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Rommie E. Amaro - Publications

Affiliations: 
University of California, San Diego, La Jolla, CA 
Area:
Computational and Theoretical Biophysics
Website:
http://www-chem.ucsd.edu/faculty/profiles/amaro_rommie_e.html
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Year Citation  Score
2023 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, ... ... Amaro RE, et al. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nature Communications. 14: 6169. PMID 37794035 DOI: 10.1038/s41467-023-41756-y  0.79
2023 Hock MT, Teitgen AE, McCabe KJ, Hirakis SP, Huber GA, Regnier M, Amaro RE, McCammon JA, McCulloch AD. Multiscale computational modeling of the effects of 2'-deoxy-ATP on cardiac muscle calcium handling. Journal of Applied Physics. 134: 074905. PMID 37601331 DOI: 10.1063/5.0157935  0.368
2023 Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. Cell Reports. Physical Science. 4: 101346. PMID 37077408 DOI: 10.1016/j.xcrp.2023.101346  0.775
2023 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. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. Science Advances. 9: eade8778. PMID 36989354 DOI: 10.1126/sciadv.ade8778  0.7
2023 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, et al. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Biorxiv : the Preprint Server For Biology. PMID 36778266 DOI: 10.1101/2023.02.01.526488  0.791
2022 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, et al. Inhibition of PRMT5 by market drugs as a novel cancer therapeutic avenue. Genes & Diseases. 10: 267-283. PMID 37013054 DOI: 10.1016/j.gendis.2022.04.001  0.588
2022 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, ... ... Amaro RE, et al. #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The International Journal of High Performance Computing Applications. 37: 28-44. PMID 36647365 DOI: 10.1177/10943420221128233  0.788
2022 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, ... ... Amaro RE, et al. Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection. Nature Chemical Biology. PMID 36175661 DOI: 10.1038/s41589-022-01149-6  0.783
2022 Moghadasi SA, Heilmann E, Moraes SN, Kearns FL, von Laer D, Amaro RE, Harris RS. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. Biorxiv : the Preprint Server For Biology. PMID 35982678 DOI: 10.1101/2022.08.07.503099  0.702
2022 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, ... ... Amaro RE, et al. Discovery of compounds that reactivate p53 mutants in vitro and in vivo. Cell Chemical Biology. PMID 35948006 DOI: 10.1016/j.chembiol.2022.07.003  0.589
2022 Kearns FL, Sandoval DR, Casalino L, Clausen TM, Rosenfeld MA, Spliid CB, Amaro RE, Esko JD. Spike-heparan sulfate interactions in SARS-CoV-2 infection. Current Opinion in Structural Biology. 76: 102439. PMID 35926454 DOI: 10.1016/j.sbi.2022.102439  0.784
2022 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. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature. 608: 429-435. PMID 35922510 DOI: 10.1038/s41586-022-05013-4  0.37
2022 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, et al. CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. Nature Reviews. Chemistry. 6: 287-295. PMID 35783295 DOI: 10.1038/s41570-022-00363-z  0.557
2022 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, ... ... Amaro RE, et al. Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection. Biorxiv : the Preprint Server For Biology. PMID 35411336 DOI: 10.1101/2022.04.05.487060  0.784
2022 Gan JL, Kumar D, Chen C, Taylor BC, Jagger BR, Amaro RE, Lee CT. Benchmarking ensemble docking methods in D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design. PMID 35199221 DOI: 10.1007/s10822-021-00433-2  0.772
2022 Moeller NH, Shi K, Demir Ö, Belica C, Banerjee S, Yin L, Durfee C, Amaro RE, Aihara H. Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35165203 DOI: 10.1073/pnas.2106379119  0.627
2022 Kim SH, Kearns FL, Rosenfeld MA, Casalino L, Papanikolas MJ, Simmerling C, Amaro RE, Freeman R. : Cell Surface-Inspired Universal Sensor for Betacoronaviruses. Acs Central Science. 8: 22-42. PMID 35106370 DOI: 10.1021/acscentsci.1c01080  0.781
2021 Ahn SH, Ojha AA, Amaro RE, McCammon JA. Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling. Journal of Chemical Theory and Computation. 17: 7938-7951. PMID 34844409 DOI: 10.1021/acs.jctc.1c00770  0.363
2021 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, ... ... Amaro R, et al. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. Biorxiv : the Preprint Server For Biology. PMID 34816263 DOI: 10.1101/2021.11.12.468428  0.788
2021 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, ... ... Amaro RE, et al. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nature Chemistry. PMID 34413500 DOI: 10.1038/s41557-021-00758-3  0.759
2021 Hempel T, Del Razo MJ, Lee CT, Taylor BC, Amaro RE, Noé F. Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34321356 DOI: 10.1073/pnas.2105230118  0.762
2021 Lee C, Dommer AC, Schiffer JM, Amaro RE, Grassian VH, Prather KA. Cation-Driven Lipopolysaccharide Morphological Changes Impact Heterogeneous Reactions of Nitric Acid with Sea Spray Aerosol Particles. The Journal of Physical Chemistry Letters. 12: 5023-5029. PMID 34024101 DOI: 10.1021/acs.jpclett.1c00810  0.371
2021 Sztain T, Amaro R, McCammon JA. Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. Journal of Chemical Information and Modeling. PMID 33939913 DOI: 10.1021/acs.jcim.1c00140  0.471
2021 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. Structural Characterization of a Minimal Antibody against Human APOBEC3B. Viruses. 13. PMID 33921405 DOI: 10.3390/v13040663  0.616
2021 Moeller NH, Shi K, Demir Ö, Banerjee S, Yin L, Belica C, Durfee C, Amaro RE, Aihara H. Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Biorxiv : the Preprint Server For Biology. PMID 33821277 DOI: 10.1101/2021.04.02.438274  0.632
2021 Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, McCool RS, Kearns FL, McCammon JA, McLellan JS, Chong LT, Amaro RE. A glycan gate controls opening of the SARS-CoV-2 spike protein. Biorxiv : the Preprint Server For Biology. PMID 33619492 DOI: 10.1101/2021.02.15.431212  0.762
2021 Lirussi L, Demir Ö, You P, Sarno A, Amaro RE, Nilsen H. RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules. 11. PMID 33430019 DOI: 10.3390/biom11010076  0.557
2021 Demir Ö, Barros EP, Offutt TL, Rosenfeld M, Amaro RE. An integrated view of p53 dynamics, function, and reactivation. Current Opinion in Structural Biology. 67: 187-194. PMID 33401096 DOI: 10.1016/j.sbi.2020.11.005  0.774
