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Items: 1 to 50 of 212

1.

An imported case of e-cigarette or vaping associated lung injury (EVALI) in Barcelona.

Casanova GS, Amaro R, Soler N, Sánchez M, Badía JR, Barberà JA, Agustí A.

Eur Respir J. 2019 Dec 5. pii: 1902076. doi: 10.1183/13993003.02076-2019. [Epub ahead of print] No abstract available.

PMID:
31806720
2.

Tailor-made PEG coated iron oxide nanoparticles as contrast agents for long lasting magnetic resonance molecular imaging of solid cancers.

Lazaro-Carrillo A, Filice M, Guillén MJ, Amaro R, Viñambres M, Tabero A, Paredes KO, Villanueva A, Calvo P, Del Puerto Morales M, Marciello M.

Mater Sci Eng C Mater Biol Appl. 2020 Feb;107:110262. doi: 10.1016/j.msec.2019.110262. Epub 2019 Oct 11.

PMID:
31761230
3.

Clinical Factors Associated with a Shorter or Longer Course of Antibiotic Treatment in Patients with Exacerbations of Bronchiectasis: A Prospective Cohort Study.

Scioscia G, Amaro R, Alcaraz-Serrano V, Gabarrús A, Oscanoa P, Fernandez L, Menendez R, Mendez R, Foschino Barbaro MP, Torres A.

J Clin Med. 2019 Nov 12;8(11). pii: E1950. doi: 10.3390/jcm8111950.

4.

Chance, luck and a fortunate finding: a new species of watersnake of the genus Helicops Wagler, 1828 (Serpentes: Xenodontinae), from the Brazilian Pantanal wetlands.

Moraes-DA-Silva A, Amaro RC, Nunes PMS, Strüssmann C, Teixeira MJ, Andrade AJ, Sudré V, Recoder R, Rodrigues MT, Curcio FF.

Zootaxa. 2019 Aug 6;4651(3):zootaxa.4651.3.3. doi: 10.11646/zootaxa.4651.3.3.

PMID:
31716897
5.

Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus.

Le KP, Do PC, Amaro RE, Le L.

Evol Bioinform Online. 2019 Sep 16;15:1176934319876938. doi: 10.1177/1176934319876938. eCollection 2019.

6.

The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation.

Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ.

ACM Trans Math Softw. 2019 Aug;45(3). pii: 28. doi: 10.1145/3321515.

PMID:
31474782
7.

Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations.

Barros EP, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE.

J Chem Theory Comput. 2019 Oct 8;15(10):5703-5715. doi: 10.1021/acs.jctc.9b00483. Epub 2019 Sep 10.

PMID:
31442033
8.

An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes.

Bernetti M, Masetti M, Recanatini M, Amaro RE, Cavalli A.

J Chem Theory Comput. 2019 Oct 8;15(10):5689-5702. doi: 10.1021/acs.jctc.9b00450. Epub 2019 Sep 5.

PMID:
31436987
9.

Soluble P-Selectin in Acute Exacerbations and Stable Bronchiectasis in Adults.

Méndez R, Moscardó A, Latorre A, Feced L, González-Jiménez P, Piró A, Alcaraz-Serrano V, Scioscia G, Amaro R, Torres A, Menéndez R.

Ann Am Thorac Soc. 2019 Dec;16(12):1587-1591. doi: 10.1513/AnnalsATS.201902-140RL. No abstract available.

PMID:
31394907
10.

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.

Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE.

Structure. 2019 Aug 6;27(8):1326-1335.e4. doi: 10.1016/j.str.2019.05.012. Epub 2019 Jun 27.

PMID:
31257108
11.

Frontiers in CryoEM Modeling.

Palermo G, Sugita Y, Wriggers W, Amaro RE.

J Chem Inf Model. 2019 Jul 22;59(7):3091-3093. doi: 10.1021/acs.jcim.9b00412. Epub 2019 Jun 13. No abstract available.

12.

Surfactant Charge Modulates Structure and Stability of Lipase-Embedded Monolayers at Marine-Relevant Aerosol Surfaces.

