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Rommie Amaro

TitleProfessor
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0340
La Jolla CA 92093
Phone858-534-9629
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    Collapse Research 
    Collapse Research Activities and Funding
    AN OPEN RESOURCE FOR COLLABORATIVE BIOMEDICAL BIG DATA TRAINING
    NIH/NIGMS R25GM114821Sep 29, 2014 - Aug 31, 2017
    Role: Principal Investigator
    AN OPEN RESOURCE TO ADVANCE COMPUTER-AIDED DRUG DESIGN
    NIH/NIGMS U01GM111528Sep 15, 2014 - Aug 31, 2019
    Role: Principal Investigator
    A Structural Systems Biology Approach to Drug Discovery
    NIH DP2OD007237Sep 30, 2010 - Oct 31, 2016
    Role: Principal Investigator
    Towards a Structural Systems Biology Approach for Anti-Trypanosomal Therapeutics
    NIH/NIAID K22AI081901Aug 15, 2010 - Jul 31, 2013
    Role: Principal Investigator
    The SMD-Relaxed Complex Method for Drug Design
    NIH/NIGMS F32GM077729Sep 1, 2006 - Jun 30, 2009
    Role: Principal Investigator
    NATIONAL BIOMEDICAL COMPUTATION RESOURCE
    NIH/NIGMS P41GM103426May 6, 1997 - Apr 30, 2019
    Role: Principal Investigator
    High Performance Computing for Biomedical Research
    NIH P41RR006009Sep 1, 1990 - Jul 31, 2013
    Role: Co-Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang DB, Wang VY, Amaro R, Huxford T, Ghosh G. Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor ?B RelA Subunit. Biochemistry. 2018 May 10. PMID: 29708732.
      View in: PubMed
    2. Bohl TE, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir Ö, Kurahashi K, Amaro R, 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 Apr 06. PMID: 29626094.
      View in: PubMed
    3. Amaro R, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophys J. 2018 Mar 29. PMID: 29606412.
      View in: PubMed
    4. Grogan F, Holst M, Lindblom L, Amaro R. Reliability assessment for large-scale molecular dynamics approximations. J Chem Phys. 2017 Dec 21; 147(23):234106. PMID: 29272950.
      View in: PubMed
    5. Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro R, Aihara H. Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 2017 Dec 12; 7(1):17415. PMID: 29234087.
      View in: PubMed
    6. 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 R. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des. 2018 Jan; 32(1):1-20. PMID: 29204945.
      View in: PubMed
    7. Prabhu L, Chen L, Wei H, Demir Ö, Safa A, Zeng L, Amaro R, 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 Nov 21; 13(12):2509-2520. PMID: 29099132.
      View in: PubMed
    8. Amaro R. Toward Understanding "the Ways" of Allosteric Drugs. ACS Cent Sci. 2017 Sep 27; 3(9):925-926. PMID: 28979932.
      View in: PubMed
    9. Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro R. POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput. 2017 Sep 12; 13(9):4584-4592. PMID: 28800393.
      View in: PubMed
    10. Hirakis SP, Malmstrom RD, Amaro R. 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 08 01; 56(30):3885-3888. PMID: 28661131.
      View in: PubMed
    11. Purawat S, Ieong PU, Malmstrom RD, Chan GJ, Yeung AK, Walker RC, Altintas I, Amaro R. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. Biophys J. 2017 Jun 20; 112(12):2469-2474. PMID: 28636905.
      View in: PubMed
    12. Cheng KJ, Demir Ö, Amaro R. A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases. Genes (Basel). 2017 Jun 20; 8(6). PMID: 28632168.
      View in: PubMed
    13. 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 Jun 20; 8(25):39963-39977. PMID: 28591716.
      View in: PubMed
    14. Buffalo CZ, Bahn-Suh AJ, Hirakis SP, Biswas T, Amaro R, Nizet V, Ghosh P. Erratum: Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol. 2017 Jun 12; 2:17107. PMID: 28604710.
      View in: PubMed
    15. Amaro R, Villa E, Luthey-Schulten Z. Biography of Klaus Schulten. J Phys Chem B. 2017 04 20; 121(15):3206. PMID: 28423903.
