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Rommie Amaro

TitleResearcher
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. Wagner JR, Demir O, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model. 2018 Aug 21. PMID: 30130104.
      View in: PubMed
    2. Jagger BR, Lee CT, Amaro RE. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 2018 Aug 02. PMID: 30070844.
      View in: PubMed
    3. 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 May 19. PMID: 29787764.
      View in: PubMed
    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 ?B RelA Subunit. Biochemistry. 2018 May 10. PMID: 29708732.
      View in: PubMed
    5. 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 Apr 06. PMID: 29626094.
      View in: PubMed
    6. Amaro RE, 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
    7. 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
    8. 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 Dec 12; 7(1):17415. PMID: 29234087.
      View in: PubMed
    9. 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 Jan; 32(1):1-20. PMID: 29204945.
      View in: PubMed
    10. 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 Nov 21; 13(12):2509-2520. PMID: 29099132.
      View in: PubMed
    11. Amaro RE. Toward Understanding "the Ways" of Allosteric Drugs. ACS Cent Sci. 2017 Sep 27; 3(9):925-926. PMID: 28979932.
      View in: PubMed
    12. 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 Sep 12; 13(9):4584-4592. PMID: 28800393.
      View in: PubMed
    13. 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 08 01; 56(30):3885-3888. PMID: 28661131.
      View in: PubMed
    14. 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 Jun 20; 112(12):2469-2474. PMID: 28636905.
      View in: PubMed
    15. Cheng KJ, Demir Ö, Amaro RE. A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases. Genes (Basel). 2017 Jun 20; 8(6). PMID: 28632168.
      View in: PubMed
    16. 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
    17. Buffalo CZ, Bahn-Suh AJ, Hirakis SP, Biswas T, Amaro RE, 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
    18. Amaro RE, Villa E, Luthey-Schulten Z. Biography of Klaus Schulten. J Phys Chem B. 2017 04 20; 121(15):3206. PMID: 28423903.
      View in: PubMed
    19. 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. J Comput Sci. 2017 May; 20:205-214. PMID: 29104704.
      View in: PubMed
    20. 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 RIa. Biochemistry. 2017 03 14; 56(10):1536-1545. PMID: 28221775.
      View in: PubMed
    21. 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 04 20; 121(15):3597-3606. PMID: 28191969.
      View in: PubMed
    22. 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 Feb 17; 12(2):422-434. PMID: 27977118.
      View in: PubMed
    23. Akbar R, Jusoh SA, Amaro RE, 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
    24. 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 02; 24(2):131-139. PMID: 27991903.
      View in: PubMed
    25. Amaro RE. A Reflection on Klaus Schulten. J Chem Theory Comput. 2017 01 10; 13(1):1-2. PMID: 28068772.
      View in: PubMed
    26. 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 Oct 18; 111(8):1631-1640. PMID: 27760351.
      View in: PubMed
    27. 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 12 15; 44(22):10862-10878. PMID: 27744351.
      View in: PubMed
    28. Offutt TL, Swift RV, Amaro RE. 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
    29. 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 RE, 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
    30. 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 Sep 05; 1(11):16155. PMID: 27595425.
      View in: PubMed
    31. Amaro RE, 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
    32. Amaro RE. Drug Discovery Gets a Boost from Data Science. Structure. 2016 08 02; 24(8):1225-1226. PMID: 27486914.
      View in: PubMed
    33. 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 08 02; 24(8):1248-1256. PMID: 27396830; PMCID: PMC4972691 [Available on 08/02/17].
    34. 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 06 13; 6:27806. PMID: 27291296.
      View in: PubMed
    35. 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 Jun; 80:1791-1800. PMID: 27478519.
      View in: PubMed
    36. Votapka LW, Lee CT, Amaro RE. Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B. 2016 08 25; 120(33):8606-16. PMID: 27154639.
      View in: PubMed
    37. 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 08 25; 120(33):8590-9. PMID: 27141956.
      View in: PubMed
    38. 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 05 23; 56(5):830-42. PMID: 27097522.
      View in: PubMed
    39. 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 04 25; 56(4):721-33. PMID: 27043429.
      View in: PubMed
    40. 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 06 08; 116(11):6370-90. PMID: 27074285; PMCID: PMC4901368.