2020 Barros EP, Demir Ö, Soto J, Cocco MJ, Amaro RE. Markov state models and NMR uncover an overlooked allosteric loop in p53. Chemical Science. 12: 1891-1900. PMID 34163952 DOI: 10.1039/d0sc05053a  0.628
2020 Casalino L, Gaieb Z, Goldsmith JA, Hjorth CK, Dommer AC, Harbison AM, Fogarty CA, Barros EP, Taylor BC, McLellan JS, Fadda E, Amaro RE. Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. Acs Central Science. 6: 1722-1734. PMID 33140034 DOI: 10.1021/acscentsci.0c01056  0.775
2020 Seitz C, Casalino L, Konecny R, Huber G, Amaro RE, McCammon JA. Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase. Biophysical Journal. PMID 33130120 DOI: 10.1016/j.bpj.2020.10.024  0.435
2020 Salamango DJ, McCann JL, Demir Ö, Becker JT, Wang J, Lingappa JR, Temiz NA, Brown WL, Amaro RE, Harris RS. Functional and Structural Insights into a Vif/PPP2R5 Complex Elucidated using Patient HIV-1 Isolates and Computational Modeling. Journal of Virology. PMID 32847850 DOI: 10.1128/Jvi.00631-20  0.641
2020 Sztain T, Amaro R, McCammon JA. Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease. Biorxiv : the Preprint Server For Biology. PMID 32743587 DOI: 10.1101/2020.07.23.218784  0.465
2020 Parks C, Gaieb Z, Amaro RE. An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models. Frontiers in Molecular Biosciences. 7: 93. PMID 32671093 DOI: 10.3389/Fmolb.2020.00093  0.322
2020 Jagger BR, Ojha AA, Amaro RE. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. Journal of Chemical Theory and Computation. PMID 32579371 DOI: 10.1021/Acs.Jctc.0C00495  0.38
2020 Casalino L, Gaieb Z, Dommer AC, Harbison AM, Fogarty CA, Barros EP, Taylor BC, Fadda E, Amaro RE. Shielding and Beyond: The Roles of Glycans in SARS-CoV-2 Spike Protein. Biorxiv : the Preprint Server For Biology. PMID 32577644 DOI: 10.1101/2020.06.11.146522  0.768
2020 Ahn SH, Jagger BR, Amaro RE. Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. Journal of Chemical Information and Modeling. PMID 32315175 DOI: 10.1021/Acs.Jcim.9B00968  0.32
2020 Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. Plos Computational Biology. 16: e1007756. PMID 32251448 DOI: 10.1371/Journal.Pcbi.1007756  0.577
2020 Shi K, Demir Ö, Carpenter MA, Banerjee S, Harki DA, Amaro RE, Harris RS, Aihara H. Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B. Faseb Bioadvances. 2: 49-58. PMID 32123856 DOI: 10.1096/fba.2019-00068  0.636
2020 Durrant JD, Kochanek SE, Casalino L, Ieong PU, Dommer AC, Amaro RE. Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. Acs Central Science. 6: 189-196. PMID 32123736 DOI: 10.1021/Acscentsci.9B01071  0.396
2020 Jagger BR, Kochanek SE, Haldar S, Amaro RE, Mulholland AJ. Multiscale simulation approaches to modeling drug-protein binding. Current Opinion in Structural Biology. 61: 213-221. PMID 32113133 DOI: 10.1016/J.Sbi.2020.01.014  0.379
2020 Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophysical Journal. PMID 32032503 DOI: 10.1016/J.Bpj.2019.11.3400  0.581
2020 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. D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. Journal of Computer-Aided Molecular Design. PMID 31974851 DOI: 10.1007/S10822-020-00289-Y  0.337
2020 Wauer NA, Dommer AC, Amaro RE. Molecular Insights into the Activity and Structural Impacts of Enzymes Across the Dynamic pH Environment in Sea Spray Aerosols Biophysical Journal. 118: 528a. DOI: 10.1016/J.Bpj.2019.11.2899  0.31
2020 Pecora de Barros E, Demir O, Amaro RE. Uncovering the Dynamical Landscape of P53 DNA Binding Domain with Markov State Models Biophysical Journal. 118: 320a. DOI: 10.1016/J.Bpj.2019.11.1799  0.638
2020 Demir O, Amaro RE. Investigating Full-Length p53 Tetramer Dynamics with Multi-Microsecond Molecular Dynamics Simulations Biophysical Journal. 118: 208a. DOI: 10.1016/J.Bpj.2019.11.1247  0.641
2020 Taylor BC, Lee CT, Amaro RE. Using Molecular Simulations to Inform Drug Development Efforts for the GPCR CCR2 Biophysical Journal. 118: 207a. DOI: 10.1016/J.Bpj.2019.11.1242  0.766
2019 Le KP, Do PC, Amaro RE, Le L. Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus. Evolutionary Bioinformatics Online. 15: 1176934319876938. PMID 31555044 DOI: 10.1177/1176934319876938  0.301
2019 Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. Acm Transactions On Mathematical Software. Association For Computing Machinery. 45. PMID 31474782 DOI: 10.1145/3321515  0.547
2019 Pecora de Barros E, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 31442033 DOI: 10.1021/Acs.Jctc.9B00483  0.383
2019 Bernetti M, Masetti M, Recanatini M, Amaro RE, Cavalli A. An Integrated Markov State Model and Path Metadynamics Approach to Characterize Drug Binding Processes. Journal of Chemical Theory and Computation. PMID 31436987 DOI: 10.1021/Acs.Jctc.9B00450  0.39
2019 Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE. Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure (London, England : 1993). PMID 31257108 DOI: 10.1016/J.Str.2019.05.012  0.326
2019 Taylor BC, Lee CT, Amaro RE. Structural basis for ligand modulation of the CCR2 conformational landscape. Proceedings of the National Academy of Sciences of the United States of America. PMID 30975755 DOI: 10.1073/Pnas.1814131116  0.791
2019 Yang PC, Purawat S, Ieong PU, Jeng MT, DeMarco KR, Vorobyov I, McCulloch AD, Altinas I, Amaro RE, Clancy CE. A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. Plos Computational Biology. 15: e1006856. PMID 30849072 DOI: 10.1371/Journal.Pcbi.1006856  0.305
2019 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. D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. Journal of Computer-Aided Molecular Design. PMID 30632055 DOI: 10.1007/S10822-018-0180-4  0.333
2019 Jagger BR, Lee CT, McCammon JA, Amaro RE. Computational Predictions of Drug-Protein Binding Kinetics with a Hybrid Molecular Dynamics, Brownian Dynamics, and Milestoning Approach Biophysical Journal. 116: 562a. DOI: 10.1016/J.Bpj.2018.11.3020  0.631
2019 Seitz C, Casalino L, Huber G, Konecny R, Huang Y, Amaro R, McCammon JA. How does Glycosylation Affect Drug Binding on Influenza? The Roles of Electrostatics and Sterics Examined through Brownian Dynamics Simulations Biophysical Journal. 116: 483a. DOI: 10.1016/J.Bpj.2018.11.2610  0.513
2019 Amaro RE. Protein Dynamics in Cellular Environments Biophysical Journal. 116: 297a. DOI: 10.1016/J.Bpj.2018.11.1608  0.328
2019 Laughlin JG, Lee CT, McCammon JA, Amaro RE, Holst M, Rangamani P. Modeling the Impact of Spine Apparatus on Signaling and Regulation in Realistic Dendritic Spine Geometries Biophysical Journal. 116: 237a. DOI: 10.1016/J.Bpj.2018.11.1303  0.529