Luo M, Dommer AC, Schiffer JM, Rez DJ, Mitchell AR, Amaro RE, Grassian VH.

Langmuir. 2019 Jul 9;35(27):9050-9060. doi: 10.1021/acs.langmuir.9b00689. Epub 2019 Jun 25.

PMID:
31188612
13.

A Celebration of Women in Computational Chemistry.

Wahab HA, Amaro RE, Cournia Z.

J Chem Inf Model. 2019 May 28;59(5):1683-1692. doi: 10.1021/acs.jcim.9b00368. No abstract available.

PMID:
31132853
14.

Exascale Computing: A New Dawn for Computational Biology.

Lee CT, Amaro RE.

Comput Sci Eng. 2018 Sep-Oct;20(5):18-25. doi: 10.1109/MCSE.2018.05329812. Epub 2018 Aug 30.

15.

Structural basis for ligand modulation of the CCR2 conformational landscape.

Taylor BC, Lee CT, Amaro RE.

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8131-8136. doi: 10.1073/pnas.1814131116. Epub 2019 Apr 11.

16.

Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.

Amaro RE, Mulholland AJ.

Nat Rev Chem. 2018 Apr;2(4). pii: 0148. doi: 10.1038/s41570-018-0148. Epub 2018 Apr 11.

17.

Human Influenza A Virus Hemagglutinin Glycan Evolution Follows a Temporal Pattern to a Glycan Limit.

Altman MO, Angel M, Košík I, Trovão NS, Zost SJ, Gibbs JS, Casalino L, Amaro RE, Hensley SE, Nelson MI, Yewdell JW.

MBio. 2019 Apr 2;10(2). pii: e00204-19. doi: 10.1128/mBio.00204-19.

18.

Nebulized Amikacin and Fosfomycin for Severe Pseudomonas aeruginosa Pneumonia: An Experimental Study.

Li Bassi G, Motos A, Fernandez-Barat L, Aguilera Xiol E, Chiurazzi C, Senussi T, Saco MA, Fuster C, Carbonara M, Bobi J, Amaro R, De Rosa F, Comaru T, Yang H, Ranzani OT, Marti JD, Rinaudo M, Comino Trinidad O, Rigol M, Bringué J, Ramirez J, Nicolau DP, Pelosi P, Antonelli M, Blasi F, Artigas A, Montgomery AB, Torres A.

Crit Care Med. 2019 Jun;47(6):e470-e477. doi: 10.1097/CCM.0000000000003724.

PMID:
30882478
19.

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.

Yang PC, Purawat S, Ieong PU, Jeng MT, DeMarco KR, Vorobyov I, McCulloch AD, Altintas I, Amaro RE, Clancy CE.

PLoS Comput Biol. 2019 Mar 8;15(3):e1006856. doi: 10.1371/journal.pcbi.1006856. eCollection 2019 Mar.

20.

Will the Real Cryptic Pocket Please Stand Out?

Amaro RE.

Biophys J. 2019 Mar 5;116(5):753-754. doi: 10.1016/j.bpj.2019.01.018. Epub 2019 Jan 26. No abstract available.

PMID:
30739726
21.

Recruitment manoeuvres dislodge mucus towards the distal airways in an experimental model of severe pneumonia.

Li Bassi G, Comaru T, Martí D, Xiol EA, Chiurazzi C, Travierso C, Carbonara M, Ranzani OT, Amaro R, Frigola G, Fuster C, Saco MA, Zanella A, De Rosa F, Rigol M, Fernandez L, Luque N, Ramirez J, Blasi F, Suen J, Fraser J, Torres A.

Br J Anaesth. 2019 Feb;122(2):269-276. doi: 10.1016/j.bja.2018.07.039. Epub 2018 Nov 10.

PMID:
30686313
22.

Sea Spray Aerosol: Where Marine Biology Meets Atmospheric Chemistry.

Schiffer JM, Mael LE, Prather KA, Amaro RE, Grassian VH.

ACS Cent Sci. 2018 Dec 26;4(12):1617-1623. doi: 10.1021/acscentsci.8b00674. Epub 2018 Dec 14. Review.

23.

D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.

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.

