Amaro, Rommie
Computational Chemistry and Biophysics
Computational Chemistry and Biophysics
Contact Information
Professor and Endowed Chair, Chemistry and Biochemistry, UC San Diego
Section Chair, Biochemistry and Physics, Department of Chemistry and Biochemistry, UC San Diego
Director, Visible Molecular Cell Consortium, UC San Diego
Co-Director, Drug Design Data Resource, UC San Diego
Office: Urey Hall 3234
Phone: 858-534-9629
Email: ramaro@ucsd.edu
Web: amarolab.ucsd.edu drugdesigndata.org biochemcore.ucsd.edu vmcc.ucsd.edu
Group: View group members
Section Chair, Biochemistry and Physics, Department of Chemistry and Biochemistry, UC San Diego
Director, Visible Molecular Cell Consortium, UC San Diego
Co-Director, Drug Design Data Resource, UC San Diego
Office: Urey Hall 3234
Phone: 858-534-9629
Email: ramaro@ucsd.edu
Web: amarolab.ucsd.edu drugdesigndata.org biochemcore.ucsd.edu vmcc.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
2005 Ph.D., Chemistry, University of Illinois at Urbana-Champaign
1999 B.S., Chemical Engineering, University of Illinois at Urbana-Champaign
Appointments
2019-present Professor & Endowed Chair, Chemistry/Biochemistry, UC San Diego
2016-2019 Professor & Shuler Scholar, Chemistry/Biochemistry, UC San Diego
2015-present Director, Visible Molecular Cell Consortium, La Jolla, CA
2014-present Co-Director, Drug Discovery Data Resource, UC San Diego
2014-2016 Associate Professor, UC San Diego
2013-2020 Director, National Biomedical Computation Resource, UC San Diego
2011-2014 Assistant Professor, UC San Diego
2009-2011 Assistant Professor, Dept of Pharmaceutical Sciences, Computer Science, and Chemistry, University of California, Irvine
2000-2001 Associate Research Engineer, Kraft Foods, Inc.
2019-present Professor & Endowed Chair, Chemistry/Biochemistry, UC San Diego
2016-2019 Professor & Shuler Scholar, Chemistry/Biochemistry, UC San Diego
2015-present Director, Visible Molecular Cell Consortium, La Jolla, CA
2014-present Co-Director, Drug Discovery Data Resource, UC San Diego
2014-2016 Associate Professor, UC San Diego
2013-2020 Director, National Biomedical Computation Resource, UC San Diego
2011-2014 Assistant Professor, UC San Diego
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
2019
Lattimer Fellowship from the Division of Physical Sciences, UC San Diego
2018
UC San Diego Faculty Research Lecturer
2017
University of Minnesota, Dept. of Medicinal Chemistry Distinguished Lecturer (October 2017)
2017
SC'17 Plenary Speaker
2017
DeWitt Stetten Jr. Lecturer, NIH (October 2017)
2017
David E. Shaw Research Distinguished Lecturer (December 2017)
2016
Gordon Research Conference Computational Chemistry Keynote Lecture (July 2016)
2016
Corwin Hansch Award for Computer-Aided Drug Design (September 2016)
2016
American Chemical Society Kavli Emerging Leader in Chemistry
2015
Work featured on cover of Biophysical Journal (June 2015)
2015
Work featured on cover of ACS Biochemistry (March 2015)
2015
San Diego 78th District Woman of the Year
2015
Invited Speaker, Burroughs Wellcome “Future of Biophysics” Symposium, 59th Annual International Biophysical Society Meeting, Baltimore, Maryland
2014
Work featured on cover of Current Opinion in Structural Biology (April 2014)
2014
NVIDIA Women Who CUDA Awardee
2014
NVIDIA Compute-the-Cure Awardee
2014
Athena Pinnacle Award Nominee
2013
ACS Division of Computers in Chemistry OpenEye Outstanding Junior Faculty Award
2013
ACS ChemLuminary Award for “Innovation and Outstanding Service to Members of a Division” for the Teach- Discover-Treat initiative
2012
Hellman Fellow
2012
Chu Lectureship, Idaho State University
2010-2015
NIH Director's New Innovator Award, National Institutes of Health
2010
Presidential Early Career Award for Scientists and Engineers
2010
NIH New Innovator Awardee
2009
UCI Nominee for the Searle Scholar Award program (September 2009)
2008
Work featured on the cover of Chemical Biology & Drug Design (March 2008)
2008
UCSD Nominee for the Burroughs Wellcome Career Award at the Scientific Interface (2008)
2007
Keystone Symposia Scholarship Recipient (January 2007)
2007
Elected Alternate Councilor, American Chemical Society COMP Division (August 2007)
2007
Computer-Aided Drug Design Gordon Research Conference Fellowship Recipient (July 2007)
2007
Awarded “Best Demo” at PRAGMA-13 (August 2007)
2006–2009
NIH NRSA Ruth Kirschstein Postdoctoral Fellow, National Institutes of Health
2006
NIH Ruth Kirschstein Postdoctoral Fellow
2005
Work featured on cover of Biophysical Journal (July 2005)
2005
Work featured as cover story of NCSA Access Magazine
