Curriculum Vitae


EDUCATION

UCSDa1University of California San Diego, San Diego, California (2007-2010)

  • Ph.D., Biomedical Sciences
  • Thesis title: “Computational Drug Design Applied To Neglected Disease”
  • Recipient of the Roland K. Robins Pharmacology Dissertation Award

Brigham Young University, Provo, Utah (2004-2005)

  • M.S., Physiology and Developmental Biology

Brigham Young University, Provo, Utah (1998-1999, 2001-2005)

  • B.S., Department of Mathematics
  • Phi Kappa Phi, University Honors, Summa Cum Laude
  • Honors thesis title: “An Encompassing Three-Barrier Two-Site Analysis of Gramicidin Conductance Based on Previously Published Conductance Data”

Brigham Young University, Provo, Utah (1998-1999, 2001-2005)

  • B.A., Portuguese Language and Literature
  • Phi Kappa Phi, University Honors, Summa Cum Laude

RESEARCH EXPERIENCE

University of California San Diego, San Diego, California (2012-present)
Postdoctoral Researcher, Advisor: Rommie E. Amaro

  • Built an all-atom representation of the entire influenza virion surface based on tomographic data, with lipid bilayer, glycoproteins, and M2 cation channels.
  • Led computer-aided drug-design projects to identify novel influenza neuraminidase inhibitors.
  • Developed software to characterize potential ligand-receptor atomic interactions, even in the absence of a bound ligand.

University of California San Diego, San Diego, California (2007-2011)
Doctoral Student/Postdoctoral Researcher, Advisor: J. Andrew McCammon

A surface patch of the Influenza virion

A surface patch of the Influenza virion. © Jacob Durrant.

  • Over the course of several years, demonstrated success at using computer-aided drug-design techniques to identify small-molecule inhibitors of six different protein drug targets. These predicted inhibitors were all subsequently validated experimentally.
  • Developed a genetic algorithm to facilitate protein-inhibitor design and optimization (AutoGrow).
  • Developed machine learning techniques (neural networks) to predict the binding affinities of protein-ligand complexes (NNScore).
  • Developed various software packages for characterizing protein-ligand complexes, including software that 1) identifies hydrogen-bond networks (HBonanza), 2) identifies key atomic interactions (BINANA), and 3) calculates pocket volume (POVME).
  • Developed software packages for generating small-molecule libraries for use in virtual screening (LigMerge and AutoClickChem).
  • Explored the impact protein flexibility has on drug design. Aside from studying several specific proteins, I’ve also written a couple of reviews on this topic.
  • Data mined the Protein Data Bank to 1) identify secondary targets of a known inhibitor, and 2) position appropriate molecular fragments into known binding pockets (CrystalDock).

Brigham Young University, Provo, Utah (2003-2005)
Masters student, Advisor: David D. Busath

  • Developed a kinetic model to describe ion conductance through the gramicidin channel.
  • Explored the impact of chemical modifications to that channel on different elements of channel conductance.

Brigham Young University, Provo, Utah (2002-2003)
Undergraduate, Advisor: Eric Jellen

  • Developed an algorithm for analyzing genetic linkages affected by heterozygous translocations (QuadMap)

TEACHING EXPERIENCE

University of California San Diego, San Diego, California

  • Curriculum Development, Indiana University-Purdue University Indianapolis, 4/2013 – present
  • Instructor, National Biomedical Computation Resource, 8/2012
  • Summer Institute
  • Undergraduate-Student Mentor, Amaro Lab 6/2012 – 9/2012
  • Graduate-Student Mentor, McCammon Lab 6/2009 – 10/2011
  • Undergraduate-Student Mentor, McCammon Lab 1/2009 – 4/2011
  • Undergraduate-Student Mentor, McCammon Lab 2/2009 – 8/2009
  • Teaching Assistant, Salk Mobile Lab 1/2009 – 5/2009

Brigham Young University, Provo, Utah

  • Teaching Assistant, Physiology 1/2005 – 4/2005
  • Teaching Assistant, Genetics 9/2003 – 12/2003
  • Teaching Assistant, Genetics 7/2003 – 8/2003
  • Teaching Assistant, Genetics 9/2002 – 12/2002
  • Teaching Assistant, Calculus 8/2001 to 12/2001

AWARDS

  • 2013 I’m currently contributing to an NIH P41 renewal proposal.
  • 2013 I led the development of a DOE INCITE proposal that, if awarded, will provide our team with access to some of the largest supercomputers on earth.
  • 2012 I made important contributions to an NSF XSEDE proposal that was eventually awarded 16 million computer service units (a.k.a. CPU-hours), which collectively have an estimated dollar value of $800,000.
  • 2010 Roland K. Robins Pharmacology Dissertation Award ($500)
  • 2010 Texas Advanced Computer Center, Startup Project Allocation: “Malarial Protein Target Identification through Virtual Screening.”
  • 2009-2010 UCSD Pharmacological Sciences Training Grant ($44,600)
  • 2009 Research I designed with an undergraduate was selected by the American Society for Cell Biology (ASCB) as one of ten projects out of four thousand considered “novel and newsworthy.” The project was presented at the ASCB conference and was featured in their press book distributed to journalists.
  • 2009 Scholarship for a Medicinal Chemistry Intensive Course ($1,745)
  • 2005-2006 Federal MSTP Grant (tuition and stipend), UCSD. (~$63,000)
  • 2006 Medical School Interview Travel Expenses Grant, Brigham Young University. ($1,500)
  • 1998-1999, 2001-2004 Full Tuition Scholarship, Brigham Young University. ($10,000)
  • 2003 ORCA Grant, Brigham Young University. ($1,500)
  • Edwin Hinckley Scholarship, Brigham Young University. ($4,000)
  • Spring-Summer Scholarship, Brigham Young University. ($1,750)

OUTREACH ACTIVITIES

  1. Served on the UCSD MSTP (MD/PhD) admissions committee for two years.
  2. Peer reviewed articles for Chemical Biology & Drug Design, Future Medicinal Chemistry, and Molecular Informatics.

Everyone has their 5 minutes of fame...

Everyone has their 5 minutes of fame…

IN THE PRESS

  1. Real Science Using Stampede’s Xeon Phi. Jorge Salazar, Texas Advanced Computing Center Press Release. 12/16/2014.
  2. New Models for Powerful Flu Fighters From Existing Drugs. Tina Hesman Saey, U.S. News and World Report. 12/9/2009.
  3. Breakthrough Flu Drug Might Already Exist. Lauren Gravitz, Technology Review (MIT). 12/8/2009
  4. Blessings live in Brazil. Kate Evans, The Daily Universe (BYU). 3/8/2005.
  5. BYU student to graduate with double major and master’s degree, 4.0 GPA in five years. Lexi Allen, BYU News. 4/18/2005
  6. He’s a triple-threat guy: BYU student will pick up three degrees. Todd Hollingshead, The Salt Lake Tribune. 04/21/2005.
  7. Serve others, BYU graduates told. Laura Hancock, Deseret Morning News. 4/22/2005.
  8. Featured on Utah’s KUTV news.

LANGUAGES

Speaking Fluency: English, Portuguese, Spanish (limited)
Reading Fluency: English, Portuguese, Spanish

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