Rommie Amaro

Title(s)Professor, Molecular Biology
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    A MULTISCALE APPROACH TO TARGET THE ACHILLES HEEL OF P53 CANCER MUTANTS
    NIH R01GM132826Apr 1, 2019 - Mar 31, 2023
    Role: Principal Investigator
    AN OPEN RESOURCE FOR COLLABORATIVE BIOMEDICAL BIG DATA TRAINING
    NIH R25GM114821Sep 29, 2014 - Aug 31, 2017
    Role: Principal Investigator
    AN OPEN RESOURCE TO ADVANCE COMPUTER-AIDED DRUG DESIGN
    NIH U01GM111528Sep 15, 2014 - Aug 31, 2020
    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 K22AI081901Aug 15, 2010 - Jul 31, 2013
    Role: Principal Investigator
    The SMD-Relaxed Complex Method for Drug Design
    NIH F32GM077729Sep 1, 2006 - Jun 30, 2009
    Role: Principal Investigator
    NATIONAL BIOMEDICAL COMPUTATION RESOURCE
    NIH P41GM103426May 6, 1997 - Apr 30, 2020
    Role: Principal Investigator
    High Performance Computing for Biomedical Research
    NIH P41RR006009Sep 1, 1990 - Jul 31, 2013
    Role: Co-Investigator

    Collapse Bibliographic 
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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Binding and Activation of LRP1-Dependent Cell Signaling in Schwann Cells Using a Peptide Derived from the Hemopexin Domain of MMP-9. Biochemistry. 2024 Mar 19; 63(6):725-732. Kim JH, Shivkumar A, Norimoto M, Castro Lingl S, Seitz C, Amaro RE, Gonias SL, Yang J, Campana WM. PMID: 38450612.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    2. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci. 2023 Nov 22; 14(45):13159-13175. Ojha AA, Votapka LW, Amaro RE. PMID: 38023523; PMCID: PMC10664576.
      View in: PubMed   Mentions:
    3. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nat Commun. 2023 10 04; 14(1):6169. Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Smith CM, Li A, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Judy Shon D, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Lemmon MA, Amaro RE, Malaker SA. PMID: 37794035; PMCID: PMC10550946.
      View in: PubMed   Mentions: 4     Fields:    
    4. Multiscale computational modeling of the effects of 2'-deoxy-ATP on cardiac muscle calcium handling. J Appl Phys. 2023 Aug 21; 134(7):074905. Hock MT, Teitgen AE, McCabe KJ, Hirakis SP, Huber GA, Regnier M, Amaro RE, McCammon JA, McCulloch AD. PMID: 37601331; PMCID: PMC10435275.
      View in: PubMed   Mentions:
    5. Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. J Chem Inf Model. 2023 06 12; 63(11):3227-3229. Soares TA, Cournia Z, Naidoo K, Amaro R, Wahab H, Merz KM. PMID: 37191169.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    6. Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology. ACS Cent Sci. 2023 Jun 28; 9(6):1088-1103. Dommer AC, Wauer NA, Angle KJ, Davasam A, Rubio P, Luo M, Morris CK, Prather KA, Grassian VH, Amaro RE. PMID: 37396863; PMCID: PMC10311664.
      View in: PubMed   Mentions:
    7. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. Cell Rep Phys Sci. 2023 Apr 19; 4(4):101346. Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R. PMID: 37077408; PMCID: PMC10080732.
      View in: PubMed   Mentions: 4  
    8. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. J Chem Inf Model. 2023 04 24; 63(8):2469-2482. Ojha AA, Srivastava A, Votapka LW, Amaro RE. PMID: 37023323; PMCID: PMC10131228.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    9. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. Sci Adv. 2023 03 29; 9(13):eade8778. Moghadasi SA, Heilmann E, Khalil AM, Nnabuife C, Kearns FL, Ye C, Moraes SN, Costacurta F, Esler MA, Aihara H, von Laer D, Martinez-Sobrido L, Palzkill T, Amaro RE, Harris RS. PMID: 36989354; PMCID: PMC10058310.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    10. APOBEC3A Catalytic Inactivity Mutation Induces Tertiary Structure Destabilization. ACS Med Chem Lett. 2023 Mar 09; 14(3):338-343. Jones KFM, Shehata M, Carpenter MA, Amaro RE, Harki DA. PMID: 36923917; PMCID: PMC10009786.
      View in: PubMed   Mentions: 1  
    11. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. bioRxiv. 2023 Feb 03. Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Shon DJ, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Amaro RE, Malaker SA. PMID: 36778266; PMCID: PMC9915616.
      View in: PubMed   Mentions:
    12. DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling. J Chem Theory Comput. 2023 Feb 28; 19(4):1342-1359. Ojha AA, Thakur S, Ahn SH, Amaro RE. PMID: 36719802.
      View in: PubMed   Mentions: 3     Fields:    
    13. Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. J Chem Inf Model. 2022 Dec 26; 62(24):6287-6291. Cournia Z, Soares TA, Wahab HA, Amaro RE. PMID: 36567670.
      View in: PubMed   Mentions:    Fields:    
    14. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. bioRxiv. 2022 Dec 26. Moghadasi SA, Heilmann E, Khalil AM, Nnabuife C, Kearns FL, Ye C, Moraes SN, Costacurta F, Esler MA, Aihara H, von Laer D, Martinez-Sobrido L, Palzkill T, Amaro RE, Harris RS. PMID: 35982678; PMCID: PMC9387136.
      View in: PubMed   Mentions:
    15. Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS Cent Sci. 2022 Dec 28; 8(12):1646-1663. Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. PMID: 36589893; PMCID: PMC9801513.
      View in: PubMed   Mentions: 14  
    16. #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int J High Perform Comput Appl. 2023 Jan; 37(1):28-44. Dommer A, Casalino L, Kearns F, Rosenfeld M, Wauer N, Ahn SH, Russo J, Oliveira S, Morris C, Bogetti A, Trifan A, Brace A, Sztain T, Clyde A, Ma H, Chennubhotla C, Lee H, Turilli M, Khalid S, Tamayo-Mendoza T, Welborn M, Christensen A, Smith DG, Qiao Z, Sirumalla SK, O'Connor M, Manby F, Anandkumar A, Hardy D, Phillips J, Stern A, Romero J, Clark D, Dorrell M, Maiden T, Huang L, McCalpin J, Woods C, Gray A, Williams M, Barker B, Rajapaksha H, Pitts R, Gibbs T, Stone J, Zuckerman DM, Mulholland AJ, Miller T, Jha S, Ramanathan A, Chong L, Amaro RE. PMID: 36647365; PMCID: PMC9527558.
