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Items: 1 to 50 of 109


Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α.

Spiriti J, Subramanian SR, Palli R, Wu M, Zuckerman DM.

PLoS One. 2019 Apr 23;14(4):e0215694. doi: 10.1371/journal.pone.0215694. eCollection 2019.


Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping.

Mostofian B, Zuckerman DM.

J Chem Theory Comput. 2019 Jun 11;15(6):3499-3509. doi: 10.1021/acs.jctc.9b00015. Epub 2019 May 7.


Computational Estimation of Microsecond to Second Atomistic Folding Times.

Adhikari U, Mostofian B, Copperman J, Subramanian SR, Petersen AA, Zuckerman DM.

J Am Chem Soc. 2019 Apr 24;141(16):6519-6526. doi: 10.1021/jacs.8b10735. Epub 2019 Apr 12.


Structure of native lens connexin 46/50 intercellular channels by cryo-EM.

Myers JB, Haddad BG, O'Neill SE, Chorev DS, Yoshioka CC, Robinson CV, Zuckerman DM, Reichow SL.

Nature. 2018 Dec;564(7736):372-377. doi: 10.1038/s41586-018-0786-7. Epub 2018 Dec 12.


Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].

Grossfield A, Patrone PN, Roe DR, Schultz AJ, Siderius DW, Zuckerman DM.

Living J Comput Mol Sci. 2018;1(1). pii: 5067. doi: 10.33011/livecoms.1.1.5067. Epub 2018 Oct 27.


Diversity in Medical Device Clinical Trials: Do We Know What Works for Which Patients?

Fox-Rawlings SR, Gottschalk LB, Doamekpor LA, Zuckerman DM.

Milbank Q. 2018 Sep;96(3):499-529. doi: 10.1111/1468-0009.12344.


Preface: Special Topic on Enhanced Sampling for Molecular Systems.

Laio A, Panagiotopoulos AZ, Zuckerman DM.

J Chem Phys. 2018 Aug 21;149(7):072001. doi: 10.1063/1.5049669.


Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways.

Nunes-Alves A, Zuckerman DM, Arantes GM.

Biophys J. 2018 Mar 13;114(5):1058-1066. doi: 10.1016/j.bpj.2018.01.014.


Supramolecular self assembly of nanodrill-like structures for intracellular delivery.

Ashwanikumar N, Plaut JS, Mostofian B, Patel S, Kwak P, Sun C, McPhail K, Zuckerman DM, Esener SC, Sahay G.

J Control Release. 2018 Jul 28;282:76-89. doi: 10.1016/j.jconrel.2018.02.041. Epub 2018 Mar 1.


Clinically Observed Estrogen Receptor Alpha Mutations within the Ligand-Binding Domain Confer Distinguishable Phenotypes.

Jia S, Miedel MT, Ngo M, Hessenius R, Chen N, Wang P, Bahreini A, Li Z, Ding Z, Shun TY, Zuckerman DM, Taylor DL, Puhalla SL, Lee AV, Oesterreich S, Stern AM.

Oncology. 2018;94(3):176-189. doi: 10.1159/000485510. Epub 2018 Jan 6.


Systematic Testing of Belief-Propagation Estimates for Absolute Free Energies in Atomistic Peptides and Proteins.

Donovan-Maiye RM, Langmead CJ, Zuckerman DM.

J Chem Theory Comput. 2018 Jan 9;14(1):426-443. doi: 10.1021/acs.jctc.7b00775. Epub 2017 Dec 22.


Can the FDA Help Reduce Drug Prices or the Cost of Medical Care?

Zuckerman DM.

Am J Public Health. 2017 Nov;107(11):1752-1754. doi: 10.2105/AJPH.2017.304093. No abstract available.


Electronic Health Records.

Ronquillo JG, Zuckerman DM.

Ann Intern Med. 2017 Apr 4;166(7):536. doi: 10.7326/L17-0050. No abstract available.


Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio.