    41. 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 Dec 01; 13(9):1781-8. PMID: 26628363; PMCID: PMC4684092.
    42. Votapka LW, Amaro RE. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol. 2015 Oct; 11(10):e1004381. PMID: 26505480; PMCID: PMC4624728.
    43. 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 Feb 18; 44(3):e24. PMID: 26400159; PMCID: PMC4756849.
    44. 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; 6:250. PMID: 26441670; PMCID: PMC4563169.
    45. 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 Sep 28; 55(9):1953-61. PMID: 26286148; PMCID: PMC4780411.
    46. Malmstrom RD, Kornev AP, Taylor SS, Amaro RE. Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nat Commun. 2015 Jul 06; 6:7588. PMID: 26145448.
      View in: PubMed
    47. Ieong P, Amaro RE, 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.
    48. Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, 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.
    49. Ikram NK, Durrant JD, Muchtaridi M, Zalaludin AS, Purwitasari N, Mohamed N, Rahim AS, Lam CK, Normi YM, Rahman NA, Amaro RE, 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.
    50. Sørensen J, Demir Ö, Swift RV, Feher VA, Amaro RE. Molecular docking to flexible targets. Methods Mol Biol. 2015; 1215:445-69. PMID: 25330975.
      View in: PubMed
    51. Durrant JD, Amaro RE. Machine-learning techniques applied to antibacterial drug discovery. Chem Biol Drug Des. 2015 Jan; 85(1):14-21. PMID: 25521642; PMCID: PMC4273861.
    52. 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.
    53. Durrant JD, Votapka L, Sørensen J, Amaro RE. 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
    54. Durrant JD, Amaro RE. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol. 2014 Jul; 10(7):e1003720. PMID: 25032790; PMCID: PMC4102414.
    55. Malmstrom RD, Lee CT, Van Wart A, Amaro RE. 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.
      View in: PubMed
    56. Demir O, Labaied M, Merritt C, Stuart K, Amaro RE. 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.
    57. Durrant JD, Amaro RE. 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.
    58. Amaro RE, Bansal M. Editorial overview: Theory and simulation: Tools for solving the insolvable. Curr Opin Struct Biol. 2014 Apr; 25:iv-v. PMID: 24835772.
      View in: PubMed
    59. Feher VA, Durrant JD, Van Wart AT, Amaro RE. Computational approaches to mapping allosteric pathways. Curr Opin Struct Biol. 2014 Apr; 25:98-103. PMID: 24667124; PMCID: PMC4040315.
    60. Van Wart AT, Durrant J, Votapka L, Amaro RE. 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
    61. Chen E, Swift RV, Alderson N, Feher VA, Feng GS, Amaro RE. Computation-guided discovery of influenza endonuclease inhibitors. ACS Med Chem Lett. 2014 Jan 09; 5(1):61-64. PMID: 24490002.
      View in: PubMed
    62. Ieong PU, Sørensen J, Vemu PL, Wong CW, Demir Ö, Williams NP, Wang J, Crawl D, Swift RV, Malmstrom RD, Altintas I, Amaro RE. 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
    63. Rathore A, Carpenter MA, Demir Ö, Ikeda T, Li M, Shaban NM, Law EK, Anokhin D, Brown WL, Amaro RE, 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.
    64. Park J, Czapla L, Amaro RE. 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.
    65. Feher VA, Randall A, Baldi P, Bush RM, de la Maza LM, Amaro RE. 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.
    66. Swift RV, Amaro RE. 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.
    67. 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; 4:1407. PMID: 23360998; PMCID: PMC3562459.
    68. Demir O, Amaro RE. Designing novel inhibitors of Trypanosoma brucei. Methods Mol Biol. 2013; 993:231-43. PMID: 23568474.
      View in: PubMed
    69. Swift RV, Ong CD, Amaro RE. Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme. Biochemistry. 2012 Dec 21; 51(51):10236-43. PMID: 23205906; PMCID: PMC3549306.
    70. Votapka L, Amaro RE. Multistructural hot spot characterization with FTProd. Bioinformatics. 2013 Feb 01; 29(3):393-4. PMID: 23202744; PMCID: PMC3562065.