      View in: PubMed   Mentions: 18  
    17. Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection. Nat Chem Biol. 2023 03; 19(3):275-283. Oh CK, Nakamura T, Beutler N, Zhang X, Piña-Crespo J, Talantova M, Ghatak S, Trudler D, Carnevale LN, McKercher SR, Bakowski MA, Diedrich JK, Roberts AJ, Woods AK, Chi V, Gupta AK, Rosenfeld MA, Kearns FL, Casalino L, Shaabani N, Liu H, Wilson IA, Amaro RE, Burton DR, Yates JR, Becker C, Rogers TF, Chatterjee AK, Lipton SA. PMID: 36175661; PMCID: PMC10127945.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    18. Discovery of compounds that reactivate p53 mutants in vitro and in vivo. Cell Chem Biol. 2022 09 15; 29(9):1381-1395.e13. Durairaj G, Demir Ö, Lim B, Baronio R, Tifrea D, Hall LV, DeForest JC, Lauinger L, Jebril Fallatah MM, Yu C, Bae H, Lin DW, Kim JK, Salehi F, Jang C, Qiao F, Lathrop RH, Huang L, Edwards R, Rychnovsky S, Amaro RE, Kaiser P. PMID: 35948006; PMCID: PMC9481737.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    19. Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities. bioRxiv. 2022 Aug 07. Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. PMID: 35982676; PMCID: PMC9387122.
      View in: PubMed   Mentions:
    20. Words Matter: On the Debate over Free Speech, Inclusivity, and Academic Excellence. J Phys Chem Lett. 2022 08 04; 13(30):7100-7104. Herbert JM, Head-Gordon M, Hratchian HP, Head-Gordon T, Amaro RE, Aspuru-Guzik A, Hoffmann R, Parish CA, Payne CM, Van Voorhis T. PMID: 35924341; PMCID: PMC9358646.
      View in: PubMed   Mentions: 2     Fields:    
    21. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature. 2022 08; 608(7922):429-435. Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, Suslov S, Khanna K, Birkholz EA, Armbruster E, McCammon JA, Amaro RE, Pogliano J, Corbett KD, Villa E. PMID: 35922510; PMCID: PMC9365700.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    22. Gaussian Accelerated Molecular Dynamics in OpenMM. J Phys Chem B. 2022 08 11; 126(31):5810-5820. Copeland MM, Do HN, Votapka L, Joshi K, Wang J, Amaro RE, Miao Y. PMID: 35895977.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    23. Spike-heparan sulfate interactions in SARS-CoV-2 infection. Curr Opin Struct Biol. 2022 10; 76:102439. Kearns FL, Sandoval DR, Casalino L, Clausen TM, Rosenfeld MA, Spliid CB, Amaro RE, Esko JD. PMID: 35926454; PMCID: PMC9257145.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    24. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J Chem Inf Model. 2022 07 11; 62(13):3253-3262. Votapka LW, Stokely AM, Ojha AA, Amaro RE. PMID: 35759413; PMCID: PMC9277580.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    25. Inhibition of PRMT5 by market drugs as a novel cancer therapeutic avenue. Genes Dis. 2023 Jan; 10(1):267-283. Prabhu L, Martin M, Chen L, Demir Ö, Jin J, Huang X, Motolani A, Sun M, Jiang G, Nakshatri H, Fishel ML, Sun S, Safa A, Amaro RE, Kelley MR, Liu Y, Zhang ZY, Lu T. PMID: 37013054; PMCID: PMC10066340.
      View in: PubMed   Mentions: 2  
    26. Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection. bioRxiv. 2022 Apr 05. Oh CK, Nakamura T, Beutler N, Zhang X, Piña-Crespo J, Talantova M, Ghatak S, Trudler D, Carnevale LN, McKercher SR, Bakowski MA, Diedrich JK, Roberts AJ, Woods AK, Chi V, Gupta AK, Rosenfeld MA, Kearns FL, Casalino L, Shaabani N, Liu H, Wilson IA, Amaro RE, Burton DR, Yates JR, Becker C, Rogers TF, Chatterjee AK, Lipton SA. PMID: 35411336; PMCID: PMC8996617.
      View in: PubMed   Mentions:
    27. Amino Acids Are Driven to the Interface by Salts and Acidic Environments. J Phys Chem Lett. 2022 Mar 31; 13(12):2824-2829. Angle KJ, Nowak CM, Davasam A, Dommer AC, Wauer NA, Amaro RE, Grassian VH. PMID: 35324217.
      View in: PubMed   Mentions: 3     Fields:    
    28. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Rep. 2022 Mar 22; 38(12):110578. Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. PMID: 35320719.
      View in: PubMed   Mentions:    Fields:    
    29. Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proc Natl Acad Sci U S A. 2022 03 01; 119(9). Moeller NH, Shi K, Demir Ö, Belica C, Banerjee S, Yin L, Durfee C, Amaro RE, Aihara H. PMID: 35165203; PMCID: PMC8892293.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansCells
    30. Benchmarking ensemble docking methods in D3R Grand Challenge 4. J Comput Aided Mol Des. 2022 02; 36(2):87-99. Gan JL, Kumar D, Chen C, Taylor BC, Jagger BR, Amaro RE, Lee CT. PMID: 35199221; PMCID: PMC8907095.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    31. CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. Nat Rev Chem. 2022 Apr; 6(4):287-295. Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, Gilson MK, Gordijo CR, Hessler G, Hillisch A, Hogner A, Irwin JJ, Jansen JM, Kuhn D, Leach AR, Lee AA, Lessel U, Morgan MR, Moult J, Muegge I, Oprea TI, Perry BG, Riley P, Rousseaux SAL, Saikatendu KS, Santhakumar V, Schapira M, Scholten C, Todd MH, Vedadi M, Volkamer A, Willson TM. PMID: 35783295; PMCID: PMC9246350.
      View in: PubMed   Mentions: 10  
    32. Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations. Biomolecules. 2022 01 22; 12(2). Oliveira AA, Róg T, da Silva ABF, Amaro RE, Johnson MS, Postila PA. PMID: 35204684; PMCID: PMC8961577.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    33. GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses. ACS Cent Sci. 2022 Jan 26; 8(1):22-42. Kim SH, Kearns FL, Rosenfeld MA, Casalino L, Papanikolas MJ, Simmerling C, Amaro RE, Freeman R. PMID: 35106370; PMCID: PMC8796303.
      View in: PubMed   Mentions: 19  
    34. Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling. J Chem Theory Comput. 2021 Dec 14; 17(12):7938-7951. Ahn SH, Ojha AA, Amaro RE, McCammon JA. PMID: 34844409; PMCID: PMC8983023.
      View in: PubMed   Mentions: 4     Fields:    
    35. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. bioRxiv. 2021 Nov 15. Dommer A, Casalino L, Kearns F, Rosenfeld M, Wauer N, Ahn SH, Russo J, Oliveira S, Morris C, Bogetti A, Trifan A, Brace A, Sztain T, Clyde A, Ma H, Chennubhotla C, Lee H, Turilli M, Khalid S, Tamayo-Mendoza T, Welborn M, Christensen A, Smith DGA, Qiao Z, Sirumalla SK, O'Connor M, Manby F, Anandkumar A, Hardy D, Phillips J, Stern A, Romero J, Clark D, Dorrell M, Maiden T, Huang L, McCalpin J, Woods C, Gray A, Williams M, Barker B, Rajapaksha H, Pitts R, Gibbs T, Stone J, Zuckerman D, Mulholland A, Miller T, Jha S, Ramanathan A, Chong L, Amaro R. PMID: 34816263; PMCID: PMC8609898.