J Comput Aided Mol Des. 2019 Jan;33(1):1-18. doi: 10.1007/s10822-018-0180-4. Epub 2019 Jan 10.

PMID:
30632055
24.

Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.

Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE.

Biophys J. 2019 Jan 22;116(2):205-214. doi: 10.1016/j.bpj.2018.09.035. Epub 2018 Dec 8.

PMID:
30606449
25.

A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target.

Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW.

ACS Cent Sci. 2018 Nov 28;4(11):1570-1577. doi: 10.1021/acscentsci.8b00666. Epub 2018 Nov 9.

26.

Dynamics and Molecular Mechanisms of p53 Transcriptional Activation.

Offutt TL, Ieong PU, Demir Ö, Amaro RE.

Biochemistry. 2018 Nov 20;57(46):6528-6537. doi: 10.1021/acs.biochem.8b01005. Epub 2018 Nov 12.

PMID:
30388364
27.

Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester.

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.

J Med Chem. 2018 Dec 13;61(23):10463-10472. doi: 10.1021/acs.jmedchem.8b00975. Epub 2018 Nov 28.

PMID:
30380865
28.

A new cryptic species of Oreobates (Anura: Craugastoridae) from the seasonally dry tropical forest of central Brazil.

Vaz-Silva W, Maciel NM, De Andrade SP, Amaro RC.

Zootaxa. 2018 Jun 26;4441(1):89-108. doi: 10.11646/zootaxa.4441.1.5.

PMID:
30314022
29.

Women in Computational Chemistry.

Wahab HA, Amaro RE, Cournia Z.

J Chem Inf Model. 2018 Nov 26;58(11):2175-2177. doi: 10.1021/acs.jcim.8b00642. Epub 2018 Oct 2. No abstract available.

PMID:
30277769
30.

Synthetic repetitive extragenic palindromic (REP) sequence as an efficient mRNA stabilizer for protein production and metabolic engineering in prokaryotic cells.

Deng C, Lv X, Li J, Liu Y, Du G, Amaro RL, Liu L.

Biotechnol Bioeng. 2019 Jan;116(1):5-18. doi: 10.1002/bit.26841. Epub 2018 Oct 27.

PMID:
30229865
31.

APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction.

Salamango DJ, Becker JT, McCann JL, Cheng AZ, Demir Ö, Amaro RE, Brown WL, Shaban NM, Harris RS.

Mol Cell Biol. 2018 Nov 13;38(23). pii: e00356-18. doi: 10.1128/MCB.00356-18. Print 2018 Dec 1.

32.

Determinants of Oligonucleotide Selectivity of APOBEC3B.

Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE.

J Chem Inf Model. 2019 May 28;59(5):2264-2273. doi: 10.1021/acs.jcim.8b00427. Epub 2018 Sep 10.

PMID:
30130104
33.

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.

Jagger BR, Lee CT, Amaro RE.

J Phys Chem Lett. 2018 Sep 6;9(17):4941-4948. doi: 10.1021/acs.jpclett.8b02047. Epub 2018 Aug 16.

34.

The efficacy of inhaled antibiotics in non-cystic fibrosis bronchiectasis.

Amaro R, Panagiotaraka M, Alcaraz V, Torres A.

Expert Rev Respir Med. 2018 Aug;12(8):683-691. doi: 10.1080/17476348.2018.1500179. Epub 2018 Jul 25. Review.

PMID:
30010445
35.

Increased Levels of AIM2 and Circulating Mitochondrial DNA in Type 2 Diabetes.

Cataño Cañizales YG, Uresti Rivera EE, García Jacobo RE, Portales Perez DP, Yadira B, Rodriguez Rivera JG, Amaro RG, Enciso Moreno JA, García Hernández MH.

Iran J Immunol. 2018 Jun;15(2):142-155. doi: IJIv15i2A7.

36.

Screening for Latent Tuberculosis Infection in Patients who are Candidate for Biological Therapies in Spain? A Multidisciplinary Survey.

Quirós S, de la Rosa D, Uranga A, Madero R, Amaro R, Bruguera N, García JA, Gómez C, Iturbe D, Lera R, Luque L, Martínez AJ, Mínguez P, Navarro A, Sánchez G, Suárez-Cuartín G.