    71. Jansen JM, Amaro RE, 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.
      View in: PubMed
    72. Jansen JM, Cornell W, Tseng YJ, Amaro RE. Teach-Discover-Treat (TDT): collaborative computational drug discovery for neglected diseases. J Mol Graph Model. 2012 Sep; 38:360-2. PMID: 23085175; PMCID: PMC3508335.
    73. Vanwart AT, Eargle J, Luthey-Schulten Z, Amaro RE. 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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    74. Votapka L, Demir O, Swift RV, Walker RC, Amaro RE. 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.
    75. Demir Ö, Amaro RE. 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.
    76. Gabrielsen M, Beckham KS, Feher VA, Zetterström CE, Wang D, Müller S, Elofsson M, Amaro RE, 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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    77. Nichols SE, Swift RV, Amaro RE. Rational prediction with molecular dynamics for hit identification. Curr Top Med Chem. 2012; 12(18):2002-12. PMID: 23110535; PMCID: PMC3636520.
    78. Amaro RE, Li WW. Molecular-level simulation of pandemic influenza glycoproteins. Methods Mol Biol. 2012; 819:575-94. PMID: 22183559; PMCID: PMC3352029.
    79. Swift RV, Amaro RE. Modeling the pharmacodynamics of passive membrane permeability. J Comput Aided Mol Des. 2011 Nov; 25(11):1007-17. PMID: 22042376; PMCID: PMC3223344.
    80. 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 Oct; 7(10):e1002238. PMID: 22028641; PMCID: PMC3197647.
    81. Torres R, Swift RV, Chim N, Wheatley N, Lan B, Atwood BR, Pujol C, Sankaran B, Bliska JB, Amaro RE, 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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    82. Amaro RE, 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.
    83. 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 Aug 24; 4(8):e803. PMID: 20808768; PMCID: PMC2927429.
    84. 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.
    85. Sung JC, Van Wynsberghe AW, Amaro RE, 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.
    86. Durrant JD, Amaro RE, 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.
    87. Amaro RE, Li WW. Emerging methods for ensemble-based virtual screening. Curr Top Med Chem. 2010; 10(1):3-13. PMID: 19929833; PMCID: PMC3086266.
    88. Newhouse EI, Xu D, Markwick PR, Amaro RE, 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.
    89. Swift RV, Amaro RE. 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.
      View in: PubMed
    90. Amaro RE, 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.
    91. Xu D, Newhouse EI, Amaro RE, 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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    92. Swift RV, Durrant J, Amaro RE, McCammon JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 2009 Feb 03; 48(4):709-19. PMID: 19133737; PMCID: PMC2651658.
    93. Durrant JD, Amaro RE, McCammon JA. AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des. 2009 Feb; 73(2):168-78. PMID: 19207419; PMCID: PMC2724963.
    94. Wong S, Amaro RE, 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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    95. 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 Nov 11; 105(45):17278-83. PMID: 18981420.
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    96. 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 Jul 10; 51(13):3878-94. PMID: 18558668; PMCID: PMC2652358.
    97. 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 Feb; 71(2):106-16. PMID: 18205727; PMCID: PMC2438278.
    98. 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 Sep; 22(9):693-705. PMID: 18196463; PMCID: PMC2516539.
    99. Amaro RE, 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.
    100. Amaro RE, Minh DD, Cheng LS, Lindstrom WM, Olson AJ, Lin JH, Li WW, McCammon JA. Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc. 2007 Jun 27; 129(25):7764-5. PMID: 17539643.
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    101. Amaro RE, Sethi A, Myers RS, Davisson VJ, Luthey-Schulten ZA. A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry. 2007 Feb 27; 46(8):2156-73. PMID: 17261030.
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    102. Myers RS, Amaro RE, Luthey-Schulten ZA, Davisson VJ. Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase. Biochemistry. 2005 Sep 13; 44(36):11974-85. PMID: 16142895.
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    103. Amaro RE, Myers RS, Davisson VJ, Luthey-Schulten ZA. Structural elements in IGP synthase exclude water to optimize ammonia transfer. Biophys J. 2005 Jul; 89(1):475-87. PMID: 15849257; PMCID: PMC1366548.
    104. Amaro R, Tajkhorshid E, Luthey-Schulten Z. Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF. Proc Natl Acad Sci U S A. 2003 Jun 24; 100(13):7599-604. PMID: 12799468; PMCID: PMC164632.