      View in: PubMed   Mentions: 1  
    36. Advancing Women in Chemistry. J Chem Inf Model. 2021 11 22; 61(11):5305-5306. Cournia Z, Soares TA, Wahab HA, Amaro RE. PMID: 34668709.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    37. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Rep. 2021 10 19; 37(3):109840. Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. PMID: 34686332; PMCID: PMC8641752.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    38. SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Proc Natl Acad Sci U S A. 2021 09 07; 118(36). Andreano E, Piccini G, Licastro D, Casalino L, Johnson NV, Paciello I, Dal Monego S, Pantano E, Manganaro N, Manenti A, Manna R, Casa E, Hyseni I, Benincasa L, Montomoli E, Amaro RE, McLellan JS, Rappuoli R. PMID: 34417349; PMCID: PMC8433494.
      View in: PubMed   Mentions: 271     Fields:    Translation:HumansAnimalsCells
    39. AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int J High Perform Comput Appl. 2021 Sep; 35(5):432-451. Casalino L, Dommer AC, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti AT, Clyde A, Ma H, Lee H, Turilli M, Khalid S, Chong LT, Simmerling C, Hardy DJ, Maia JD, Phillips JC, Kurth T, Stern AC, Huang L, McCalpin JD, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. PMID: 38603008; PMCID: PMC8064023.
      View in: PubMed   Mentions:
    40. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nat Chem. 2021 10; 13(10):963-968. Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. PMID: 34413500; PMCID: PMC8488004.
      View in: PubMed   Mentions: 134     Fields:    Translation:HumansCells
    41. Calcium bridging drives polysaccharide co-adsorption to a proxy sea surface microlayer. Phys Chem Chem Phys. 2021 Aug 04; 23(30):16401-16416. Carter-Fenk KA, Dommer AC, Fiamingo ME, Kim J, Amaro RE, Allen HC. PMID: 34318808.
      View in: PubMed   Mentions:    Fields:    
    42. Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes. Proc Natl Acad Sci U S A. 2021 08 03; 118(31). Hempel T, Del Razo MJ, Lee CT, Taylor BC, Amaro RE, Noé F. PMID: 34321356; PMCID: PMC8346863.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    43. A critical overview of computational approaches employed for COVID-19 drug discovery. Chem Soc Rev. 2021 Aug 21; 50(16):9121-9151. Muratov EN, Amaro R, Andrade CH, Brown N, Ekins S, Fourches D, Isayev O, Kozakov D, Medina-Franco JL, Merz KM, Oprea TI, Poroikov V, Schneider G, Todd MH, Varnek A, Winkler DA, Zakharov AV, Cherkasov A, Tropsha A. PMID: 34212944; PMCID: PMC8371861.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCellsPHPublic Health
    44. Cation-Driven Lipopolysaccharide Morphological Changes Impact Heterogeneous Reactions of Nitric Acid with Sea Spray Aerosol Particles. J Phys Chem Lett. 2021 May 27; 12(20):5023-5029. Lee C, Dommer AC, Schiffer JM, Amaro RE, Grassian VH, Prather KA. PMID: 34024101.
      View in: PubMed   Mentions: 1     Fields:    
    45. A glycan gate controls opening of the SARS-CoV-2 spike protein. bioRxiv. 2021 May 17. Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. PMID: 33619492; PMCID: PMC7899456.
      View in: PubMed   Mentions:
    46. Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. J Chem Inf Model. 2021 07 26; 61(7):3495-3501. Sztain T, Amaro R, McCammon JA. PMID: 33939913; PMCID: PMC8117783.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    47. Development of Dimethylisoxazole-Attached Imidazo[1,2-a]pyridines as Potent and Selective CBP/P300 Inhibitors. J Med Chem. 2021 05 13; 64(9):5787-5801. Muthengi A, Wimalasena VK, Yosief HO, Bikowitz MJ, Sigua LH, Wang T, Li D, Gaieb Z, Dhawan G, Liu S, Erickson J, Amaro RE, Schönbrunn E, Qi J, Zhang W. PMID: 33872011; PMCID: PMC8856734.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    48. Structural Characterization of a Minimal Antibody against Human APOBEC3B. Viruses. 2021 04 12; 13(4). Tang H, Demir Ö, Kurniawan F, Brown WL, Shi K, Moeller NH, Carpenter MA, Belica C, Orellana K, Du G, LeBeau AM, Amaro RE, Harris RS, Aihara H. PMID: 33921405; PMCID: PMC8070380.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    49. Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. bioRxiv. 2021 Apr 04. Moeller NH, Shi K, Demir Ö, Banerjee S, Yin L, Belica C, Durfee C, Amaro RE, Aihara H. PMID: 33821277; PMCID: PMC8020977.
      View in: PubMed   Mentions:
    50. Disease-related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors. Elife. 2021 03 04; 10. Rathinaswamy MK, Gaieb Z, Fleming KD, Borsari C, Harris NJ, Moeller BE, Wymann MP, Amaro RE, Burke JE. PMID: 33661099; PMCID: PMC7955810.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    51. A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors. Biophys J. 2021 03 16; 120(6):983-993. Oliveira ASF, Ibarra AA, Bermudez I, Casalino L, Gaieb Z, Shoemark DK, Gallagher T, Sessions RB, Amaro RE, Mulholland AJ. PMID: 33609494; PMCID: PMC7889469.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    52. Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nat Commun. 2021 02 08; 12(1):856. Klima JC, Doyle LA, Lee JD, Rappleye M, Gagnon LA, Lee MY, Barros EP, Vorobieva AA, Dou J, Bremner S, Quon JS, Chow CM, Carter L, Mack DL, Amaro RE, Vaughan JC, Berndt A, Stoddard BL, Baker D. PMID: 33558528; PMCID: PMC7870846.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    53. RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules. 2021 01 08; 11(1). Lirussi L, Demir Ö, You P, Sarno A, Amaro RE, Nilsen H. PMID: 33430019; PMCID: PMC7826747.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    54. An integrated view of p53 dynamics, function, and reactivation. Curr Opin Struct Biol. 2021 04; 67:187-194. Demir Ö, Barros EP, Offutt TL, Rosenfeld M, Amaro RE. PMID: 33401096; PMCID: PMC8985518.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    55. SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. bioRxiv. 2020 Dec 28. Andreano E, Piccini G, Licastro D, Casalino L, Johnson NV, Paciello I, Dal Monego S, Pantano E, Manganaro N, Manenti A, Manna R, Casa E, Hyseni I, Benincasa L, Montomoli E, Amaro RE, McLellan JS, Rappuoli R. PMID: 33398278; PMCID: PMC7781313.
      View in: PubMed   Mentions: 1  
    56. COVID19 - Computational Chemists Meet the Moment. J Chem Inf Model. 2020 12 28; 60(12):5724-5726. Mulholland AJ, Amaro RE. PMID: 33378852.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    57. Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J Chem Inf Model. 2020 12 28; 60(12):5868-5869. Merz KM, Amaro R, Cournia Z, Rarey M, Soares T, Tropsha A, Wahab HA, Wang R. PMID: 33378854.
      View in: PubMed   Mentions: 6     Fields:    
    58. Markov state models and NMR uncover an overlooked allosteric loop in p53. Chem Sci. 2020 Dec 16; 12(5):1891-1900. Barros EP, Demir Ö, Soto J, Cocco MJ, Amaro RE. PMID: 34163952; PMCID: PMC8179107.
