Rommie Amaro
Computational Chemistry and Biophysics

Contact Information

Assistant Professor, Chemistry and Biochemistry
American Chemical Society, Division of Computers in Chemistry, Alternate Councilor
National Biomedical Computation Resource, Affiliate

Office: Urey Hall 3234
Phone: 858-534-9629
Email: ramaro@ucsd.edu
Web: amarolab.ucsd.edu
Group: View group members

Education
2005 Ph.D., Chemistry, University of Illinois at Urbana-Champaign
1999 B.S., Chemical Engineering, University of Illinois at Urbana-Champaign

Appointments
2009-2011 Assistant Professor, Dept of Pharmaceutical Sciences, Computer Science, and Chemistry, University of California, Irvine
2000-2001 Associate Research Engineer, , Kraft Foods, Inc.

Awards and Academic Honors

2010

Presidential Early Career Award for Scientists and Engineers

2010

NIH New Innovator Awardee

2006

NIH Ruth Kirschstein Postdoctoral Fellow

2002

NCSA Performance Capability Champion Award

1999

UIUC All-Campus Teaching Award, Outstanding Teacher of Freshman (General Chemistry)

Research Interests

The Amaro lab is broadly concerned with the development and application of state-of-the-art computational and theoretical techniques to investigate the structure, function, and dynamics of complex biological systems. At the interface of chemistry, biology, physics, and pharmacology, our research integrates both applied and basic science components, with goals to bridge the interface between basic and clinical research. Fundamental enzymological and drug discovery studies are tightly coupled to a wide range of biochemical and biophysical experiments that allow us to engage in dynamic and exciting collaborations with various experimental labs.

Primary Research Area
Physical/Analytical Chemistry

Interdisciplinary interests

Computational and Theoretical
Biophysics

Selected Publications

Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM, "Mechanism of 150-cavity formation in influenza neuraminidase.", Nat Commun, 2011, Vol. 2, 388 [View Abstract]

Demir Ö, Baronio R, Salehi F, Wassman CD, Hall L, Hatfield GW, Chamberlin R, Kaiser P, Lathrop RH, Amaro RE, "Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants.", PLoS Comput Biol, 2011, Vol. 7, Issue 10, e1002238 [View Abstract]

Swift RV, Amaro RE, "Modeling the pharmacodynamics of passive membrane permeability.", J Comput Aided Mol Des, 2011, Vol. 25, Issue 11, 1007-17 [View Abstract]

Durrant JD, Hall L, Swift RV, Landon M, Schnaufer A, Amaro RE, "Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1.", PLoS Negl Trop Dis, 2010, Vol. 4, Issue 8, e803 [View Abstract]

Amaro RE, Baron R, McCammon JA, "An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.", J Comput Aided Mol Des, 2008, Vol. 22, Issue 9, 693-705 [View Abstract]

Amaro RE, Schnaufer A, Interthal H, Hol W, Stuart KD, McCammon JA, "Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei.", Proc Natl Acad Sci U S A, 2008, Vol. 105, Issue 45, 17278-83 [View Abstract]

Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA, "Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.", J Med Chem, 2008, Vol. 51, Issue 13, 3878-94 [View Abstract]

Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, Vajda S, "Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.", Chem Biol Drug Des, 2008, Vol. 71, Issue 2, 106-16 [View Abstract]