2005
Selected as a Student Facilitator at the Council for Chemical Research Annual Meeting
2002
NCSA Performance Capability Champion Award
2001-2004
UIUC Department of Chemistry Graduate Fellowship, Graduate College MAPP Fellow
2000
DNA Spark Award, Kraft Foods for “diligence, dedication, and enthusiasm”
2000
Above and Beyond Call of Duty Award, Kraft Foods
1999
UIUC All-Campus Teaching Award, Outstanding Teacher of Freshman (General Chemistry)
1995–1999
Ameritech Minority Engineering Scholarship, MChEP Air Products Scholar, Chancellor’s Scholar, President’s Scholar, Unofficial List of Excellent Teache
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
Physical/Analytical Chemistry
Interdisciplinary interests
Computational and Theoretical
Biophysics
Biophysics
Outreach Activities
http://biochemcore.ucsd.edu
Selected Publications
- 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, 7969-7981 [View]
- 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 [View]
- 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 [View]
- 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 [View]
- 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, [View]
- 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 [View]
- Schiffer JM, Luo M, Dommer AC, Thoron G, Pendergraft M, Santander MV, Lucero D, Pecora de Barros E, Prather KA, Grassian VH, Amaro RE "Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols.", J Phys Chem Lett, 2018, Vol. 9, Issue 14, 3839-3849 [View]
- Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE "Determinants of Oligonucleotide Selectivity of APOBEC3B.", J Chem Inf Model, 2018, [View]
- Wahab HA, Amaro RE, Cournia Z "Women in Computational Chemistry.", J Chem Inf Model, 2018, [View]
- Akbar R, Jusoh SA, Amaro RE, Helms V "ENRI: A tool for selecting structure-based virtual screening target conformations.", Chem Biol Drug Des, 2017, Vol. 89, Issue 5, 762-771 [View]
- Amaro RE "Toward Understanding "the Ways" of Allosteric Drugs.", ACS Cent Sci, 2017, Vol. 3, Issue 9, 925-926 [View]
- Amaro RE, Villa E, Luthey-Schulten Z "Biography of Klaus Schulten.", J Phys Chem B, 2017, Vol. 121, Issue 15, 3206 [View]
- Cheng KJ, Demir Ö, Amaro RE "A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases.", Genes (Basel), 2017, Vol. 8, Issue 6, [View]
- Demir Ö, Ieong PU, Amaro RE "Full-length p53 tetramer bound to DNA and its quaternary dynamics.", Oncogene, 2017, Vol. 36, Issue 10, 1451-1460 [View]
- Grogan F, Holst M, Lindblom L, Amaro R "Reliability assessment for large-scale molecular dynamics approximations.", J Chem Phys, 2017, Vol. 147, Issue 23, 234106 [View]
- Hirakis SP, Malmstrom RD, Amaro RE "Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism.", Biochemistry, 2017, Vol. 56, Issue 30, 3885-3888 [View]
- Ottilie S, Goldgof GM, Calvet CM, Jennings GK, LaMonte G, Schenken J, Vigil E, Kumar P, McCall LI, Lopes ES, Gunawan F, Yang J, Suzuki Y, Siqueira-Neto JL, McKerrow JH, Amaro RE, Podust LM, Durrant JD, Winzeler EA "Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast.", ACS Chem Biol, 2017, Vol. 12, Issue 2, 422-434 [View]
- P Barros E, Malmstrom RD, Nourbakhsh K, Del Rio JC, Kornev AP, Taylor SS, Amaro RE "Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα.", Biochemistry, 2017, Vol. 56, Issue 10, 1536-1545 [View]
- Prabhu L, Chen L, Wei H, Demir Ö, Safa A, Zeng L, Amaro RE, O'Neil BH, Zhang ZY, Lu T "Development of an AlphaLISA high throughput technique to screen for small molecule inhibitors targeting protein arginine methyltransferases.", Mol Biosyst, 2017, Vol. 13, Issue 12, 2509-2520 [View]
- Prabhu L, Wei H, Chen L, Demir Ö, Sandusky G, Sun E, Wang J, Mo J, Zeng L, Fishel M, Safa A, Amaro R, Korc M, Zhang ZY, Lu T "Adapting AlphaLISA high throughput screen to discover a novel small-molecule inhibitor targeting protein arginine methyltransferase 5 in pancreatic and colorectal cancers.", Oncotarget, 2017, Vol. 8, Issue 25, 39963-39977 [View]
- Purawat S, Ieong PU, Malmstrom RD, Chan GJ, Yeung AK, Walker RC, Altintas I, Amaro RE "A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.", Biophys J, 2017, Vol. 112, Issue 12, 2469-2474 [View]
- Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K,Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir Ö, Amaro RE, Harki DA, Harris RS, Aihara H "Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.", Nat Struct Mol Biol, 2017, Vol. 24, Issue 2, 131-139 [View]
- Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H "Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.", Sci Rep, 2017, Vol. 7, Issue 1, 17415 [View]