      View in: PubMed   Mentions: 9  
    59. A multiscale coarse-grained model of the SARS-CoV-2 virion. Biophys J. 2021 03 16; 120(6):1097-1104. Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. PMID: 33253634; PMCID: PMC7695975.
      View in: PubMed   Mentions: 58     Fields:    Translation:Cells
    60. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. bioRxiv. 2020 Nov 20. Casalino L, Dommer A, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti A, Ma H, Lee H, Turilli M, Khalid S, Chong L, Simmerling C, Hardy DJ, Maia JDC, Phillips JC, Kurth T, Stern A, Huang L, McCalpin J, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. PMID: 33236007; PMCID: PMC7685317.
      View in: PubMed   Mentions:
    61. The flexibility of ACE2 in the context of SARS-CoV-2 infection. Biophys J. 2021 03 16; 120(6):1072-1084. Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. PMID: 33189680; PMCID: PMC7661960.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    62. OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring-Flip Frequencies Determined by Integrated Use of 1 H NMR Spectroscopy and Molecular Dynamics Simulations. Chembiochem. 2021 02 02; 22(3):565-570. Martin BT, Malmstrom RD, Amaro RE, Wüthrich K. PMID: 32975902.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    63. Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase. Biophys J. 2020 12 01; 119(11):2275-2289. Seitz C, Casalino L, Konecny R, Huber G, Amaro RE, McCammon JA. PMID: 33130120; PMCID: PMC7732775.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    64. Functional and Structural Insights into a Vif/PPP2R5 Complex Elucidated Using Patient HIV-1 Isolates and Computational Modeling. J Virol. 2020 10 14; 94(21). Salamango DJ, McCann JL, Demir Ö, Becker JT, Wang J, Lingappa JR, Temiz NA, Brown WL, Amaro RE, Harris RS. PMID: 32847850; PMCID: PMC7565612.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    65. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. bioRxiv. 2020 Oct 02. Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. PMID: 33024966; PMCID: PMC7536869.
      View in: PubMed   Mentions:
    66. Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. ACS Cent Sci. 2020 Oct 28; 6(10):1722-1734. Casalino L, Gaieb Z, Goldsmith JA, Hjorth CK, Dommer AC, Harbison AM, Fogarty CA, Barros EP, Taylor BC, McLellan JS, Fadda E, Amaro RE. PMID: 33140034; PMCID: PMC7523240.
      View in: PubMed   Mentions: 382  
    67. The flexibility of ACE2 in the context of SARS-CoV-2 infection. bioRxiv. 2020 Sep 16. Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. PMID: 32995769; PMCID: PMC7523095.
      View in: PubMed   Mentions:
    68. Biomolecular Simulations in the Time of COVID19, and After. Comput Sci Eng. 2020 Nov-Dec; 22(6):30-36. Amaro RE, Mulholland AJ. PMID: 33100917; PMCID: PMC7584139.
      View in: PubMed   Mentions: 12  
    69. Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors. bioRxiv. 2020 Sep 14. Oliveira ASF, Ibarra AA, Bermudez I, Casalino L, Gaieb Z, Shoemark DK, Gallagher T, Sessions RB, Amaro RE, Mulholland AJ. PMID: 32743575; PMCID: PMC7386492.
      View in: PubMed   Mentions:
    70. Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. bioRxiv. 2020 Sep 04. Casalino L, Gaieb Z, Goldsmith JA, Hjorth CK, Dommer AC, Harbison AM, Fogarty CA, Barros EP, Taylor BC, McLellan JS, Fadda E, Amaro RE. PMID: 32577644; PMCID: PMC7302197.
      View in: PubMed   Mentions:
    71. Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations. Front Mol Biosci. 2020; 7:194. Palermo G, Bonvin AMJJ, Dal Peraro M, Amaro RE, Tozzini V. PMID: 33005628; PMCID: PMC7484804.
      View in: PubMed   Mentions: 4  
    72. Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease. bioRxiv. 2020 Jul 24. Sztain T, Amaro R, McCammon JA. PMID: 32743587; PMCID: PMC7386507.
      View in: PubMed   Mentions:
    73. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. J Chem Theory Comput. 2020 Aug 11; 16(8):5348-5357. Jagger BR, Ojha AA, Amaro RE. PMID: 32579371.
      View in: PubMed   Mentions: 13     Fields:    
    74. Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. J Chem Inf Model. 2020 07 27; 60(7):3328-3330. Mazzolari A, Nunes-Alves A, Wahab HA, Amaro RE, Cournia Z, Merz KM. PMID: 32623887.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    75. An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models. Front Mol Biosci. 2020; 7:93. Parks C, Gaieb Z, Amaro RE. PMID: 32671093; PMCID: PMC7328444.
      View in: PubMed   Mentions: 6  
    76. Insights into the behavior of nonanoic acid and its conjugate base at the air/water interface through a combined experimental and theoretical approach. Chem Sci. 2020 Oct 21; 11(39):10647-10656. Luo M, Wauer NA, Angle KJ, Dommer AC, Song M, Nowak CM, Amaro RE, Grassian VH. PMID: 33144932; PMCID: PMC7583472.
      View in: PubMed   Mentions: 3  
    77. Faces of Contemporary CryoEM Information and Modeling. J Chem Inf Model. 2020 05 26; 60(5):2407-2409. Palermo G, Sugita Y, Wriggers W, Amaro RE. PMID: 32452204; PMCID: PMC7838532.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    78. Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. J Chem Inf Model. 2020 11 23; 60(11):5340-5352. Ahn SH, Jagger BR, Amaro RE. PMID: 32315175.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    79. A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. J Chem Inf Model. 2020 06 22; 60(6):2653-2656. Amaro RE, Mulholland AJ. PMID: 32255648.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCellsPHPublic Health
    80. 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput Biol. 2020 04; 16(4):e1007756. Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. PMID: 32251448; PMCID: PMC7162555.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    81. Multiscale simulation approaches to modeling drug-protein binding. Curr Opin Struct Biol. 2020 04; 61:213-221. Jagger BR, Kochanek SE, Haldar S, Amaro RE, Mulholland AJ. PMID: 32113133.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    82. Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Cent Sci. 2020 Feb 26; 6(2):189-196. Durrant JD, Kochanek SE, Casalino L, Ieong PU, Dommer AC, Amaro RE. PMID: 32123736; PMCID: PMC7048371.
      View in: PubMed   Mentions: 40  
    83. Drug Design Data Resource, Grand Challenge 4, second of two issues. J Comput Aided Mol Des. 2020 02; 34(2):97. Gilson MK, Amaro RE. PMID: 32016636.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    84. D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des. 2020 02; 34(2):99-119. Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK. PMID: 31974851; PMCID: PMC7261493.
      View in: PubMed   Mentions: 42     Fields:    Translation:Humans
    85. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophys J. 2020 03 10; 118(5):1003-1008. Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. PMID: 32032503; PMCID: PMC7063475.
      View in: PubMed   Mentions: 10     Fields:    
    86. Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B. FASEB Bioadv. 2020 Jan; 2(1):49-58. Shi K, Demir Ö, Carpenter MA, Banerjee S, Harki DA, Amaro RE, Harris RS, Aihara H. PMID: 32123856; PMCID: PMC6996314.