      View in: PubMed
    16. Purawat S, Cowart C, Amaro R, Altintas I. Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research. J Comput Sci. 2017 May; 20:205-214. PMID: 29104704.
      View in: PubMed
    17. P Barros E, Malmstrom RD, Nourbakhsh K, Del Rio JC, Kornev AP, Taylor SS, Amaro R. Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIa. Biochemistry. 2017 03 14; 56(10):1536-1545. PMID: 28221775.
      View in: PubMed
    18. Votapka LW, Jagger BR, Heyneman AL, Amaro R. 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 04 20; 121(15):3597-3606. PMID: 28191969.
      View in: PubMed
    19. 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 R, Podust LM, Durrant JD, Winzeler EA. Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast. ACS Chem Biol. 2017 Feb 17; 12(2):422-434. PMID: 27977118.
      View in: PubMed
    20. Akbar R, Jusoh SA, Amaro R, Helms V. ENRI: A tool for selecting structure-based virtual screening target conformations. Chem Biol Drug Des. 2017 May; 89(5):762-771. PMID: 27995760.
      View in: PubMed
    21. Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir Ö, Amaro R, Harki DA, Harris RS, Aihara H. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol. 2017 02; 24(2):131-139. PMID: 27991903.
      View in: PubMed
    22. Amaro R. A Reflection on Klaus Schulten. J Chem Theory Comput. 2017 01 10; 13(1):1-2. PMID: 28068772.
      View in: PubMed
    23. Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro R. Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophys J. 2016 Oct 18; 111(8):1631-1640. PMID: 27760351.
      View in: PubMed
    24. Offutt TL, Swift RV, Amaro R. Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. J Chem Inf Model. 2016 10 24; 56(10):1923-1935. PMID: 27662181.
      View in: PubMed
    25. Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB, Carlson HA, Burley SK, Walters WP, Amaro R, Feher VA, Gilson MK. D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des. 2016 09; 30(9):651-668. PMID: 27696240.
      View in: PubMed
    26. Buffalo CZ, Bahn-Suh AJ, Hirakis SP, Biswas T, Amaro R, Nizet V, Ghosh P. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol. 2016 Sep 05; 1(11):16155. PMID: 27595425.
      View in: PubMed
    27. Amaro R, Madura JD, Wong CF. Tribute to J. Andrew McCammon. J Phys Chem B. 2016 08 25; 120(33):8055-6. PMID: 27558538.
      View in: PubMed
    28. Amaro R. Drug Discovery Gets a Boost from Data Science. Structure. 2016 08 02; 24(8):1225-1226. PMID: 27486914.
      View in: PubMed
    29. Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro R, Komives EA. Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure. 2016 08 02; 24(8):1248-1256. PMID: 27396830; PMCID: PMC4972691 [Available on 08/02/17].
    30. 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 R, Suzuki Y, Winzeler EA. Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. Sci Rep. 2016 06 13; 6:27806. PMID: 27291296.
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    31. Purawat S, Cowart C, Amaro R, Altintas I. Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research. Procedia Comput Sci. 2016 Jun; 80:1791-1800. PMID: 27478519.
      View in: PubMed
    32. Votapka LW, Lee CT, Amaro R. Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B. 2016 08 25; 120(33):8606-16. PMID: 27154639.
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    33. Durrant JD, Bush RM, Amaro R. Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants. J Phys Chem B. 2016 08 25; 120(33):8590-9. PMID: 27141956.
      View in: PubMed
    34. Swift RV, Jusoh SA, Offutt TL, Li ES, Amaro R. Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. J Chem Inf Model. 2016 05 23; 56(5):830-42. PMID: 27097522.
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    35. Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro R, Chipot C, Wang Y, Gumbart JC. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model. 2016 04 25; 56(4):721-33. PMID: 27043429.
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    36. Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro R. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 2016 06 08; 116(11):6370-90. PMID: 27074285; PMCID: PMC4901368.
    37. Richards C, Albin JS, Demir Ö, Shaban NM, Luengas EM, Land AM, Anderson BD, Holten JR, Anderson JS, Harki DA, Amaro R, Harris RS. The Binding Interface between Human APOBEC3F and HIV-1 Vif Elucidated by Genetic and Computational Approaches. Cell Rep. 2015 Dec 01; 13(9):1781-8. PMID: 26628363; PMCID: PMC4684092.