2018 Lee CT, Amaro RE. Exascale Computing: A New Dawn for Computational Biology. Computing in Science & Engineering. 20: 18-25. PMID 30983889 DOI: 10.1109/Mcse.2018.05329812  0.475
2018 Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophysical Journal. PMID 30606449 DOI: 10.1016/J.Bpj.2018.09.035  0.496
2018 Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW. A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target. Acs Central Science. 4: 1570-1577. PMID 30555910 DOI: 10.1021/Acscentsci.8B00666  0.396
2018 Offutt TL, Ieong PU, Demir O, Amaro RE. Dynamics and Molecular Mechanisms of p53 Transcriptional Activation. Biochemistry. PMID 30388364 DOI: 10.1021/Acs.Biochem.8B01005  0.645
2018 Castro-Falcón G, Seiler G, Demir O, Rathinaswamy M, Hamelin D, Hoffmann RM, Makowski S, Letzel AC, Field S, Burke J, Amaro RE, Hughes CC. Neolymphostin A is a Covalent Phosphoinositide-3-kinase (PI3-K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor that Employs an Unusual Electrophilic Vinylogous Ester. Journal of Medicinal Chemistry. PMID 30380865 DOI: 10.1021/Acs.Jmedchem.8B00975  0.609
2018 Salamango DJ, Becker JT, McCann JL, Cheng AZ, Demir Ö, Amaro RE, Brown WL, Shaban NM, Harris RS. APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction. Molecular and Cellular Biology. PMID 30224517 DOI: 10.1128/Mcb.00356-18  0.634
2018 Wagner JR, Demir O, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. Determinants of Oligonucleotide Selectivity of APOBEC3B. Journal of Chemical Information and Modeling. PMID 30130104 DOI: 10.1021/Acs.Jcim.8B00427  0.688
2018 Jagger BR, Lee CT, Amaro RE. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. The Journal of Physical Chemistry Letters. PMID 30070844 DOI: 10.1021/Acs.Jpclett.8B02047  0.548
2018 Salamango DJ, McCann JL, Demir Ö, Brown WL, Amaro RE, Harris RS. APOBEC3B Nuclear Localization Requires two Distinct N-Terminal Domain Surfaces. Journal of Molecular Biology. PMID 29787764 DOI: 10.1016/J.Jmb.2018.04.044  0.627
2018 Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang D, Wang VY, Amaro RE, Huxford T, Ghosh G. Protein co-factors are essential for high affinity DNA binding by the nuclear factor κB RelA subunit. Biochemistry. PMID 29708732 DOI: 10.1021/Acs.Biochem.8B00158  0.314
2018 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. The Journal of Biological Chemistry. PMID 29626094 DOI: 10.1074/Jbc.Ra118.002503  0.657
2018 Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophysical Journal. PMID 29606412 DOI: 10.1016/J.Bpj.2018.02.038  0.763
2018 Grogan F, Holst M, Lindblom L, Amaro R. Reliability assessment for large-scale molecular dynamics approximations. The Journal of Chemical Physics. 147: 234106. PMID 29272950 DOI: 10.1063/1.5009431  0.33
2018 Seitz C, Autin L, Amaro R, McCammon JA, Olson AJ. Cellpacking: Examining Influenza Virulence through Software-Engineered Protein Packing Biophysical Journal. 114: 680a. DOI: 10.1016/J.Bpj.2017.11.3670  0.422
2018 Pecora de Barros E, Amaro RE. Investigating the Dynamics of Designed Ligand-Binding Proteins Biophysical Journal. 114: 527a. DOI: 10.1016/J.Bpj.2017.11.2880  0.346
2018 Taylor BC, Kufareva I, Handel T, Amaro RE. Investigating Chemokine Receptor CCR2 Dynamics and Druggability by Ensemble Based Approaches Biophysical Journal. 114: 399a. DOI: 10.1016/J.Bpj.2017.11.2205  0.731
2018 Lee CT, Moody J, Holst MJ, McCammon JA, Amaro RE. Gamer 2.0: Software Toolkit for Adaptive Mesh Generation from Structural Biological Datasets Biophysical Journal. 114: 344a. DOI: 10.1016/J.Bpj.2017.11.1921  0.557
2018 Kochanek SE, Durrant JD, Amaro RE. Influenza Viral Envelope Simulation Reveals Novel Druggable Pockets on Surface Glycoproteins Biophysical Journal. 114: 341a. DOI: 10.1016/J.Bpj.2017.11.1904  0.31
2017 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. Scientific Reports. 7: 17415. PMID 29234087 DOI: 10.1038/S41598-017-17694-3  0.658
2017 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. Journal of Computer-Aided Molecular Design. PMID 29204945 DOI: 10.1007/S10822-017-0088-4  0.319
2017 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. Molecular Biosystems. PMID 29099132 DOI: 10.1039/C7Mb00391A  0.638
2017 Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE. POVME 3.0: Software for Mapping Binding Pocket Flexibility. Journal of Chemical Theory and Computation. PMID 28800393 DOI: 10.1021/Acs.Jctc.7B00500  0.379
2017 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 association mechanism. Biochemistry. PMID 28661131 DOI: 10.1021/Acs.Biochem.7B00461  0.355
2017 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. Biophysical Journal. 112: 2469-2474. PMID 28636905 DOI: 10.1016/J.Bpj.2017.04.055  0.331
2017 Cheng KJ, Demir Ö, Amaro RE. A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases. Genes. 8. PMID 28632168 DOI: 10.3390/Genes8060166  0.647
2017 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. PMID 28591716 DOI: 10.18632/Oncotarget.18102  0.623
2017 Pecora de Barros E, Malmstrom RD, Nourbakhsh K, Del Rio JC, Kornev AP, Taylor SS, Amaro RE. Electrostatic interactions as mediators in the allosteric activation of PKA RIα. Biochemistry. PMID 28221775 DOI: 10.1021/Acs.Biochem.6B01152  0.387
2017 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. The Journal of Physical Chemistry. B. PMID 28191969 DOI: 10.1021/Acs.Jpcb.6B09388  0.314
2017 Demir O, Wagner JR, Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Harki D, Aihara H, Amaro RE, Harris RS. Abstract 5236: The dynamic interplay between the cancer genome mutating enzyme APOBEC3B and DNA substrates Cancer Research. 77: 5236-5236. DOI: 10.1158/1538-7445.Am2017-5236  0.614
2017 Schiffer JM, Tien Nguyen T, Demir O, Chan G, Amaro RE, Ghosh G. Construing the Dynamic Complexity at a Plausible IKK2-Nemo Interface Biophysical Journal. 112: 352a. DOI: 10.1016/J.Bpj.2016.11.1912  0.617
2017 Lee C, Moody J, Andrew McCammon J, Holst M, Amaro RE. Investigating Transport Properties with Multi-Scale Computable Mesh Models from Heterogeneous Structural Datasets Biophysical Journal. 112: 293a. DOI: 10.1016/J.Bpj.2016.11.1586  0.513
2016 Akbar R, Jusoh SA, Amaro RE, Helms V. ENRI: A tool for selecting structure-based virtual screening target conformations. Chemical Biology & Drug Design. PMID 27995760 DOI: 10.1111/Cbdd.12900  0.337
2016 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. Nature Structural & Molecular Biology. PMID 27991903 DOI: 10.1038/Nsmb.3344  0.654
2016 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, et al. Rapid Chagas disease drug target discovery using directed evolution in drug-sensitive yeast. Acs Chemical Biology. PMID 27977118 DOI: 10.1021/Acschembio.6B01037  0.377