      View in: PubMed   Mentions: 4  
    87. Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus. Evol Bioinform Online. 2019; 15:1176934319876938. Le KP, Do PC, Amaro RE, Le L. PMID: 31555044; PMCID: PMC6747855.
      View in: PubMed   Mentions: 2  
    88. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations. J Chem Theory Comput. 2019 Oct 08; 15(10):5703-5715. Barros EP, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE. PMID: 31442033; PMCID: PMC7532806.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    89. An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes. J Chem Theory Comput. 2019 Oct 08; 15(10):5689-5702. Bernetti M, Masetti M, Recanatini M, Amaro RE, Cavalli A. PMID: 31436987.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    90. The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. ACM Trans Math Softw. 2019 Aug; 45(3). Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. PMID: 31474782; PMCID: PMC6716611.
      View in: PubMed   Mentions: 3  
    91. Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure. 2019 08 06; 27(8):1326-1335.e4. Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE. PMID: 31257108; PMCID: PMC6685748.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    92. Surfactant Charge Modulates Structure and Stability of Lipase-Embedded Monolayers at Marine-Relevant Aerosol Surfaces. Langmuir. 2019 07 09; 35(27):9050-9060. Luo M, Dommer AC, Schiffer JM, Rez DJ, Mitchell AR, Amaro RE, Grassian VH. PMID: 31188612.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    93. Frontiers in CryoEM Modeling. J Chem Inf Model. 2019 07 22; 59(7):3091-3093. Palermo G, Sugita Y, Wriggers W, Amaro RE. PMID: 31192591; PMCID: PMC6646052.
      View in: PubMed   Mentions: 2     Fields:    
    94. A Celebration of Women in Computational Chemistry. J Chem Inf Model. 2019 05 28; 59(5):1683-1692. Wahab HA, Amaro RE, Cournia Z. PMID: 31132853.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    95. Structural basis for ligand modulation of the CCR2 conformational landscape. Proc Natl Acad Sci U S A. 2019 04 23; 116(17):8131-8136. Taylor BC, Lee CT, Amaro RE. PMID: 30975755; PMCID: PMC6486717.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    96. Human Influenza A Virus Hemagglutinin Glycan Evolution Follows a Temporal Pattern to a Glycan Limit. mBio. 2019 04 02; 10(2). Altman MO, Angel M, Košík I, Trovão NS, Zost SJ, Gibbs JS, Casalino L, Amaro RE, Hensley SE, Nelson MI, Yewdell JW. PMID: 30940704; PMCID: PMC6445938.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    97. A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. PLoS Comput Biol. 2019 03; 15(3):e1006856. Yang PC, Purawat S, Ieong PU, Jeng MT, DeMarco KR, Vorobyov I, McCulloch AD, Altintas I, Amaro RE, Clancy CE. PMID: 30849072; PMCID: PMC6426265.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    98. Will the Real Cryptic Pocket Please Stand Out? Biophys J. 2019 03 05; 116(5):753-754. Amaro RE. PMID: 30739726; PMCID: PMC6400825.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    99. D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J Comput Aided Mol Des. 2019 01; 33(1):1-18. Gaieb Z, Parks CD, Chiu M, Yang H, Shao C, Walters WP, Lambert MH, Nevins N, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK. PMID: 30632055; PMCID: PMC6472484.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    100. Unification of hydrogen-enhanced damage understanding through strain-life experiments for modeling. Eng Fract Mech. 2019; 216. Martin ML, Looney C, Bradley P, Lauria D, Amaro R, Slifka AJ. PMID: 32165761; PMCID: PMC7067297.
      View in: PubMed   Mentions:
    101. Sea Spray Aerosol: Where Marine Biology Meets Atmospheric Chemistry. ACS Cent Sci. 2018 Dec 26; 4(12):1617-1623. Schiffer JM, Mael LE, Prather KA, Amaro RE, Grassian VH. PMID: 30648145; PMCID: PMC6311946.
      View in: PubMed   Mentions: 1  
    102. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J. 2019 01 22; 116(2):205-214. Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. PMID: 30606449; PMCID: PMC6349996.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    103. Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester. J Med Chem. 2018 12 13; 61(23):10463-10472. Castro-Falcón G, Seiler GS, Demir Ö, Rathinaswamy MK, Hamelin D, Hoffmann RM, Makowski SL, Letzel AC, Field SJ, Burke JE, Amaro RE, Hughes CC. PMID: 30380865; PMCID: PMC6688905.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    104. APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction. Mol Cell Biol. 2018 12 01; 38(23). Salamango DJ, Becker JT, McCann JL, Cheng AZ, Demir Ö, Amaro RE, Brown WL, Shaban NM, Harris RS. PMID: 30224517; PMCID: PMC6234287.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    105. Dynamics and Molecular Mechanisms of p53 Transcriptional Activation. Biochemistry. 2018 11 20; 57(46):6528-6537. Offutt TL, Ieong PU, Demir Ö, Amaro RE. PMID: 30388364; PMCID: PMC7560988.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    106. A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target. ACS Cent Sci. 2018 Nov 28; 4(11):1570-1577. Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW. PMID: 30555910; PMCID: PMC6276040.
      View in: PubMed   Mentions: 14  
    107. Women in Computational Chemistry. J Chem Inf Model. 2018 11 26; 58(11):2175-2177. Wahab HA, Amaro RE, Cournia Z. PMID: 30277769.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    108. Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model. 2019 05 28; 59(5):2264-2273. Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. PMID: 30130104; PMCID: PMC6644697.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    109. Exascale Computing: A New Dawn for Computational Biology. Comput Sci Eng. 2018 Sep-Oct; 20(5):18-25. Lee CT, Amaro RE. PMID: 30983889; PMCID: PMC6458592.
      View in: PubMed   Mentions: 8  
    110. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 2018 Sep 06; 9(17):4941-4948. Jagger BR, Lee CT, Amaro RE. PMID: 30070844; PMCID: PMC6443090.
      View in: PubMed   Mentions: 15     Fields:    
    111. Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols. J Phys Chem Lett. 2018 Jul 19; 9(14):3839-3849. Schiffer JM, Luo M, Dommer AC, Thoron G, Pendergraft M, Santander MV, Lucero D, Pecora de Barros E, Prather KA, Grassian VH, Amaro RE. PMID: 29916254.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    112. APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces. J Mol Biol. 2018 08 17; 430(17):2695-2708. Salamango DJ, McCann JL, Demir Ö, Brown WL, Amaro RE, Harris RS. PMID: 29787764; PMCID: PMC6456046.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    113. Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit. Biochemistry. 2018 05 22; 57(20):2943-2957. Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang DB, Wang VY, Amaro RE, Huxford T, Ghosh G. PMID: 29708732; PMCID: PMC5993198.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    114. Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures. Nat Rev Chem. 2018 Apr; 2(4). Amaro RE, Mulholland AJ. PMID: 30949587; PMCID: PMC6445369.
