UNM HSC School of Medicine

Division of Biocomputing

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Recent publications:

"In vivo effects of a GPR30 antagonist", Megan K Dennis, Ritwik Burai, Chinnasamy Ramesh, Whitney K Petrie, Sara N Alcon, Tapan K Nayak, Cristian G Bologa, Andrei Leitao, Eugen Brailoiu, Elena Deliu, Nae J Dun, Larry A Sklar, Helen J Hathaway, Jeffrey B Arterburn, Tudor I Oprea & Eric R Prossnitz, Nat. Chem. Biol. 5, 421-427 (2009)
  * This study, conducted primarily at UNM, with help from Prof. Jeff Arterburn at New Mexico State University and the group of Prof. Nae Dun, Temple University Medical School, integrated virtual and experimental methods to describe the in vitro and in vivo effects of the first antagonist of GPER, a G-protein estrogen receptor.
 
"A crowdsourcing evaluation of the NIH chemical probes", Tudor I Oprea, Cristian G Bologa, Scott Boyer, Ramona F Curpan, Robert C Glen, Andrew L Hopkins, Christopher A Lipinski, Garland R Marshall, Yvonne C Martin, Liliana Ostopovici-Halip, Gilbert Rishton, Oleg Ursu, Roy J Vaz, Chris Waller, Herbert Waldmann  &  Larry A Sklar, Nat. Chem. Bio., 5, 441 - 447 (2009).
 
* Originated and conducted by UNM Biocomputing, this survey of experts evaluated 64 of the chemical probes resulting from the NIH Roadmap Molecular Libraries Program by means of crowdsourcing. Crowdsourcing is a distributed problem-solving method based on outsourcing. Here, 12 experts in drug discovery have given their vote of confidence to the 64 chemical probes.
 
* See also: Howe, J., Crowdsourcing: Why the Power of the Crowd Is Driving the Future of Business, Crown Business (2008).
 

"Interactive exploration of chemical space with Scaffold Hunter", Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I Oprea, Petra Mutzel & Herbert Waldmann, Nat. Chem. Biol. 5, 581-583 (2009), doi:10.1038/nchembio.187.
  * This brief communication, from the Max Planck Institute in Dortmund (MPID) , describes the development of an interactive tool, ScaffoldHunter, conceptualized by MPID chemists with contributions from Tudor Oprea, and programmed by computational science students from the Dortmund Technical University (Germany). ScaffoldHunter reads data from bioactivity screens, automatically generates scaffolds for compound classes present in the data sets, and correlates them in tree-like (inspired by Cytoscape) arrangements that represent the hierarchical relationships between scaffolds and the molecules represented by them. ScaffoldHunter is freely available from the Nature Chemical Biology website [link].
 
"Bioactivity-guided mapping and navigation of chemical space", Steffen Renner, Willem A L van Otterlo, Marta Dominguez Seoane, Sabine Möcklinghoff, Bettina Hofmann, Stefan Wetzel1, Ansgar Schuffenhauer, Peter Ertl, Tudor I Oprea, Dieter Steinhilber, Luc Brunsveld, Daniel Rauh & Herbert Waldmann, Nat. Chem. Biol. 5, 585-592 (2009) doi:10.1038/nchembio.188.
  * This paper, also from the MPID, uses Scaffold Hunter to provide empirical evidence that hierarchical analyses and organization of a compound library in scaffold trees together with brachiation (a "lateral" tree jump), along lines of documented bioactivity is an efficient way to navigate in both chemical and biological space, as documented for 5-lipoxygenase and estrogen receptor alpha.
 
   

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