2016 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. Biophysical Journal. 111: 1631-1640. PMID 27760351 DOI: 10.1016/J.Bpj.2016.08.041  0.321
2016 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 Research. PMID 27744351 DOI: 10.1093/Nar/Gkw917  0.622
2016 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. Journal of Computer-Aided Molecular Design. 30: 651-668. PMID 27696240 DOI: 10.1007/S10822-016-9946-8  0.35
2016 Offutt TL, Swift RV, Amaro RE. Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 27662181 DOI: 10.1021/Acs.Jcim.6B00261  0.37
2016 Demir Ö, Ieong PU, Amaro RE. Full-length p53 tetramer bound to DNA and its quaternary dynamics. Oncogene. 36: 1451-1460. PMID 27641333 DOI: 10.1038/Onc.2016.321  0.642
2016 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 (London, England : 1993). PMID 27396830 DOI: 10.1016/J.Str.2016.05.016  0.573
2016 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, ... ... Amaro RE, et al. Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. Scientific Reports. 6: 27806. PMID 27291296 DOI: 10.1038/Srep27806  0.31
2016 Votapka LW, Lee CT, Amaro RE. Two Relations to Estimate Membrane Permeability Using Milestoning. The Journal of Physical Chemistry. B. PMID 27154639 DOI: 10.1021/Acs.Jpcb.6B02814  0.453
2016 Durrant JD, Bush RM, Amaro RE. Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants. The Journal of Physical Chemistry. B. PMID 27141956 DOI: 10.1021/Acs.Jpcb.6B02655  0.407
2016 Swift RV, Jusoh SA, Offutt TL, Li ES, Amaro RE. Knowledge-Based Methods to Train and Optimize Virtual Screening Ensembles. Journal of Chemical Information and Modeling. PMID 27097522 DOI: 10.1021/Acs.Jcim.5B00684  0.34
2016 Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chemical Reviews. PMID 27074285 DOI: 10.1021/Acs.Chemrev.5B00631  0.584
2016 Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley C, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-based approaches for determining membrane permeability of small compounds. Journal of Chemical Information and Modeling. PMID 27043429 DOI: 10.1021/Acs.Jcim.6B00022  0.489
2016 Malmstrom RD, Kornev AP, Taylor SS, Amaro RE. Protein-Ligand Interactions through the Computational Microscope: Allostery in a Canonical Signaling Domain Biophysical Journal. 110: 52a. DOI: 10.1016/J.Bpj.2015.11.346  0.397
2016 Schiffer J, Sida R, Arciniega D, Malmstrom R, Feher V, Amaro R. Seeing the Unseen: Sampling the Excited State of T4 Lysozyme L99A with Simulations on the Anton Supercomputer Biophysical Journal. 110: 11a-12a. DOI: 10.1016/J.Bpj.2015.11.120  0.318
2015 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 Reports. PMID 26628363 DOI: 10.1016/J.Celrep.2015.10.067  0.66
2015 Votapka LW, Amaro RE. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. Plos Computational Biology. 11: e1004381. PMID 26505480 DOI: 10.1371/Journal.Pcbi.1004381  0.329
2015 Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD. Bridging scales through multiscale modeling: a case study on protein kinase A. Frontiers in Physiology. 6: 250. PMID 26441670 DOI: 10.3389/Fphys.2015.00250  0.373
2015 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 Research. PMID 26400159 DOI: 10.1093/Nar/Gkv938  0.341
2015 Durrant JD, Carlson KE, Martin TA, Offutt TL, Mayne CG, Katzenellenbogen JA, Amaro RE. Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. Journal of Chemical Information and Modeling. 55: 1953-61. PMID 26286148 DOI: 10.1021/Acs.Jcim.5B00241  0.338
2015 Malmstrom RD, Kornev AP, Taylor SS, Amaro RE. Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nature Communications. 6: 7588. PMID 26145448 DOI: 10.1038/Ncomms8588  0.379
2015 Votapka LW, Amaro RE. 38 Multiscale estimation of binding kinetics using molecular dynamics, brownian dynamics, and milestoning. Journal of Biomolecular Structure & Dynamics. 33: 26-7. PMID 26103249 DOI: 10.1080/07391102.2015.1032587  0.336
2015 Ieong P, Amaro RE, Li WW. Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin. Biophysical Journal. 108: 2704-12. PMID 26039171 DOI: 10.1016/J.Bpj.2015.04.025  0.305
2015 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. 54: 1673-80. PMID 25654263 DOI: 10.1021/Bi501420N  0.593
2015 Sørensen J, Demir Ö, Swift RV, Feher VA, Amaro RE. Molecular docking to flexible targets. Methods in Molecular Biology (Clifton, N.J.). 1215: 445-69. PMID 25330975 DOI: 10.1007/978-1-4939-1465-4_20  0.646
2015 Singharoy A, Chandler D, Durrant J, Sener M, Amaro R, Schulten K. The Do's and Do Not's of a 100 Million Atom Molecular Dynamics Simulation Biophysical Journal. 108: 158a. DOI: 10.1016/J.Bpj.2014.11.872  0.326
2014 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 Computer Science. 29: 1745-1755. PMID 29399238 DOI: 10.1016/j.procs.2014.05.159  0.633
2014 Malmstrom RD, Lee CT, Van Wart A, Amaro RE. On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. Journal of Chemical Theory and Computation. 10: 2648-2657. PMID 25473382 DOI: 10.1021/Ct5002363  0.782
2014 Durrant JD, Votapka L, Sørensen J, Amaro RE. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. Journal of Chemical Theory and Computation. 10: 5047-5056. PMID 25400521 DOI: 10.1021/Ct500381C  0.368
2014 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. Biophysical Journal. 107: 1675-85. PMID 25296321 DOI: 10.1016/J.Bpj.2014.08.008  0.48
2014 Demir O, Labaied M, Merritt C, Stuart K, Amaro RE. Computer-aided discovery of Trypanosoma brucei RNA-editing terminal uridylyl transferase 2 inhibitors. Chemical Biology & Drug Design. 84: 131-9. PMID 24903413 DOI: 10.1111/Cbdd.12302  0.651
2014 Van Wart AT, Durrant J, Votapka L, Amaro RE. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. Journal of Chemical Theory and Computation. 10: 511-517. PMID 24803851 DOI: 10.1021/Ct4008603  0.753
2014 Feher VA, Durrant JD, Van Wart AT, Amaro RE. Computational approaches to mapping allosteric pathways. Current Opinion in Structural Biology. 25: 98-103. PMID 24667124 DOI: 10.1016/J.Sbi.2014.02.004  0.749
2014 Chen E, Swift RV, Alderson N, Feher VA, Feng GS, Amaro RE. Computation-guided discovery of influenza endonuclease inhibitors. Acs Medicinal Chemistry Letters. 5: 61-64. PMID 24490002 DOI: 10.1021/Ml4003474  0.32
2013 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. Journal of Molecular Biology. 425: 4442-54. PMID 23938202 DOI: 10.1016/J.Jmb.2013.07.040  0.345
2013 Feher VA, Randall A, Baldi P, Bush RM, de la Maza LM, Amaro RE. A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins. Plos One. 8: e68934. PMID 23935908 DOI: 10.1371/Journal.Pone.0068934  0.324