Anandakrishnan R, Zuckerman DM.

PLoS One. 2017 Mar 20;12(3):e0173500. doi: 10.1371/journal.pone.0173500. eCollection 2017.


Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.

Zuckerman DM, Chong LT.

Annu Rev Biophys. 2017 May 22;46:43-57. doi: 10.1146/annurev-biophys-070816-033834. Epub 2017 Mar 1. Review.


Path-sampling strategies for simulating rare events in biomolecular systems.

Chong LT, Saglam AS, Zuckerman DM.

Curr Opin Struct Biol. 2017 Apr;43:88-94. doi: 10.1016/ Epub 2016 Dec 13. Review.


Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg2+ Titration Analysis for HIV-1 Ribonuclease H Domain.

Karki I, Christen MT, Spiriti J, Slack RL, Oda M, Kanaori K, Zuckerman DM, Ishima R.

J Phys Chem B. 2016 Dec 15;120(49):12420-12431. Epub 2016 Dec 5.


A Major Shortcoming in the Public Health Legacy of the Obama Administration.

Zuckerman DM.

Am J Public Health. 2017 Jan;107(1):29-30. No abstract available.


Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process.

Anandakrishnan R, Zhang Z, Donovan-Maiye R, Zuckerman DM.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11220-11225. Epub 2016 Sep 19.


Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide.

Zwier MC, Pratt AJ, Adelman JL, Kaus JW, Zuckerman DM, Chong LT.

J Phys Chem Lett. 2016 Sep 1;7(17):3440-5. doi: 10.1021/acs.jpclett.6b01502. Epub 2016 Aug 22.


Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.

Suárez E, Adelman JL, Zuckerman DM.

J Chem Theory Comput. 2016 Aug 9;12(8):3473-81. doi: 10.1021/acs.jctc.6b00339. Epub 2016 Jul 11.


Breast Implants, Self-Esteem, Quality of Life, and the Risk of Suicide.

Zuckerman DM, Kennedy CE, Terplan M.

Womens Health Issues. 2016 Jul-Aug;26(4):361-5. doi: 10.1016/j.whi.2016.03.002. Epub 2016 Apr 16. No abstract available.


Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.

Donovan RM, Tapia JJ, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, Zuckerman DM.

PLoS Comput Biol. 2016 Feb 4;12(2):e1004611. doi: 10.1371/journal.pcbi.1004611. eCollection 2016 Feb.


21st Century Cures Act and similar policy efforts: at what cost?

Zuckerman DM, Jury NJ, Silcox CE.

BMJ. 2015 Nov 23;351:h6122. doi: 10.1136/bmj.h6122. No abstract available.


WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis.

Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suárez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT.

J Chem Theory Comput. 2015 Feb 10;11(2):800-9. doi: 10.1021/ct5010615.


Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.

Suárez E, Pratt AJ, Chong LT, Zuckerman DM.

Protein Sci. 2016 Jan;25(1):67-78. doi: 10.1002/pro.2738. Epub 2015 Sep 9.


Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase.

Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R.

Proteins. 2015 Aug;83(8):1526-38. doi: 10.1002/prot.24843. Epub 2015 Jul 1.


Cell rejuvenation and social behaviors promoted by LPS exchange in myxobacteria.

Vassallo C, Pathak DT, Cao P, Zuckerman DM, Hoiczyk E, Wall D.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2939-46. doi: 10.1073/pnas.1503553112. Epub 2015 May 18.


Sufficiency of Information in 510(k) Summaries-Reply.

Zuckerman DM, Brown P.

JAMA Intern Med. 2015 May;175(5):864. doi: 10.1001/jamainternmed.2015.84. No abstract available.


The bactofilin cytoskeleton protein BacM of Myxococcus xanthus forms an extended β-sheet structure likely mediated by hydrophobic interactions.

Zuckerman DM, Boucher LE, Xie K, Engelhardt H, Bosch J, Hoiczyk E.