- Votapka LW, Jagger BR, Heyneman AL, Amaro RE "SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.", J Phys Chem B, 2017, Vol. 121, Issue 15, 3597-3606 [View]
- Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE "POVME 3.0: Software for Mapping Binding Pocket Flexibility.", J Chem Theory Comput, 2017, Vol. 13, Issue 9, 4584-4592 [View]
- Buffalo CZ, Bahn-Suh AJ, Hirakis SP, Biswas T, Amaro RE, Nizet V, Ghosh P "Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein.", Nat Microbiol, 2016, Vol. 1, Issue 11, 16155 [View]
- Durrant JD, Bush RM, Amaro RE "Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants.", J Phys Chem B, 2016, Vol. 120, Issue 33, 8590-9 [View]
- Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK "D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.", J Comput Aided Mol Des, 2016, Vol. 30, Issue 9, 651-668 [View]
- Goldgof GM, Durrant JD, Ottilie S, Vigil E, Allen KE, Gunawan F, Kostylev M, Henderson KA, Yang J, Schenken J, LaMonte GM, Manary MJ, Murao A, Nachon M, Stanhope R, Prescott M, McNamara CW, Slayman CW, Amaro RE, Suzuki Y, Winzeler EA "Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor.", Sci Rep, 2016, Vol. 6, 27806 [View]
- Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC "Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.", J Chem Inf Model, 2016, Vol. 56, Issue 4, 721-33 [View]
- Liang C, Li Y, Luo J "A Novel Method to Detect Functional microRNA Regulatory Modules by Bicliques Merging.", IEEE/ACM Trans Comput Biol Bioinform, 2016, Vol. 13, Issue 3, 549-56 [View]
- Offutt TL, Swift RV, Amaro RE "Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations.", J Chem Inf Model, 2016, Vol. 56, Issue 10, 1923-1935 [View]
- Purawat S, Cowart C, Amaro RE, Altintas I "Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research.", Procedia Comput Sci, 2016, Vol. 80, 1791-1800 [View]
- Rajappa-Titu L, Suematsu T, Munoz-Tello P, Long M, Demir Ö, Cheng KJ, Stagno JR, Luecke H, Amaro RE, Aphasizheva I, Aphasizhev R, Thore S "RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting.", Nucleic Acids Res, 2016, Vol. 44, Issue 22, 10862-10878 [View]
- Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE "Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A.", Biophys J, 2016, Vol. 111, Issue 8, 1631-1640 [View]
- Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA "Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer.", Structure, 2016, Vol. 24, Issue 8, 1248-1256 [View]
- Swift RV, Jusoh SA, Offutt TL, Li ES, Amaro RE "Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles.", J Chem Inf Model, 2016, Vol. 56, Issue 5, 830-42 [View]
- Votapka LW, Lee CT, Amaro RE "Two Relations to Estimate Membrane Permeability Using Milestoning.", J Phys Chem B, 2016, Vol. 120, Issue 33, 8606-16 [View]
- Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE "Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.", Chem Rev, 2016, Vol. 116, Issue 11, 6370-90 [View]
- Zimmermann S, Hall L, Riley S, Sørensen J, Amaro RE, Schnaufer A "A novel high-throughput activity assay for the Trypanosoma brucei editosome enzyme REL1 and other RNA ligases.", Nucleic Acids Res, 2016, Vol. 44, Issue 3, e24 [View]
- Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD "Bridging scales through multiscale modeling: a case study on protein kinase A.", Front Physiol, 2015, Vol. 6, 250 [View]
- Durrant JD, Carlson KE, Martin TA, Offutt TL, Mayne CG, Katzenellenbogen JA, Amaro RE "Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands.", J Chem Inf Model, 2015, Vol. 55, Issue 9, 1953-61 [View]
- 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 [View]
- 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
- Votapka LW, Amaro RE "Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.", PLoS Comput Biol, 2015, Vol. 11, Issue 10, e1004381 [View]
- Jacob D. Durrant, Rommie E. Amaro "LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry", PLOS Computational Biology, 2014, Vol. 10, Issue 7, e1003720
- Wassman CD, Baronio R, Demir Ö, Wallentine BD, Chen CK, Hall LV, Salehi F, Lin DW, Chung BP, Hatfield GW, Richard Chamberlin A, Luecke H, Lathrop RH, Kaiser P, Amaro RE, "Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53.", Nat Commun, 2013, Vol. 4, 1407 [View]
- 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]
- 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]
- Swift RV, Amaro RE, "Modeling the pharmacodynamics of passive membrane permeability.", J Comput Aided Mol Des, 2011, Vol. 25, Issue 11, 1007-17 [View]
- 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]