2013 Park J, Czapla L, Amaro RE. Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding. Journal of Chemical Information and Modeling. 53: 2047-56. PMID 23927370 DOI: 10.1021/Ci400225W  0.391
2013 Demir O, Amaro RE. Designing novel inhibitors of Trypanosoma brucei. Methods in Molecular Biology (Clifton, N.J.). 993: 231-43. PMID 23568474 DOI: 10.1007/978-1-62703-342-8_15  0.663
2013 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. Nature Communications. 4: 1407. PMID 23360998 DOI: 10.1038/Ncomms2361  0.307
2013 Votapka L, Amaro RE. Multistructural hot spot characterization with FTProd. Bioinformatics (Oxford, England). 29: 393-4. PMID 23202744 DOI: 10.1093/Bioinformatics/Bts689  0.4
2013 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? Chemical Biology & Drug Design. 81: 61-71. PMID 23066853 DOI: 10.1111/Cbdd.12074  0.32
2013 Votapka LW, Czapla L, Zhenirovskyy M, Amaro RE. DelEnsembleElec: Computing ensemble-averaged electrostatics using DelPhi Communications in Computational Physics. 13: 256-268. DOI: 10.4208/Cicp.170711.111111S  0.342
2012 Swift RV, Ong CD, Amaro RE. Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme. Biochemistry. 51: 10236-43. PMID 23205906 DOI: 10.1021/Bi301224B  0.302
2012 Vanwart AT, Eargle J, Luthey-Schulten Z, Amaro RE. Exploring residue component contributions to dynamical network models of allostery. Journal of Chemical Theory and Computation. 8: 2949-2961. PMID 23139645 DOI: 10.1021/Ct300377A  0.785
2012 Nichols SE, Swift RV, Amaro RE. Rational prediction with molecular dynamics for hit identification. Current Topics in Medicinal Chemistry. 12: 2002-12. PMID 23110535 DOI: 10.2174/156802612804910313  0.396
2012 Votapka L, Demir O, Swift RV, Walker RC, Amaro RE. Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. Journal of Molecular and Genetic Medicine : An International Journal of Biomedical Research. 6: 293-300. PMID 22872804 DOI: 10.4172/1747-0862.1000052  0.668
2012 Demir Ö, Amaro RE. Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. Journal of Chemical Information and Modeling. 52: 1308-18. PMID 22512810 DOI: 10.1021/Ci3001327  0.657
2012 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. 7: e32217. PMID 22384182 DOI: 10.1371/Journal.Pone.0032217  0.341
2012 Amaro RE, Li WW. Molecular-level simulation of pandemic influenza glycoproteins. Methods in Molecular Biology (Clifton, N.J.). 819: 575-94. PMID 22183559 DOI: 10.1007/978-1-61779-465-0_34  0.342
2011 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 Computational Biology. 7: e1002238. PMID 22028641 DOI: 10.1371/Journal.Pcbi.1002238  0.323
2011 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. 6: e25084. PMID 21966419 DOI: 10.1371/Journal.Pone.0025084  0.384
2011 Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM. Mechanism of 150-cavity formation in influenza neuraminidase. Nature Communications. 2: 388. PMID 21750542 DOI: 10.1038/Ncomms1390  0.332
2010 Durrant JD, Hall L, Swift RV, Landon M, Schnaufer A, Amaro RE. Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1. Plos Neglected Tropical Diseases. 4: e803. PMID 20808768 DOI: 10.1371/Journal.Pntd.0000803  0.379
2010 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: Structure, Function and Bioinformatics. 78: 2523-2532. PMID 20602360 DOI: 10.1002/Prot.22761  0.648
2010 Sung JC, Van Wynsberghe AW, Amaro RE, Li WW, McCammon JA. Role of secondary sialic acid binding sites in influenza N1 neuraminidase. Journal of the American Chemical Society. 132: 2883-5. PMID 20155919 DOI: 10.1021/Ja9073672  0.486
2010 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 Computational Biology. 6: e1000648. PMID 20098496 DOI: 10.1371/Journal.Pcbi.1000648  0.487
2010 Amaro RE, Li WW. Emerging methods for ensemble-based virtual screening. Current Topics in Medicinal Chemistry. 10: 3-13. PMID 19929833 DOI: 10.2174/156802610790232279  0.373
2010 Xu D, Newhouse EI, 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 Biophysical Journal. 98: 568a. DOI: 10.1016/J.Bpj.2009.12.3082  0.525
2009 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. Journal of the American Chemical Society. 131: 17430-42. PMID 19891427 DOI: 10.1021/Ja904052Q  0.522
2009 Wong S, Amaro RE, McCammon JA. MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface. Journal of Chemical Theory and Computation. 5: 422-429. PMID 19461869 DOI: 10.1021/Ct8003707  0.485
2009 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. Journal of Molecular Biology. 387: 465-91. PMID 19356594 DOI: 10.1016/J.Jmb.2009.01.040  0.514
2009 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. Journal of the American Chemical Society. 131: 4702-9. PMID 19296611 DOI: 10.1021/Ja8085643  0.52
2009 Durrant JD, Amaro RE, McCammon JA. AutoGrow: a novel algorithm for protein inhibitor design. Chemical Biology & Drug Design. 73: 168-78. PMID 19207419 DOI: 10.1111/J.1747-0285.2008.00761.X  0.462
2009 Swift RV, Durrant J, Amaro RE, McCammon JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 48: 709-19. PMID 19133737 DOI: 10.1021/Bi8018114  0.444
2008 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. Proceedings of the National Academy of Sciences of the United States of America. 105: 17278-83. PMID 18981420 DOI: 10.1073/Pnas.0805820105  0.509
2008 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. Journal of Medicinal Chemistry. 51: 3878-94. PMID 18558668 DOI: 10.1021/Jm8001197  0.526
2008 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. Chemical Biology & Drug Design. 71: 106-16. PMID 18205727 DOI: 10.1111/J.1747-0285.2007.00614.X  0.495
2008 Amaro RE, Baron R, McCammon JA. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. Journal of Computer-Aided Molecular Design. 22: 693-705. PMID 18196463 DOI: 10.1007/S10822-007-9159-2  0.527
2007 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 Neglected Tropical Diseases. 1: e68. PMID 18060084 DOI: 10.1371/Journal.Pntd.0000068  0.547
2007 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. Journal of the American Chemical Society. 129: 7764-5. PMID 17539643 DOI: 10.1021/Ja0723535  0.517
2007 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. 46: 2156-73. PMID 17261030 DOI: 10.1021/Bi061708E  0.699
2005 Myers RS, Amaro RE, Luthey-Schulten ZA, Davisson VJ. Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase. Biochemistry. 44: 11974-85. PMID 16142895 DOI: 10.1021/Bi050706B  0.594
2005 Amaro RE, Myers RS, Davisson VJ, Luthey-Schulten ZA. Structural elements in IGP synthase exclude water to optimize ammonia transfer. Biophysical Journal. 89: 475-87. PMID 15849257 DOI: 10.1529/Biophysj.104.058651  0.59