PLoS One. 2015 Mar 24;10(3):e0121074. doi: 10.1371/journal.pone.0121074. eCollection 2015.


Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations.

Spiriti J, Zuckerman DM.

J Chem Theory Comput. 2014 Nov 11;10(11):5161-5177. Epub 2014 Oct 9.


Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.

Suárez E, Lettieri S, Zwier MC, Stringer CA, Subramanian SR, Chong LT, Zuckerman DM.

J Chem Theory Comput. 2014 Jul 8;10(7):2658-2667. Epub 2014 Mar 3.


Lack of diversity in cancer drug clinical trials may exacerbate racial disparities in mortality rates.

Doamekpor LA, Zuckerman DM.

Cancer Epidemiol. 2014 Oct;38(5):645-6. doi: 10.1016/j.canep.2014.06.007. Epub 2014 Jul 19. No abstract available.


Comment on "Silicone wristbands as personal passive samplers".

Mazzucco AE, Zuckerman DM.

Environ Sci Technol. 2014;48(15):8926. doi: 10.1021/es502594c. Epub 2014 Jul 10. No abstract available.


Regulatory reticence and medical devices.

Fox DM, Zuckerman DM.

Milbank Q. 2014 Mar;92(1):151-9. doi: 10.1111/1468-0009.12044. No abstract available.


Three basic residues of intracellular loop 3 of the beta-1 adrenergic receptor are required for golgin-160-dependent trafficking.

Gilbert CE, Zuckerman DM, Currier PL, Machamer CE.

Int J Mol Sci. 2014 Feb 20;15(2):2929-45. doi: 10.3390/ijms15022929.


Sambucus nigra extracts inhibit infectious bronchitis virus at an early point during replication.

Chen C, Zuckerman DM, Brantley S, Sharpe M, Childress K, Hoiczyk E, Pendleton AR.

BMC Vet Res. 2014 Jan 16;10:24. doi: 10.1186/1746-6148-10-24.


Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.

Donovan RM, Sedgewick AJ, Faeder JR, Zuckerman DM.

J Chem Phys. 2013 Sep 21;139(11):115105. doi: 10.1063/1.4821167.


Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.

Mamonov AB, Lettieri S, Ding Y, Sarver JL, Palli R, Cunningham TF, Saxena S, Zuckerman DM.

J Chem Theory Comput. 2012 Aug 14;8(8):2921-2929. Epub 2012 Jun 15.


Simulations of the alternating access mechanism of the sodium symporter Mhp1.

Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, Grabe M.

Biophys J. 2011 Nov 16;101(10):2399-407. doi: 10.1016/j.bpj.2011.09.061. Epub 2011 Nov 15.


Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?

Bhatt D, Zuckerman DM.

J Chem Theory Comput. 2011 Aug 9;7(8):2520-2527.


Differential regulation of two palmitoylation sites in the cytoplasmic tail of the beta1-adrenergic receptor.

Zuckerman DM, Hicks SW, Charron G, Hang HC, Machamer CE.

J Biol Chem. 2011 May 27;286(21):19014-23. doi: 10.1074/jbc.M110.189977. Epub 2011 Apr 4.


Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.

Lettieri S, Mamonov AB, Zuckerman DM.

J Comput Chem. 2011 Apr 30;32(6):1135-43. doi: 10.1002/jcc.21695. Epub 2010 Nov 29.


Equilibrium sampling in biomolecular simulations.

Zuckerman DM.

Annu Rev Biophys. 2011;40:41-62. doi: 10.1146/annurev-biophys-042910-155255. Review.


Medical device recalls and the FDA approval process.

Zuckerman DM, Brown P, Nissen SE.

Arch Intern Med. 2011 Jun 13;171(11):1006-11. doi: 10.1001/archinternmed.2011.30. Epub 2011 Feb 14.


Automated sampling assessment for molecular simulations using the effective sample size.

Zhang X, Bhatt D, Zuckerman DM.

J Chem Theory Comput. 2010 Sep 1;6(10):3048-3057.

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