    38. Votapka LW, Amaro R. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol. 2015 Oct; 11(10):e1004381. PMID: 26505480; PMCID: PMC4624728.
    39. Zimmermann S, Hall L, Riley S, Sørensen J, Amaro R, Schnaufer A. A novel high-throughput activity assay for the Trypanosoma brucei editosome enzyme REL1 and other RNA ligases. Nucleic Acids Res. 2016 Feb 18; 44(3):e24. PMID: 26400159; PMCID: PMC4756849.
    40. Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro R, McCulloch AD. Bridging scales through multiscale modeling: a case study on protein kinase A. Front Physiol. 2015; 6:250. PMID: 26441670; PMCID: PMC4563169.
    41. Durrant JD, Carlson KE, Martin TA, Offutt TL, Mayne CG, Katzenellenbogen JA, Amaro R. Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. J Chem Inf Model. 2015 Sep 28; 55(9):1953-61. PMID: 26286148; PMCID: PMC4780411.
    42. Malmstrom RD, Kornev AP, Taylor SS, Amaro R. Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nat Commun. 2015 Jul 06; 6:7588. PMID: 26145448.
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    43. Ieong P, Amaro R, Li WW. Molecular dynamics analysis of antibody recognition and escape by human H1N1 influenza hemagglutinin. Biophys J. 2015 Jun 02; 108(11):2704-12. PMID: 26039171; PMCID: PMC4457473.
    44. Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro R, Komives EA. How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry. 2015 Mar 03; 54(8):1673-80. PMID: 25654263; PMCID: PMC4348336.
    45. Ikram NK, Durrant JD, Muchtaridi M, Zalaludin AS, Purwitasari N, Mohamed N, Rahim AS, Lam CK, Normi YM, Rahman NA, Amaro R, Wahab HA. A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity. J Chem Inf Model. 2015 Feb 23; 55(2):308-16. PMID: 25555059; PMCID: PMC4340357.
    46. Sørensen J, Demir Ö, Swift RV, Feher VA, Amaro R. Molecular docking to flexible targets. Methods Mol Biol. 2015; 1215:445-69. PMID: 25330975.
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    47. Durrant JD, Amaro R. Machine-learning techniques applied to antibacterial drug discovery. Chem Biol Drug Des. 2015 Jan; 85(1):14-21. PMID: 25521642; PMCID: PMC4273861.
    48. Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M. Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics. Biophys J. 2014 Oct 07; 107(7):1675-85. PMID: 25296321; PMCID: PMC4190606.
    49. Durrant JD, Votapka L, Sørensen J, Amaro R. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput. 2014 Nov 11; 10(11):5047-5056. PMID: 25400521.
      View in: PubMed
    50. Durrant JD, Amaro R. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol. 2014 Jul; 10(7):e1003720. PMID: 25032790; PMCID: PMC4102414.
    51. Malmstrom RD, Lee CT, Van Wart A, Amaro R. On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput. 2014 Jul 08; 10(7):2648-2657. PMID: 25473382.
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    52. Demir O, Labaied M, Merritt C, Stuart K, Amaro R. Computer-aided discovery of Trypanosoma brucei RNA-editing terminal uridylyl transferase 2 inhibitors. Chem Biol Drug Des. 2014 Aug; 84(2):131-9. PMID: 24903413; PMCID: PMC4317284.
    53. Durrant JD, Amaro R. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinformatics. 2014 May 23; 15:159. PMID: 24886360; PMCID: PMC4094277.
    54. Amaro R, Bansal M. Editorial overview: Theory and simulation: Tools for solving the insolvable. Curr Opin Struct Biol. 2014 Apr; 25:iv-v. PMID: 24835772.
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    55. Feher VA, Durrant JD, Van Wart AT, Amaro R. Computational approaches to mapping allosteric pathways. Curr Opin Struct Biol. 2014 Apr; 25:98-103. PMID: 24667124; PMCID: PMC4040315.