      View in: PubMed   Mentions: 38  
    115. The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. J Biol Chem. 2018 05 25; 293(21):7969-7981. Bohl HO, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir Ö, Kurahashi K, Amaro RE, Wang Z, Aihara H. PMID: 29626094; PMCID: PMC5971466.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    116. Ensemble Docking in Drug Discovery. Biophys J. 2018 05 22; 114(10):2271-2278. Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. PMID: 29606412; PMCID: PMC6129458.
      View in: PubMed   Mentions: 157     Fields:    Translation:Cells
    117. Reliability assessment for large-scale molecular dynamics approximations. J Chem Phys. 2017 Dec 21; 147(23):234106. Grogan F, Holst M, Lindblom L, Amaro R. PMID: 29272950; PMCID: PMC5739912.
      View in: PubMed   Mentions: 3     Fields:    
    118. Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 2017 12 12; 7(1):17415. Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H. PMID: 29234087; PMCID: PMC5727031.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    119. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des. 2018 01; 32(1):1-20. 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. PMID: 29204945; PMCID: PMC5767524.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansCells
    120. 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. Prabhu L, Chen L, Wei H, Demir Ö, Safa A, Zeng L, Amaro RE, O'Neil BH, Zhang ZY, Lu T. PMID: 29099132; PMCID: PMC5759323.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    121. Toward Understanding "the Ways" of Allosteric Drugs. ACS Cent Sci. 2017 Sep 27; 3(9):925-926. Amaro RE. PMID: 28979932; PMCID: PMC5620975.
      View in: PubMed   Mentions: 3  
    122. POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput. 2017 Sep 12; 13(9):4584-4592. Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE. PMID: 28800393; PMCID: PMC5751414.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansCells
    123. 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. Hirakis SP, Malmstrom RD, Amaro RE. PMID: 28661131; PMCID: PMC5751417.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    124. A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases. Genes (Basel). 2017 Jun 20; 8(6). Cheng KJ, Demir Ö, Amaro RE. PMID: 28632168; PMCID: PMC5485530.
      View in: PubMed   Mentions:    Fields:    
    125. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. Biophys J. 2017 Jun 20; 112(12):2469-2474. Purawat S, Ieong PU, Malmstrom RD, Chan GJ, Yeung AK, Walker RC, Altintas I, Amaro RE. PMID: 28636905; PMCID: PMC5479118.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    126. 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. 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. PMID: 28591716; PMCID: PMC5522311.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    127. Erratum: Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol. 2017 Jun 12; 2:17107. Buffalo CZ, Bahn-Suh AJ, Hirakis SP, Biswas T, Amaro RE, Nizet V, Ghosh P. PMID: 28604710.
      View in: PubMed   Mentions: 1     Fields:    
    128. Biography of Klaus Schulten. J Phys Chem B. 2017 04 20; 121(15):3206. Amaro RE, Villa E, Luthey-Schulten Z. PMID: 28423903.
      View in: PubMed   Mentions:    Fields:    
    129. 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. Purawat S, Cowart C, Amaro RE, Altintas I. PMID: 29104704; PMCID: PMC5663195.
      View in: PubMed   Mentions: 1  
    130. Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα. Biochemistry. 2017 03 14; 56(10):1536-1545. P Barros E, Malmstrom RD, Nourbakhsh K, Del Rio JC, Kornev AP, Taylor SS, Amaro RE. PMID: 28221775; PMCID: PMC5495472.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    131. 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. Votapka LW, Jagger BR, Heyneman AL, Amaro RE. PMID: 28191969; PMCID: PMC5562489.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    132. Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast. ACS Chem Biol. 2017 02 17; 12(2):422-434. 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. PMID: 27977118; PMCID: PMC5649375.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    133. ENRI: A tool for selecting structure-based virtual screening target conformations. Chem Biol Drug Des. 2017 05; 89(5):762-771. Akbar R, Jusoh SA, Amaro RE, Helms V. PMID: 27995760.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    134. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol. 2017 02; 24(2):131-139. 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. PMID: 27991903; PMCID: PMC5296220.
      View in: PubMed   Mentions: 134     Fields:    Translation:HumansCells
    135. A Reflection on Klaus Schulten. J Chem Theory Comput. 2017 01 10; 13(1):1-2. Amaro RE. PMID: 28068772.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    136. 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. Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE. PMID: 27760351; PMCID: PMC5071553.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    137. RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting. Nucleic Acids Res. 2016 12 15; 44(22):10862-10878. 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. PMID: 27744351; PMCID: PMC5159558.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    138. Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. J Chem Inf Model. 2016 10 24; 56(10):1923-1935. Offutt TL, Swift RV, Amaro RE. PMID: 27662181; PMCID: PMC5323360.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    139. D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des. 2016 09; 30(9):651-668. 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. PMID: 27696240; PMCID: PMC5562487.
      View in: PubMed   Mentions: 104     Fields:    Translation:Cells
    140. Full-length p53 tetramer bound to DNA and its quaternary dynamics. Oncogene. 2017 03 09; 36(10):1451-1460. Demir Ö, Ieong PU, Amaro RE. PMID: 27641333; PMCID: PMC5344712.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    141. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol. 2016 Sep 05; 1(11):16155. Buffalo CZ, Bahn-Suh AJ, Hirakis SP, Biswas T, Amaro RE, Nizet V, Ghosh P. PMID: 27595425; PMCID: PMC5014329.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    142. Tribute to J. Andrew McCammon. J Phys Chem B. 2016 08 25; 120(33):8055-6. Amaro RE, Madura JD, Wong CF. PMID: 27558538.
      View in: PubMed   Mentions:    Fields:    
    143. Drug Discovery Gets a Boost from Data Science. Structure. 2016 08 02; 24(8):1225-1226. Amaro RE. PMID: 27486914.
      View in: PubMed   Mentions:    Fields:    
    144. 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. Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. PMID: 27396830; PMCID: PMC4972691.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    145. Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. Sci Rep. 2016 06 13; 6:27806. 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, Murray R, Prescott M, McNamara CW, Slayman CW, Amaro RE, Suzuki Y, Winzeler EA. PMID: 27291296; PMCID: PMC4904242.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    146. 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. Purawat S, Cowart C, Amaro RE, Altintas I. PMID: 27478519; PMCID: PMC4966614.
      View in: PubMed   Mentions: 3  
    147. Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B. 2016 08 25; 120(33):8606-16. Votapka LW, Lee CT, Amaro RE. PMID: 27154639; PMCID: PMC5002937.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    148. 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. Durrant JD, Bush RM, Amaro RE. PMID: 27141956; PMCID: PMC5002936.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    149. Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. J Chem Inf Model. 2016 05 23; 56(5):830-42. Swift RV, Jusoh SA, Offutt TL, Li ES, Amaro RE. PMID: 27097522; PMCID: PMC4881196.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    150. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model. 2016 04 25; 56(4):721-33. Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. PMID: 27043429; PMCID: PMC5280572.
      View in: PubMed   Mentions: 65     Fields:    Translation:Cells
    151. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 2016 06 08; 116(11):6370-90. Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. PMID: 27074285; PMCID: PMC4901368.
