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

96 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.44
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  0.36
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  0.84
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  0.84
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  0.36
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  0.44
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  0.6
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  0.84
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  0.36
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  0.36
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  0.44
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  0.68
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  0.68
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  0.72
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  0.68
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  0.64
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  0.44
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  0.68
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  0.44
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  0.44
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  0.72
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  0.72
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  0.84
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.68
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  0.6
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.68
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
2013 Votapka L, Amaro RE. Multistructural hot spot characterization with FTProd. Bioinformatics (Oxford, England). 29: 393-4. PMID 23202744 DOI: 10.1093/bioinformatics/bts689  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.44
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  0.72
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  0.72
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  0.72
2012 Swift RV, Amaro RE. Chapter 12: Molecular simulation in computer-aided drug design: Algorithms and applications Rsc Biomolecular Sciences. 281-315.  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.44
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.44
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.44
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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