    56. Van Wart AT, Durrant J, Votapka L, Amaro R. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. J Chem Theory Comput. 2014 Feb 11; 10(2):511-517. PMID: 24803851.
      View in: PubMed
    57. Chen E, Swift RV, Alderson N, Feher VA, Feng GS, Amaro R. Computation-guided discovery of influenza endonuclease inhibitors. ACS Med Chem Lett. 2014 Jan 09; 5(1):61-64. PMID: 24490002.
      View in: PubMed
    58. Ieong PU, Sørensen J, Vemu PL, Wong CW, Demir Ö, Williams NP, Wang J, Crawl D, Swift RV, Malmstrom RD, Altintas I, Amaro R. Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations. Procedia Comput Sci. 2014; 29:1745-1755. PMID: 29399238.
      View in: PubMed
    59. Rathore A, Carpenter MA, Demir Ö, Ikeda T, Li M, Shaban NM, Law EK, Anokhin D, Brown WL, Amaro R, Harris RS. The local dinucleotide preference of APOBEC3G can be altered from 5'-CC to 5'-TC by a single amino acid substitution. J Mol Biol. 2013 Nov 15; 425(22):4442-54. PMID: 23938202; PMCID: PMC3812309.
    60. Park J, Czapla L, Amaro R. Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding. J Chem Inf Model. 2013 Aug 26; 53(8):2047-56. PMID: 23927370; PMCID: PMC3787069.
    61. Feher VA, Randall A, Baldi P, Bush RM, de la Maza LM, Amaro R. A 3-dimensional trimeric ß-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins. PLoS One. 2013; 8(7):e68934. PMID: 23935908; PMCID: PMC3723809.
    62. Swift RV, Amaro R. Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR? Chem Biol Drug Des. 2013 Jan; 81(1):61-71. PMID: 23066853; PMCID: PMC3527668.
    63. 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 R. Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Nat Commun. 2013; 4:1407. PMID: 23360998; PMCID: PMC3562459.
    64. Demir O, Amaro R. Designing novel inhibitors of Trypanosoma brucei. Methods Mol Biol. 2013; 993:231-43. PMID: 23568474.
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    65. Swift RV, Ong CD, Amaro R. Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme. Biochemistry. 2012 Dec 21; 51(51):10236-43. PMID: 23205906; PMCID: PMC3549306.
    66. Votapka L, Amaro R. Multistructural hot spot characterization with FTProd. Bioinformatics. 2013 Feb 01; 29(3):393-4. PMID: 23202744; PMCID: PMC3562065.
    67. Jansen JM, Amaro R, Cornell W, Tseng YJ, Walters WP. Computational chemistry and drug discovery: a call to action. Future Med Chem. 2012 Oct; 4(15):1893-6. PMID: 23088271.
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    68. Jansen JM, Cornell W, Tseng YJ, Amaro R. Teach-Discover-Treat (TDT): collaborative computational drug discovery for neglected diseases. J Mol Graph Model. 2012 Sep; 38:360-2. PMID: 23085175; PMCID: PMC3508335.
    69. Vanwart AT, Eargle J, Luthey-Schulten Z, Amaro R. Exploring residue component contributions to dynamical network models of allostery. J Chem Theory Comput. 2012 Aug 14; 8(8):2949-2961. PMID: 23139645.
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    70. Votapka L, Demir O, Swift RV, Walker RC, Amaro R. Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med. 2012; 6:293-300. PMID: 22872804; PMCID: PMC3410406.
    71. Demir Ö, Amaro R. Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. J Chem Inf Model. 2012 May 25; 52(5):1308-18. PMID: 22512810; PMCID: PMC3362124.
    72. Gabrielsen M, Beckham KS, Feher VA, Zetterström CE, Wang D, Müller S, Elofsson M, Amaro R, Byron O, Roe AJ. Structural characterisation of Tpx from Yersinia pseudotuberculosis reveals insights into the binding of salicylidene acylhydrazide compounds. PLoS One. 2012; 7(2):e32217. PMID: 22384182.
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    73. Nichols SE, Swift RV, Amaro R. Rational prediction with molecular dynamics for hit identification. Curr Top Med Chem. 2012; 12(18):2002-12. PMID: 23110535; PMCID: PMC3636520.