2004 Amaro R, Luthey-Schulten Z. Molecular dynamics simulations of substrate channeling through an α-β Barrel protein Chemical Physics. 307: 147-155. DOI: 10.1016/J.Chemphys.2004.05.019  0.59
2003 Amaro R, Tajkhorshidt E, Luthey-Schulten Z. Developing an energy landscape for the novel function of a (β/α)8 barrel: Ammonia conduction through HisF Proceedings of the National Academy of Sciences of the United States of America. 100: 7599-7604. PMID 12799468 DOI: 10.1073/Pnas.1331150100  0.575
2001 O'Donoghue P, Amaro RE, Luthey-Schulten Z. On the structure of hisH: protein structure prediction in the context of structural and functional genomics. Journal of Structural Biology. 134: 257-68. PMID 11551184 DOI: 10.1006/Jsbi.2001.4390  0.738
Low-probability matches (unlikely to be authored by this person)
2012 Jansen JM, Cornell W, Tseng YJ, Amaro RE. Teach-Discover-Treat (TDT): collaborative computational drug discovery for neglected diseases. Journal of Molecular Graphics & Modelling. 38: 360-2. PMID 23085175 DOI: 10.1016/J.Jmgm.2012.07.007  0.299
2016 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. Nature Microbiology. 1: 16155. PMID 27595425 DOI: 10.1038/Nmicrobiol.2016.155  0.298
2019 Luo M, Dommer A, Schiffer JM, Rez DJ, Mitchell A, Amaro RE, Grassian VH. Surfactant Charge Modulates Structure and Stability of Lipase-Embedded Monolayers at Marine-Relevant Aerosol Surfaces. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 31188612 DOI: 10.1021/Acs.Langmuir.9B00689  0.298
2018 Jagger BR, Votapka LW, Amaro RE. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Multiscale Approach for the Calculation of Protein-Ligand Association and Dissociation Kinetics Biophysical Journal. 114: 42a. DOI: 10.1016/J.Bpj.2017.11.281  0.296
2020 Palermo G, Bonvin AMJJ, Dal Peraro M, Amaro RE, Tozzini V. Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations. Frontiers in Molecular Biosciences. 7: 194. PMID 33005628 DOI: 10.3389/Fmolb.2020.00194  0.295
2009 Swift RV, Amaro RE. Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opinion On Drug Discovery. 4: 1281-1294. PMID 20354588 DOI: 10.1517/17460440903373617  0.294
2014 Durrant JD, Amaro RE. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. Bmc Bioinformatics. 15: 159. PMID 24886360 DOI: 10.1186/1471-2105-15-159  0.293
2020 Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. The flexibility of ACE2 in the context of SARS-CoV-2 infection. Biophysical Journal. PMID 33189680 DOI: 10.1016/j.bpj.2020.10.036  0.293
2020 Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. The flexibility of ACE2 in the context of SARS-CoV-2 infection. Biorxiv : the Preprint Server For Biology. PMID 32995769 DOI: 10.1101/2020.09.16.300459  0.291
2019 Altman MO, Angel M, Košík I, Trovão NS, Zost SJ, Gibbs JS, Casalino L, Amaro RE, Hensley SE, Nelson MI, Yewdell JW. Human Influenza A Virus Hemagglutinin Glycan Evolution Follows a Temporal Pattern to a Glycan Limit. Mbio. 10. PMID 30940704 DOI: 10.1128/Mbio.00204-19  0.29
2018 Schiffer JM, Luo M, Dommer AC, Thoron G, Pendergraft MA, Santander MV, Lucero D, Pecora de Barros E, Prather KA, Grassian VH, Amaro RE. Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols. The Journal of Physical Chemistry Letters. PMID 29916254 DOI: 10.1021/Acs.Jpclett.8B01363  0.29
2018 Schiffer JM, Mael LE, Prather KA, Amaro RE, Grassian VH. Sea Spray Aerosol: Where Marine Biology Meets Atmospheric Chemistry. Acs Central Science. 4: 1617-1623. PMID 30648145 DOI: 10.1021/Acscentsci.8B00674  0.288
2011 Swift RV, Amaro RE. Modeling the pharmacodynamics of passive membrane permeability. Journal of Computer-Aided Molecular Design. 25: 1007-17. PMID 22042376 DOI: 10.1007/S10822-011-9480-7  0.288
2020 Ahn S, Jagger B, Amaro RE. Ranking of Ligand Binding Kinetics using a Weighted Ensemble Approach and Comparison with Milestoning Biophysical Journal. 118: 305a. DOI: 10.1016/J.Bpj.2019.11.1725  0.288
2015 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. Journal of Chemical Information and Modeling. 55: 308-16. PMID 25555059 DOI: 10.1021/Ci500405G  0.287
2018 Schiffer J, Amaro R. Atomic-Level Insights into the Dynamics of Enzymes and Intrinsically Disordered Proteins within Sea Spray Aerosol Particles Biophysical Journal. 114: 431a. DOI: 10.1016/J.Bpj.2017.11.2389  0.284
2024 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, ... ... Amaro RE, et al. AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. The International Journal of High Performance Computing Applications. 35: 432-451. PMID 38603008 DOI: 10.1177/10943420211006452  0.284
2020 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, ... ... Amaro RE, et al. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. Biorxiv : the Preprint Server For Biology. PMID 33236007 DOI: 10.1101/2020.11.19.390187  0.284
2012 Jansen JM, Amaro RE, Cornell W, Tseng YJ, Walters WP. Computational chemistry and drug discovery: a call to action. Future Medicinal Chemistry. 4: 1893-6. PMID 23088271 DOI: 10.4155/Fmc.12.137  0.281
2020 Tao A, Pecora E, Barros d, Amaro RE. Improving the Speed and Generality of Machine Learning Approaches to Ligand-binding Protein Design Biophysical Journal. 118: 361a. DOI: 10.1016/J.Bpj.2019.11.2076  0.28
2015 Durrant JD, Amaro RE. Machine-learning techniques applied to antibacterial drug discovery. Chemical Biology & Drug Design. 85: 14-21. PMID 25521642 DOI: 10.1111/Cbdd.12423  0.276
2019 Kochanek SE, Amaro RE. Markov State Model of Influenza Hemagglutinin Reveals Structural Basis for Group 1 Influenza Inhibition by Arbidol Biophysical Journal. 116: 163a-164a. DOI: 10.1016/J.Bpj.2018.11.909  0.276
2017 Amaro RE. Toward Understanding "the Ways" of Allosteric Drugs. Acs Central Science. 3: 925-926. PMID 28979932 DOI: 10.1021/Acscentsci.7B00396  0.273
2020 Amaro RE, Mulholland AJ. A Community Letter Regarding Sharing Bimolecular Simulation Data for COVID-19. Journal of Chemical Information and Modeling. PMID 32255648 DOI: 10.1021/Acs.Jcim.0C00319  0.271
2014 Durrant JD, Amaro RE. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. Plos Computational Biology. 10: e1003720. PMID 25032790 DOI: 10.1371/Journal.Pcbi.1003720  0.268
2018 Nguyen TTT, Schiffer J, Ghosh G, Amaro R. How Lymphoma Mutation Disrupts Functional Conformation of IKK2 Under the Lens of Computational Microscope Biophysical Journal. 114: 48a. DOI: 10.1016/J.Bpj.2017.11.316  0.264
2019 Casalino L, Seitz C, Wilson IA, Amaro RE. Influenza Virulence and Transmissibility through the Computational Microscope Biophysical Journal. 116: 342a. DOI: 10.1016/J.Bpj.2018.11.1862  0.264