Arch Bronconeumol. 2018 Oct;54(10):510-517. doi: 10.1016/j.arbres.2018.04.004. Epub 2018 Jun 23. English, Spanish.

37.

Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols.

Schiffer JM, Luo M, Dommer AC, Thoron G, Pendergraft M, Santander MV, Lucero D, Pecora de Barros E, Prather KA, Grassian VH, Amaro RE.

J Phys Chem Lett. 2018 Jul 19;9(14):3839-3849. doi: 10.1021/acs.jpclett.8b01363. Epub 2018 Jun 29.

PMID:
29916254
38.

APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces.

Salamango DJ, McCann JL, Demir Ö, Brown WL, Amaro RE, Harris RS.

J Mol Biol. 2018 Aug 17;430(17):2695-2708. doi: 10.1016/j.jmb.2018.04.044. Epub 2018 May 19.

39.

Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit.

Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang DB, Wang VY, Amaro RE, Huxford T, Ghosh G.

Biochemistry. 2018 May 22;57(20):2943-2957. doi: 10.1021/acs.biochem.8b00158. Epub 2018 May 10.

40.

The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release.

Bohl TE, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir Ö, Kurahashi K, Amaro RE, Wang Z, Aihara H.

J Biol Chem. 2018 May 25;293(21):7969-7981. doi: 10.1074/jbc.RA118.002503. Epub 2018 Apr 6.

41.

Ensemble Docking in Drug Discovery.

Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC.

Biophys J. 2018 May 22;114(10):2271-2278. doi: 10.1016/j.bpj.2018.02.038. Epub 2018 Mar 30. Review.

42.

Initial Inflammatory Profile in Community-acquired Pneumonia Depends on Time since Onset of Symptoms.

Méndez R, Menéndez R, Cillóniz C, Amara-Elori I, Amaro R, González P, Posadas T, Gimeno A, España PP, Almirall J, Torres A.

Am J Respir Crit Care Med. 2018 Aug 1;198(3):370-378. doi: 10.1164/rccm.201709-1908OC.

43.

Reliability assessment for large-scale molecular dynamics approximations.

Grogan F, Holst M, Lindblom L, Amaro R.

J Chem Phys. 2017 Dec 21;147(23):234106. doi: 10.1063/1.5009431.

44.

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.

Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H.

Sci Rep. 2017 Dec 12;7(1):17415. doi: 10.1038/s41598-017-17694-3.

45.

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

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.

J Comput Aided Mol Des. 2018 Jan;32(1):1-20. doi: 10.1007/s10822-017-0088-4. Epub 2017 Dec 4.

46.

Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research.

Purawat S, Cowart C, Amaro RE, Altintas I.

J Comput Sci. 2017 May;20:205-214. doi: 10.1016/j.jocs.2017.03.010. Epub 2017 Mar 15.

47.

Development of an AlphaLISA high throughput technique to screen for small molecule inhibitors targeting protein arginine methyltransferases.

Prabhu L, Chen L, Wei H, Demir Ö, Safa A, Zeng L, Amaro RE, O'Neil BH, Zhang ZY, Lu T.

Mol Biosyst. 2017 Nov 21;13(12):2509-2520. doi: 10.1039/c7mb00391a.

48.

Toward Understanding "the Ways" of Allosteric Drugs.

Amaro RE.

ACS Cent Sci. 2017 Sep 27;3(9):925-926. doi: 10.1021/acscentsci.7b00396. Epub 2017 Sep 13. No abstract available.

49.

POVME 3.0: Software for Mapping Binding Pocket Flexibility.

Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE.

J Chem Theory Comput. 2017 Sep 12;13(9):4584-4592. doi: 10.1021/acs.jctc.7b00500. Epub 2017 Aug 30.

50.

Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism.

Hirakis SP, Malmstrom RD, Amaro RE.

Biochemistry. 2017 Aug 1;56(30):3885-3888. doi: 10.1021/acs.biochem.7b00461. Epub 2017 Jul 17.

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