    74. Amaro R, Li WW. Molecular-level simulation of pandemic influenza glycoproteins. Methods Mol Biol. 2012; 819:575-94. PMID: 22183559; PMCID: PMC3352029.
    75. Swift RV, Amaro R. Modeling the pharmacodynamics of passive membrane permeability. J Comput Aided Mol Des. 2011 Nov; 25(11):1007-17. PMID: 22042376; PMCID: PMC3223344.
    76. Demir Ö, Baronio R, Salehi F, Wassman CD, Hall L, Hatfield GW, Chamberlin R, Kaiser P, Lathrop RH, Amaro R. Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants. PLoS Comput Biol. 2011 Oct; 7(10):e1002238. PMID: 22028641; PMCID: PMC3197647.
    77. Torres R, Swift RV, Chim N, Wheatley N, Lan B, Atwood BR, Pujol C, Sankaran B, Bliska JB, Amaro R, Goulding CW. Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis. PLoS One. 2011; 6(9):e25084. PMID: 21966419.
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    78. Amaro R, Swift RV, Votapka L, Li WW, Walker RC, Bush RM. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011 Jul 12; 2:388. PMID: 21750542; PMCID: PMC3144582.
    79. Durrant JD, Hall L, Swift RV, Landon M, Schnaufer A, Amaro R. Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1. PLoS Negl Trop Dis. 2010 Aug 24; 4(8):e803. PMID: 20808768; PMCID: PMC2927429.
    80. Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins. 2010 Aug 15; 78(11):2523-32. PMID: 20602360; PMCID: PMC2902668.
    81. Sung JC, Van Wynsberghe AW, Amaro R, Li WW, McCammon JA. Role of secondary sialic acid binding sites in influenza N1 neuraminidase. J Am Chem Soc. 2010 Mar 10; 132(9):2883-5. PMID: 20155919; PMCID: PMC2835425.
    82. Durrant JD, Amaro R, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne PE, McCammon JA. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol. 2010 Jan 22; 6(1):e1000648. PMID: 20098496; PMCID: PMC2799658.
    83. Amaro R, Li WW. Emerging methods for ensemble-based virtual screening. Curr Top Med Chem. 2010; 10(1):3-13. PMID: 19929833; PMCID: PMC3086266.
    84. Newhouse EI, Xu D, Markwick PR, Amaro R, Pao HC, Wu KJ, Alam M, McCammon JA, Li WW. Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc. 2009 Dec 02; 131(47):17430-42. PMID: 19891427; PMCID: PMC2782351.
    85. Swift RV, Amaro R. Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opin Drug Discov. 2009 Dec 01; 4(12):1281-1294. PMID: 20354588.
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    86. Amaro R, Cheng X, Ivanov I, Xu D, McCammon JA. Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc. 2009 Apr 08; 131(13):4702-9. PMID: 19296611; PMCID: PMC2665887.
    87. Xu D, Newhouse EI, Amaro R, Pao HC, Cheng LS, Markwick PR, McCammon JA, Li WW, Arzberger PW. Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. J Mol Biol. 2009 Mar 27; 387(2):465-91. PMID: 19356594.
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    88. Swift RV, Durrant J, Amaro R, McCammon JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 2009 Feb 03; 48(4):709-19. PMID: 19133737; PMCID: PMC2651658.
    89. Durrant JD, Amaro R, McCammon JA. AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des. 2009 Feb; 73(2):168-78. PMID: 19207419; PMCID: PMC2724963.
    90. Wong S, Amaro R, McCammon JA. MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface. J Chem Theory Comput. 2009 Feb 10; 5(2):422-429. PMID: 19461869.
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    91. Amaro R, 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 Nov 11; 105(45):17278-83. PMID: 18981420.
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    92. Cheng LS, Amaro R, 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 Jul 10; 51(13):3878-94. PMID: 18558668; PMCID: PMC2652358.
    93. Landon MR, Amaro R, 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 Feb; 71(2):106-16. PMID: 18205727; PMCID: PMC2438278.
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    95. Amaro R, Swift RV, McCammon JA. Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei. PLoS Negl Trop Dis. 2007 Nov 14; 1(2):e68. PMID: 18060084; PMCID: PMC2100368.
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