      View in: PubMed   Mentions: 69     Fields:    Translation:Cells
    152. 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. Richards C, Albin JS, Demir Ö, Shaban NM, Luengas EM, Land AM, Anderson BD, Holten JR, Anderson JS, Harki DA, Amaro RE, Harris RS. PMID: 26628363; PMCID: PMC4684092.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    153. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol. 2015 Oct; 11(10):e1004381. Votapka LW, Amaro RE. PMID: 26505480; PMCID: PMC4624728.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    154. 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. Zimmermann S, Hall L, Riley S, Sørensen J, Amaro RE, Schnaufer A. PMID: 26400159; PMCID: PMC4756849.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    155. Bridging scales through multiscale modeling: a case study on protein kinase A. Front Physiol. 2015; 6:250. Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD. PMID: 26441670; PMCID: PMC4563169.
      View in: PubMed   Mentions: 10  
    156. Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. J Chem Inf Model. 2015 Sep 28; 55(9):1953-61. Durrant JD, Carlson KE, Martin TA, Offutt TL, Mayne CG, Katzenellenbogen JA, Amaro RE. PMID: 26286148; PMCID: PMC4780411.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    157. Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nat Commun. 2015 Jul 06; 6:7588. Malmstrom RD, Kornev AP, Taylor SS, Amaro RE. PMID: 26145448; PMCID: PMC4504738.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    158. Molecular dynamics analysis of antibody recognition and escape by human H1N1 influenza hemagglutinin. Biophys J. 2015 Jun 02; 108(11):2704-12. Ieong P, Amaro RE, Li WW. PMID: 26039171; PMCID: PMC4457473.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    159. How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry. 2015 Mar 03; 54(8):1673-80. Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives EA. PMID: 25654263; PMCID: PMC4348336.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    160. A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity. J Chem Inf Model. 2015 Feb 23; 55(2):308-16. Ikram NK, Durrant JD, Muchtaridi M, Zalaludin AS, Purwitasari N, Mohamed N, Rahim AS, Lam CK, Normi YM, Rahman NA, Amaro RE, Wahab HA. PMID: 25555059; PMCID: PMC4340357.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    161. Molecular docking to flexible targets. Methods Mol Biol. 2015; 1215:445-69. Sørensen J, Demir Ö, Swift RV, Feher VA, Amaro RE. PMID: 25330975.
      View in: PubMed   Mentions: 9     Fields:    
    162. Machine-learning techniques applied to antibacterial drug discovery. Chem Biol Drug Des. 2015 Jan; 85(1):14-21. Durrant JD, Amaro RE. PMID: 25521642; PMCID: PMC4273861.
      View in: PubMed   Mentions: 20     Fields:    
    163. 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. Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M. PMID: 25296321; PMCID: PMC4190606.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    164. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput. 2014 Nov 11; 10(11):5047-5056. Durrant JD, Votapka L, Sørensen J, Amaro RE. PMID: 25400521; PMCID: PMC4230373.
      View in: PubMed   Mentions: 103     Fields:    
    165. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol. 2014 Jul; 10(7):e1003720. Durrant JD, Amaro RE. PMID: 25032790; PMCID: PMC4102414.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    166. On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput. 2014 Jul 08; 10(7):2648-2657. Malmstrom RD, Lee CT, Van Wart A, Amaro RE. PMID: 25473382; PMCID: PMC4248791.
      View in: PubMed   Mentions: 37     Fields:    
    167. Computer-aided discovery of Trypanosoma brucei RNA-editing terminal uridylyl transferase 2 inhibitors. Chem Biol Drug Des. 2014 Aug; 84(2):131-9. Demir O, Labaied M, Merritt C, Stuart K, Amaro RE. PMID: 24903413; PMCID: PMC4317284.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    168. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinformatics. 2014 May 23; 15:159. Durrant JD, Amaro RE. PMID: 24886360; PMCID: PMC4094277.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    169. Editorial overview: Theory and simulation: Tools for solving the insolvable. Curr Opin Struct Biol. 2014 Apr; 25:iv-v. Amaro RE, Bansal M. PMID: 24835772.
      View in: PubMed   Mentions: 1     Fields:    
    170. Computational approaches to mapping allosteric pathways. Curr Opin Struct Biol. 2014 Apr; 25:98-103. Feher VA, Durrant JD, Van Wart AT, Amaro RE. PMID: 24667124; PMCID: PMC4040315.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    171. 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. Van Wart AT, Durrant J, Votapka L, Amaro RE. PMID: 24803851; PMCID: PMC3958135.
      View in: PubMed   Mentions: 61     Fields:    
    172. Computation-guided discovery of influenza endonuclease inhibitors. ACS Med Chem Lett. 2014 Jan 09; 5(1):61-64. Chen E, Swift RV, Alderson N, Feher VA, Feng GS, Amaro RE. PMID: 24490002; PMCID: PMC3904387.
      View in: PubMed   Mentions: 11  
    173. Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations. Procedia Comput Sci. 2014; 29:1745-1755. Ieong PU, Sørensen J, Vemu PL, Wong CW, Demir Ö, Williams NP, Wang J, Crawl D, Swift RV, Malmstrom RD, Altintas I, Amaro RE. PMID: 29399238; PMCID: PMC5796787.
      View in: PubMed   Mentions: 5  
    174. 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. Rathore A, Carpenter MA, Demir Ö, Ikeda T, Li M, Shaban NM, Law EK, Anokhin D, Brown WL, Amaro RE, Harris RS. PMID: 23938202; PMCID: PMC3812309.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    175. Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding. J Chem Inf Model. 2013 Aug 26; 53(8):2047-56. Park J, Czapla L, Amaro RE. PMID: 23927370; PMCID: PMC3787069.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    176. A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins. PLoS One. 2013; 8(7):e68934. Feher VA, Randall A, Baldi P, Bush RM, de la Maza LM, Amaro RE. PMID: 23935908; PMCID: PMC3723809.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    177. 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. Swift RV, Amaro RE. PMID: 23066853; PMCID: PMC3527668.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    178. Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Nat Commun. 2013; 4:1407. 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. PMID: 23360998; PMCID: PMC3562459.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansCells
    179. Designing novel inhibitors of Trypanosoma brucei. Methods Mol Biol. 2013; 993:231-43. Demir O, Amaro RE. PMID: 23568474.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    180. Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme. Biochemistry. 2012 Dec 21; 51(51):10236-43. Swift RV, Ong CD, Amaro RE. PMID: 23205906; PMCID: PMC3549306.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    181. Multistructural hot spot characterization with FTProd. Bioinformatics. 2013 Feb 01; 29(3):393-4. Votapka L, Amaro RE. PMID: 23202744; PMCID: PMC3562065.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    182. Computational chemistry and drug discovery: a call to action. Future Med Chem. 2012 Oct; 4(15):1893-6. Jansen JM, Amaro RE, Cornell W, Tseng YJ, Walters WP. PMID: 23088271.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    183. Teach-Discover-Treat (TDT): collaborative computational drug discovery for neglected diseases. J Mol Graph Model. 2012 Sep; 38:360-2. Jansen JM, Cornell W, Tseng YJ, Amaro RE. PMID: 23085175; PMCID: PMC3508335.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    184. Exploring residue component contributions to dynamical network models of allostery. J Chem Theory Comput. 2012 Aug 14; 8(8):2949-2961. Vanwart AT, Eargle J, Luthey-Schulten Z, Amaro RE. PMID: 23139645; PMCID: PMC3489502.
