI Interface Portal
    NIH NCATS

Overview

KMC grant awarded to UNM encompasses 3 cores: Administrative Core (AC), Data Organizing Core (DOC), and User Interface Portal (UIP).

Dr. Larry Sklar leads the AC and coordinates the functions of the different cores to address the fulfillment of milestones developed in conjunction of NIH, in addition to addressing the needs of building and maintaining an IDG consortium encompassing all KMC grantees along with all the different Technology Development centers. Much of the work entails communication and facilitation of meetings and teleconferences.

Dr. Tudor Oprea directs the DOC, which includes a collaboration between UNM and different sub-contractors at University of Miami (UofMiami), European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), and Novo Nordisk Foundation Center for Protein Research (NNFCPR) at the University of Copenhagen. DOC collects and integrates data for the four highlighted target proteins (Kinase, GPCR, Ion Channel and Nuclear Hormone Receptor).

User Interface Portal (UIP) led by group at NCATS developing PHAROS: Dr. Anton Simeonov and Dr. Rajarshi Guha. Follow link to PHAROS

Description

The overall goal of the Illuminating the Druggable Genome Knowledge Management Center (IDG KMC) is to evaluate and organize (via the Data Organizing Core, DOC), present and visualize (via the User Interface Portal, UIP) and rank (in cooperation with the IDG Consortium) all prospective disease-linked proteins, as potential druggable targets for four protein superfamilies: G-protein-coupled receptors (GPCRs), nuclear receptors (NRs), ion channels (IC) and kinases. By combining data extracted from multiple sources, coupled with algorithmic processing, prediction and human curation, the emerging knowledge will be associated with the appropriate proteins. The KMC will link disease, pathway, protein, gene, chemical, bioactivity, drug discovery and clinical information elements from databases, literature, patents and other documents in the DOC "Target Central" Resource Database. TCRD will serve as primary source for the IDG Query Platform, the UlP-developed system that will enable scientists to access, visualize and analyze IDG-specific data. Coordinating DOC and UIP activities, the Administrative Core, AC, will assist with human curation by organizing class-specific External Target Panels to categorize proteins into 4 classes (Tclin, Tchem, Tbio, and Tdark) Tissue and cellular localization for both disease and protein will serve as central filtes for ranking. The specific aims of the KMC are based on the demonstrated experience of the Oprea-Sklar team at the University of New Mexico (data capture, processing, mining and modeling), and the Simeonov-led team at NCATS (software development, visualization and modeling), supported by teams based in Denmark, Florida and UK.

Publications

George-Thompson AM, Ursu O, Babkin P, Iancu CV, Whang A, Oprea TI, Choe JY. Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluation. Scientific Reports, Epub 2016 Apr 14. PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26241209

Oprea, Tudor I; Overington, John P, Computational and Practical Aspects of Drug Repositioning., Assay Drug Dev Technol 13 (6): 299-306 (2015), PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/27074918

Links

Translational Informatics Team


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From Left: Jayme Holmes, Oleg Ursu, Jeremy J Yang, Philip Kroth, Cristian Bologa, Jerome G Abear,
Christophe Lambert, Tudor Oprea, Stephen Mathias, Lydia Montoya, Herbert Davis & Stuart Nelson.

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