2016 Amaro RE. Drug Discovery Gets a Boost from Data Science. Structure (London, England : 1993). 24: 1225-1226. PMID 27486914 DOI: 10.1016/J.Str.2016.07.003  0.262
2020 Gilson MK, Amaro RE. Drug Design Data Resource, Grand Challenge 4, second of two issues. Journal of Computer-Aided Molecular Design. PMID 32016636 DOI: 10.1007/S10822-020-00296-Z  0.253
2017 Hirakis SP, Bartol TM, Sejnowski TJ, Amaro RE. Particle-Based Approaches to Clearing Calcium: a Protein Landscape Model of the Sarco/Endoplasmic Reticulum Calcium-ATPase (SERCA) Pump for Sub-Cellular Stochastic Models Biophysical Journal. 112: 484a. DOI: 10.1016/J.Bpj.2016.11.2618  0.244
2020 Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophysical Journal. PMID 33253634 DOI: 10.1016/j.bpj.2020.10.048  0.242
2020 Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biorxiv : the Preprint Server For Biology. PMID 33024966 DOI: 10.1101/2020.10.02.323915  0.242
2014 Amaro RE, Bansal M. Editorial overview: Theory and simulation: Tools for solving the insolvable. Current Opinion in Structural Biology. 25: iv-v. PMID 24835772 DOI: 10.1016/J.Sbi.2014.04.004  0.242
2020 Dommer AC, Amaro RE. Impacts of Biochemical Complexity on Climate-Relevant Properties of Model Marine Aerosols Biophysical Journal. 118: 553a. DOI: 10.1016/J.Bpj.2019.11.3023  0.238
2018 Amaro RE, Mulholland AJ. Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures. Nature Reviews. Chemistry. 2. PMID 30949587 DOI: 10.1038/s41570-018-0148  0.231
2020 Luo M, Wauer NA, Angle KJ, Dommer AC, Song M, Nowak CM, Amaro RE, Grassian VH. Insights into the behavior of nonanoic acid and its conjugate base at the air/water interface through a combined experimental and theoretical approach Chemical Science. 11: 10647-10656. DOI: 10.1039/D0Sc02354J  0.23
2023 Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chemical Science. 14: 13159-13175. PMID 38023523 DOI: 10.1039/d3sc04195f  0.23
2019 Amaro RE. Will the Real Cryptic Pocket Please Stand Out? Biophysical Journal. PMID 30739726 DOI: 10.1016/J.Bpj.2019.01.018  0.228
2022 Votapka LW, Stokely AM, Ojha AA, Amaro RE. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. Journal of Chemical Information and Modeling. PMID 35759413 DOI: 10.1021/acs.jcim.2c00501  0.225
2019 Palermo G, Sugita Y, Wriggers W, Amaro RE. Frontiers in CryoEM Modeling. Journal of Chemical Information and Modeling. PMID 31192591 DOI: 10.1021/Acs.Jcim.9B00412  0.224
2020 Mazzolari A, Nunes-Alves A, Wahab HA, Amaro RE, Cournia Z, Merz KM. Impact of the Special Issue on Women in Computational Chemistry. Journal of Chemical Information and Modeling. PMID 32623887 DOI: 10.1021/Acs.Jcim.0C00636  0.224
2022 Copeland MM, Do HN, Votapka L, Joshi K, Wang J, Amaro RE, Miao Y. Gaussian Accelerated Molecular Dynamics in OpenMM. The Journal of Physical Chemistry. B. 126: 5810-5820. PMID 35895977 DOI: 10.1021/acs.jpcb.2c03765  0.224
2022 Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. Acs Central Science. 8: 1646-1663. PMID 36589893 DOI: 10.1021/acscentsci.2c00981  0.221
2022 Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities. Biorxiv : the Preprint Server For Biology. PMID 35982676 DOI: 10.1101/2022.08.02.502576  0.22
2017 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. Journal of Computational Science. 20: 205-214. PMID 29104704 DOI: 10.1016/J.Jocs.2017.03.010  0.219
2021 Rathinaswamy MK, Gaieb Z, Fleming KD, Borsari C, Harris NJ, Moeller BJ, Wymann MP, Amaro RE, Burke JE. Disease related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors. Elife. 10. PMID 33661099 DOI: 10.7554/eLife.64691  0.214
2021 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. Development of Dimethylisoxazole-Attached Imidazo[1,2-]pyridines as Potent and Selective CBP/P300 Inhibitors. Journal of Medicinal Chemistry. PMID 33872011 DOI: 10.1021/acs.jmedchem.0c02232  0.214
2020 McCabe KJ, Hirakis SP, Teitgen AE, Duclos AB, Regnier M, Amaro RE, McCulloch AD. Exploring the Effects of 2.Deoxy-ATP on SERCA 2A using Multiscale Modeling Biophysical Journal. 118: 260a. DOI: 10.1016/J.Bpj.2019.11.1508  0.21
2019 Wahab HA, Amaro RE, Cournia Z. A Celebration of Women in Computational Chemistry. Journal of Chemical Information and Modeling. 59: 1683-1692. PMID 31132853 DOI: 10.1021/Acs.Jcim.9B00368  0.21
2018 Wahab HA, Amaro RE, Cournia Z. Women in Computational Chemistry. Journal of Chemical Information and Modeling. PMID 30277769 DOI: 10.1021/Acs.Jcim.8B00642  0.209
2020 Palermo G, Sugita Y, Wriggers W, Amaro RE. Faces of Contemporary CryoEM Information and Modeling. Journal of Chemical Information and Modeling. 60: 2407-2409. PMID 32452204 DOI: 10.1021/Acs.Jcim.0C00481  0.208
2020 Amaro RE, Mulholland AJ. Biomolecular Simulations in the Time of COVID19, and After. Computing in Science & Engineering. 22: 30-36. PMID 33100917 DOI: 10.1109/MCSE.2020.3024155  0.206
2020 Oliveira ASF, Ibarra AA, Bermudez I, Casalino L, Gaieb Z, Shoemark DK, Gallagher T, Sessions RB, Amaro RE, Mulholland AJ. Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors and suggest subtype specificity. Biorxiv : the Preprint Server For Biology. PMID 32743575 DOI: 10.1101/2020.07.16.206680  0.202
2018 Hirakis SP, Bartol TM, Sejnowski TJ, Amaro RE. Molecules to Membranes: The Calcium Release Unit Biophysical Journal. 114: 118a. DOI: 10.1016/J.Bpj.2017.11.678  0.198
2021 Oliveira ASF, Ibarra AA, Bermudez I, Casalino L, Gaieb Z, Shoemark DK, Gallagher T, Sessions RB, Amaro RE, Mulholland AJ. A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors. Biophysical Journal. PMID 33609494 DOI: 10.1016/j.bpj.2021.01.037  0.195
2016 Bateman RM, Sharpe MD, Jagger JE, Ellis CG, Solé-Violán J, López-Rodríguez M, Herrera-Ramos E, Ruíz-Hernández J, Borderías L, Horcajada J, González-Quevedo N, Rajas O, Briones M, Rodríguez de Castro F, Rodríguez Gallego C, ... ... Amaro R, et al. Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016. Critical Care (London, England). 20: 347. PMID 31268434 DOI: 10.1186/S13054-016-1358-6  0.192
2016 Bateman RM, Sharpe MD, Jagger JE, Ellis CG, Solé-Violán J, López-Rodríguez M, Herrera-Ramos E, Ruíz-Hernández J, Borderías L, Horcajada J, González-Quevedo N, Rajas O, Briones M, Castro FRd, Gallego CR, ... ... Amaro R, et al. 36th International Symposium on Intensive Care and Emergency Medicine Critical Care. 20: 94. PMID 27885969 DOI: 10.1186/S13054-016-1208-6  0.186
2023 Jones KFM, Shehata M, Carpenter MA, Amaro RE, Harki DA. APOBEC3A Catalytic Inactivity Mutation Induces Tertiary Structure Destabilization. Acs Medicinal Chemistry Letters. 14: 338-343. PMID 36923917 DOI: 10.1021/acsmedchemlett.2c00517  0.183