      View in: PubMed   Mentions: 71     Fields:    
    185. Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med. 2012; 6:293-300. Votapka L, Demir O, Swift RV, Walker RC, Amaro RE. PMID: 22872804; PMCID: PMC3410406.
      View in: PubMed   Mentions: 2  
    186. Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. J Chem Inf Model. 2012 May 25; 52(5):1308-18. Demir Ö, Amaro RE. PMID: 22512810; PMCID: PMC3362124.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    187. Structural characterisation of Tpx from Yersinia pseudotuberculosis reveals insights into the binding of salicylidene acylhydrazide compounds. PLoS One. 2012; 7(2):e32217. Gabrielsen M, Beckham KS, Feher VA, Zetterström CE, Wang D, Müller S, Elofsson M, Amaro RE, Byron O, Roe AJ. PMID: 22384182; PMCID: PMC3288085.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    188. Rational prediction with molecular dynamics for hit identification. Curr Top Med Chem. 2012; 12(18):2002-12. Nichols SE, Swift RV, Amaro RE. PMID: 23110535; PMCID: PMC3636520.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    189. Molecular-level simulation of pandemic influenza glycoproteins. Methods Mol Biol. 2012; 819:575-94. Amaro RE, Li WW. PMID: 22183559; PMCID: PMC3352029.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    190. Modeling the pharmacodynamics of passive membrane permeability. J Comput Aided Mol Des. 2011 Nov; 25(11):1007-17. Swift RV, Amaro RE. PMID: 22042376; PMCID: PMC3223344.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    191. Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants. PLoS Comput Biol. 2011 Oct; 7(10):e1002238. Demir Ö, Baronio R, Salehi F, Wassman CD, Hall L, Hatfield GW, Chamberlin R, Kaiser P, Lathrop RH, Amaro RE. PMID: 22028641; PMCID: PMC3197647.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    192. Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis. PLoS One. 2011; 6(9):e25084. Torres R, Swift RV, Chim N, Wheatley N, Lan B, Atwood BR, Pujol C, Sankaran B, Bliska JB, Amaro RE, Goulding CW. PMID: 21966419; PMCID: PMC3180442.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    193. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011 Jul 12; 2:388. Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM. PMID: 21750542; PMCID: PMC3144582.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    194. Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1. PLoS Negl Trop Dis. 2010 Aug 24; 4(8):e803. Durrant JD, Hall L, Swift RV, Landon M, Schnaufer A, Amaro RE. PMID: 20808768; PMCID: PMC2927429.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    195. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins. 2010 Aug 15; 78(11):2523-32. Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA. PMID: 20602360; PMCID: PMC2902668.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    196. Role of secondary sialic acid binding sites in influenza N1 neuraminidase. J Am Chem Soc. 2010 Mar 10; 132(9):2883-5. Sung JC, Van Wynsberghe AW, Amaro RE, Li WW, McCammon JA. PMID: 20155919; PMCID: PMC2835425.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    197. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol. 2010 Jan 22; 6(1):e1000648. Durrant JD, Amaro RE, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne PE, McCammon JA. PMID: 20098496; PMCID: PMC2799658.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    198. Emerging methods for ensemble-based virtual screening. Curr Top Med Chem. 2010; 10(1):3-13. Amaro RE, Li WW. PMID: 19929833; PMCID: PMC3086266.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    199. 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. Newhouse EI, Xu D, Markwick PR, Amaro RE, Pao HC, Wu KJ, Alam M, McCammon JA, Li WW. PMID: 19891427; PMCID: PMC2782351.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    200. Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opin Drug Discov. 2009 Dec 01; 4(12):1281-1294. Swift RV, Amaro RE. PMID: 20354588; PMCID: PMC2846787.
      View in: PubMed   Mentions: 5     Fields:    
    201. 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. Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA. PMID: 19296611; PMCID: PMC2665887.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    202. 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. Xu D, Newhouse EI, Amaro RE, Pao HC, Cheng LS, Markwick PR, McCammon JA, Li WW, Arzberger PW. PMID: 19356594; PMCID: PMC2892341.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimalsCells
    203. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 2009 Feb 03; 48(4):709-19. Swift RV, Durrant J, Amaro RE, McCammon JA. PMID: 19133737; PMCID: PMC2651658.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    204. AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des. 2009 Feb; 73(2):168-78. Durrant JD, Amaro RE, McCammon JA. PMID: 19207419; PMCID: PMC2724963.
      View in: PubMed   Mentions: 29     Fields:    
    205. 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. Wong S, Amaro RE, McCammon JA. PMID: 19461869; PMCID: PMC2651627.
      View in: PubMed   Mentions: 35     Fields:    
    206. 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. Amaro RE, Schnaufer A, Interthal H, Hol W, Stuart KD, McCammon JA. PMID: 18981420; PMCID: PMC2577703.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansAnimalsCells
    207. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem. 2008 Jul 10; 51(13):3878-94. Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. PMID: 18558668; PMCID: PMC2652358.
      View in: PubMed   Mentions: 88     Fields:    Translation:Cells
    208. 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. Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, Vajda S. PMID: 18205727; PMCID: PMC2438278.
      View in: PubMed   Mentions: 56     Fields:    Translation:Cells
    209. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des. 2008 Sep; 22(9):693-705. Amaro RE, Baron R, McCammon JA. PMID: 18196463; PMCID: PMC2516539.
      View in: PubMed   Mentions: 146     Fields:    Translation:Cells
    210. 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. Amaro RE, Swift RV, McCammon JA. PMID: 18060084; PMCID: PMC2100368.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    211. 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. Amaro RE, Minh DD, Cheng LS, Lindstrom WM, Olson AJ, Lin JH, Li WW, McCammon JA. PMID: 17539643.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    212. A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry. 2007 Feb 27; 46(8):2156-73. Amaro RE, Sethi A, Myers RS, Davisson VJ, Luthey-Schulten ZA. PMID: 17261030.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
    213. Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase. Biochemistry. 2005 Sep 13; 44(36):11974-85. Myers RS, Amaro RE, Luthey-Schulten ZA, Davisson VJ. PMID: 16142895.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    214. Structural elements in IGP synthase exclude water to optimize ammonia transfer. Biophys J. 2005 Jul; 89(1):475-87. Amaro RE, Myers RS, Davisson VJ, Luthey-Schulten ZA. PMID: 15849257; PMCID: PMC1366548.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    215. 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. Amaro R, Tajkhorshid E, Luthey-Schulten Z. PMID: 12799468; PMCID: PMC164632.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    216. On the structure of hisH: protein structure prediction in the context of structural and functional genomics. J Struct Biol. 2001 May-Jun; 134(2-3):257-68. O'Donoghue P, Amaro RE, Luthey-Schulten Z. PMID: 11551184.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    217. Age specific prevalence of impairment and disability relating to hemiplegic stroke in the Hai District of northern Tanzania. Adult Morbidity and Mortality Project. J Neurol Neurosurg Psychiatry. 2000 Jun; 68(6):744-9. Walker RW, McLarty DG, Masuki G, Kitange HM, Whiting D, Moshi AF, Massawe JG, Amaro R, Mhina A, Alberti KG. PMID: 10811698; PMCID: PMC1736964.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
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