Rommie Amaro Explained

Rommie E. Amaro
Birth Place:	Chicago
Fields:	Computational biophysics
Workplaces:	University of California, San Diego
Alma Mater:	University of Illinois at Urbana-Champaign
Thesis Title:	Investigating the Structure and Function of IGP Synthase
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Doctoral Advisor:	Zaida Luthey-Schulten
Awards:	Presidential Early Career Award for Scientists and Engineers, 2010 San Diego 78th District Woman of the Year, 2015 ACS Kavli Emerging Leader in Chemistry National Lecturer, 2016 Corwin Hansch Award, Hansch-Fujita Society, 2016 ACM Gordon Bell Special Prize for COVID19, 2020
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Rommie E. Amaro is a professor and endowed chair of chemistry and biochemistry and the director of the National Biomedical Computation Resource at the University of California, San Diego. Her research focuses on development of computational methods in biophysics for applications to drug discovery.^{[1] [2]}

Early life and education

Amaro grew up in Chicago and obtained her bachelor's degree in chemical engineering from the University of Illinois at Urbana-Champaign (UIUC) in 1999. She spent two years as a research engineer at Kraft Foods before returning to UIUC for graduate school; she received a Ph.D. in chemistry in 2005 for work with Zaida Luthey-Schulten on computational biophysics. During her graduate work, she also helped develop National Institutes of Health (NIH) Center for Macromolecular Modeling and Bioinformatics workshops. After graduation she became a postdoctoral fellow with Andrew McCammon at University of California, San Diego on an NIH Kirschstein-National Research Service Award (NRSA) postdoctoral fellowship.^{[3] [4]}

Academic career

Amaro joined the faculty at University of California, Irvine in 2009, with partial appointments in the departments of pharmaceutical sciences, computer science, and chemistry. She received an NIH Director's New Innovator Award in 2010 and the Presidential Early Career Award for Scientists and Engineers in 2010. She returned to UCSD in 2012 in the Department of Chemistry and Biochemistry. She was the director of UCSD's National Biomedical Computation Resource from 2014-2020.^[5] She served as co-Director of the Drug Design Data Resource (D3R).^[6]

Amaro's work has emphasized the utility of GPU computing for methods development for molecular simulation. She was awarded a research grant by NVIDIA in 2013 to continue development for the CUDA platform.^{[7] [8]}

Amaro is also active in public outreach and science communication; a high-school student she co-mentored won the 2013 Siemens Competition in Math, Science & Technology, the 2013 Google Science Fair, and the 2014 Intel Science Talent Search.^[9]

Selected publications

1. Bohl TE, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir Ö, Kurahashi K, Amaro RE, Wang Z, Aihara H "The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release.", J Biol Chem, 2018, Vol. 293, Issue 21, 7969-798^[10]
2. Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE "D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.", J Comput Aided Mol Des, 2018, Vol. 32, Issue 1, 1-20^[10]
3. Jagger BR, Lee CT, Amaro RE "Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.", J Phys Chem Lett, 2018, Vol. 9, Issue 17, 4941-4948^[10]
4. Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang DB, Wang VY, Amaro RE, Huxford T, Ghosh G "Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit.", Biochemistry, 2018, Vol. 57, Issue 20, 2943–2957^[10]
5. Salamango DJ, Becker JT, McCann JL, Cheng AZ, Demir Ö, Amaro RE, Brown WL, Shaban NM, Harris RS "APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction.", Mol Cell Biol, 2018^[10]
6. Salamango DJ, McCann JL, Demir Ö, Brown WL, Amaro RE, Harris RS "APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces.", J Mol Biol, 2018, Vol. 430, Issue 17, 2695–2708^[10]
7. Richards C, Albin JS, Demir Ö, Shaban NM, Luengas EM, Land AM, Anderson BD, Holten JR, Anderson JS, Harki DA, Amaro RE, Harris RS "The Binding Interface between Human APOBEC3F and HIV-1 Vif Elucidated by Genetic and Computational Approaches.", Cell Rep, 2015, Vol. 13, Issue 9, 1781-8^[10]
8. Robert D. Malmstrom, Alexandr P. Kornev, Susan S. Taylor & Rommie E. Amaro "Allostery through the computational microscope: cAMP activation of a canonical signalling domain", Nature Communications, 2015, Vol. 6, 8588^[10]

Notes and References

1. Web site: Dr. Rommie Amaro. Amaro Lab. 11 October 2015.
2. Web site: Rommie Amaro. UCSD Faculty. 11 October 2015.
3. Web site: Ghose. Tia. Rommie Amaro: Protein Explorer. The Scientist. 11 October 2015. 1 February 2012.
4. Web site: Amaro Lab. 2020-07-12. amarolab.ucsd.edu.
5. Web site: National Biomedical Computation Resource Receives $9 Million in Funding from National Institutes of Health. California Institute for Telecommunications and Information Technology. 11 October 2015. 27 August 2014.
6. Web site: D3R Welcome... . 2022-08-31 . drugdesigndata.org.
7. Web site: Fox. Tiffany. Rommie Amaro: Computing the Cure for Cancer on Desktop 'Supercomputers'. California Institute for Telecommunications and Information Technology. 11 October 2015. 6 January 2013.
8. Web site: Austin. Liz. NVIDIA Foundation Awards $200K Grant in "Compute the Cure" Anti-Cancer Effort. NVIDIA Blog. 11 October 2015. 11 December 2013.
9. Web site: Zverina. Jan. Teen Mentored by UC San Diego Professors Wins $250,000 in Science Prizes. UC San Diego News Center. 11 October 2015. 6 May 2014.
10. Web site: Amaro, Rommie . www-chem.ucsd.edu. 2020-03-07.