2023 Ojha AA, Thakur S, Ahn SH, Amaro RE. DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling. Journal of Chemical Theory and Computation. PMID 36719802 DOI: 10.1021/acs.jctc.2c00282  0.181
2021 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, et al. A critical overview of computational approaches employed for COVID-19 drug discovery. Chemical Society Reviews. PMID 34212944 DOI: 10.1039/d0cs01065k  0.175
2023 Ojha AA, Srivastava A, Votapka LW, Amaro RE. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. Journal of Chemical Information and Modeling. PMID 37023323 DOI: 10.1021/acs.jcim.2c01589  0.174
2017 Amaro RE, Villa E, Luthey-Schulten Z. Biography of Klaus Schulten. The Journal of Physical Chemistry. B. 121: 3206. PMID 28423903 DOI: 10.1021/Acs.Jpcb.7B02141  0.173
2023 Soares TA, Cournia Z, Naidoo K, Amaro R, Wahab H, Merz KM. Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. Journal of Chemical Information and Modeling. PMID 37191169 DOI: 10.1021/acs.jcim.3c00599  0.17
2017 Amaro RE. A Reflection on Klaus Schulten. Journal of Chemical Theory and Computation. 13: 1-2. PMID 28068772 DOI: 10.1021/Acs.Jctc.6B01111  0.163
2021 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, et al. SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34417349 DOI: 10.1073/pnas.2103154118  0.163
2016 Amaro RE, Madura JD, Wong CF. Tribute to J. Andrew McCammon. The Journal of Physical Chemistry. B. 120: 8055-6. PMID 27558538 DOI: 10.1021/Acs.Jpcb.6B07015  0.159
2020 Andreano E, Piccini G, Licastro D, Casalino L, Johnson NV, Paciello I, Monego SD, Pantano E, Manganaro N, Manenti A, Manna R, Casa E, Hyseni I, Benincasa L, Montomoli E, ... Amaro RE, et al. SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Biorxiv : the Preprint Server For Biology. PMID 33398278 DOI: 10.1101/2020.12.28.424451  0.157
2012 Swift RV, Amaro RE. Chapter 12: Molecular simulation in computer-aided drug design: Algorithms and applications Rsc Biomolecular Sciences. 281-315.  0.153
2024 McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell. 187: 563-584. PMID 38306982 DOI: 10.1016/j.cell.2024.01.005  0.151
2023 Dommer AC, Wauer NA, Angle KJ, Davasam A, Rubio P, Luo M, Morris CK, Prather KA, Grassian VH, Amaro RE. Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology. Acs Central Science. 9: 1088-1103. PMID 37396863 DOI: 10.1021/acscentsci.3c00184  0.149
2017 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. Nature Microbiology. 2: 17107. PMID 28604710 DOI: 10.1038/nmicrobiol.2017.107  0.145
2022 Oliveira AA, Róg T, da Silva ABF, Amaro RE, Johnson MS, Postila PA. Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations. Biomolecules. 12. PMID 35204684 DOI: 10.3390/biom12020183  0.145
2020 Martin BT, Malmstrom RD, Amaro RE, Wüthrich K. OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring Flip Frequencies by Integrated Use of 1H-NMR and Molecular Dynamics Simulations. Chembiochem : a European Journal of Chemical Biology. PMID 32975902 DOI: 10.1002/cbic.202000517  0.137
2024 Kim JH, Shivkumar A, Norimoto M, Castro Lingl S, Seitz C, Amaro RE, Gonias SL, Yang J, Campana WM. Binding and Activation of LRP1-Dependent Cell Signaling in Schwann Cells Using a Peptide Derived from the Hemopexin Domain of MMP-9. Biochemistry. PMID 38450612 DOI: 10.1021/acs.biochem.3c00705  0.118
2021 Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Reports. 37: 109840. PMID 34686332 DOI: 10.1016/j.celrep.2021.109840  0.112
2020 Amaro RE, Mulholland AJ. Biomolecular Simulations in the Time of COVID-19, and After Computing in Science & Engineering. 22: 30-36. DOI: 10.1109/MCSE.2020.3024155  0.107
2015 Malmstrom RD, Kornev AP, Taylor SS, Amaro RE. Allostery through the computational microscope: CAMP activation of a canonical signalling domain Nature Communications. 6. DOI: 10.1038/ncomms8588  0.107
2020 Luo M, Wauer NA, Angle KJ, Dommer AC, Song M, Nowak CM, Amaro RE, Grassian VH. Insights into the behavior of nonanoic acid and its conjugate base at the air/water interface through a combined experimental and theoretical approach. Chemical Science. 11: 10647-10656. PMID 33144932 DOI: 10.1039/d0sc02354j  0.105
2021 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, et al. Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nature Communications. 12: 856. PMID 33558528 DOI: 10.1038/s41467-020-18911-w  0.104
2022 Cournia Z, Soares TA, Wahab HA, Amaro RE. Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. Journal of Chemical Information and Modeling. 62: 6287-6291. PMID 36567670 DOI: 10.1021/acs.jcim.2c01543  0.104
2022 Angle KJ, Nowak CM, Davasam A, Dommer AC, Wauer NA, Amaro RE, Grassian VH. Amino Acids Are Driven to the Interface by Salts and Acidic Environments. The Journal of Physical Chemistry Letters. 13: 2824-2829. PMID 35324217 DOI: 10.1021/acs.jpclett.2c00231  0.098
2016 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 Computer Science. 80: 1791-1800. PMID 27478519 DOI: 10.1016/j.procs.2016.05.454  0.096
2020 Mulholland AJ, Amaro RE. COVID19 - Computational Chemists Meet the Moment. Journal of Chemical Information and Modeling. 60: 5724-5726. PMID 33378852 DOI: 10.1021/acs.jcim.0c01395  0.083
2021 Carter-Fenk KA, Dommer AC, Fiamingo ME, Kim J, Amaro RE, Allen HC. Calcium bridging drives polysaccharide co-adsorption to a proxy sea surface microlayer. Physical Chemistry Chemical Physics : Pccp. PMID 34318808 DOI: 10.1039/d1cp01407b  0.081
2020 Merz KM, Amaro R, Cournia Z, Rarey M, Soares T, Tropsha A, Wahab HA, Wang R. Editorial: Method and Data Sharing and Reproducibility of Scientific Results. Journal of Chemical Information and Modeling. 60: 5868-5869. PMID 33378854 DOI: 10.1021/acs.jcim.0c01389  0.071
2022 Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Reports. 38: 110578. PMID 35320719 DOI: 10.1016/j.celrep.2022.110578  0.056
2021 Cournia Z, Soares TA, Wahab HA, Amaro RE. Advancing Women in Chemistry. Journal of Chemical Information and Modeling. 61: 5305-5306. PMID 34668709 DOI: 10.1021/acs.jcim.1c01185  0.021
2022 Herbert JM, Head-Gordon M, Hratchian HP, Head-Gordon T, Amaro RE, Aspuru-Guzik A, Hoffmann R, Parish CA, Payne CM, Van Voorhis T. Words Matter: On the Debate over Free Speech, Inclusivity, and Academic Excellence. The Journal of Physical Chemistry Letters. 13: 7100-7104. PMID 35924341 DOI: 10.1021/acs.jpclett.2c02242  0.011
2014 Ieong PU, Sørensen J, Vemu PL, Wong CW, Demir O, Williams NP, Wang J, Crawl D, Swift RV, Malmstrom RD, Altintas I, Amaro RE. Progres Procedia Computer Science. 29: 1745-1755. DOI: 10.1016/j.procs.2014.05.159  0.01
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