| Year |
Citation |
Score |
| 2023 |
Bogetti AT, Leung JMG, Russo JD, Zhang S, Thompson JP, Saglam AS, Ray D, Mostofian B, Pratt AJ, Abraham RC, Harrison PO, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, ... ... Zuckerman DM, et al. A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]. Living Journal of Computational Molecular Science. 5. PMID 37200895 DOI: 10.33011/livecoms.5.1.1655 |
0.767 |
|
| 2022 |
Russo JD, Zhang S, Leung JMG, Bogetti AT, Thompson JP, DeGrave AJ, Torrillo PA, Pratt AJ, Wong KF, Xia J, Copperman J, Adelman JL, Zwier MC, LeBard DN, Zuckerman DM, et al. WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications. Journal of Chemical Theory and Computation. PMID 35043623 DOI: 10.1021/acs.jctc.1c01154 |
0.757 |
|
| 2021 |
Suárez E, Wiewiora RP, Wehmeyer C, Noé F, Chodera JD, Zuckerman DM. What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models. Journal of Chemical Theory and Computation. PMID 33904312 DOI: 10.1021/acs.jctc.0c01154 |
0.308 |
|
| 2020 |
Copperman J, Zuckerman DM. Accelerated estimation of long-timescale kinetics from weighted ensemble simulation via non-Markovian "microbin" analysis. Journal of Chemical Theory and Computation. PMID 32990438 DOI: 10.1021/acs.jctc.0c00273 |
0.412 |
|
| 2020 |
Flores JA, Haddad BG, Dolan KA, Myers JB, Yoshioka CC, Copperman J, Zuckerman DM, Reichow SL. Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å. Nature Communications. 11: 4331. PMID 32859914 DOI: 10.1038/S41467-020-18120-5 |
0.742 |
|
| 2020 |
Bisignano P, Lee MA, George A, Zuckerman DM, Grabe M, Rosenberg JM. A kinetic mechanism for enhanced selectivity of membrane transport. Plos Computational Biology. 16: e1007789. PMID 32614861 DOI: 10.1371/Journal.Pcbi.1007789 |
0.305 |
|
| 2020 |
George A, Bisignano P, Rosenberg JM, Grabe M, Zuckerman DM. A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms. Plos Computational Biology. 16: e1007884. PMID 32614821 DOI: 10.1371/Journal.Pcbi.1007884 |
0.399 |
|
| 2020 |
Chen KY, Zuckerman DM, Nelson PC. Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells The Biophysicist. 1. DOI: 10.35459/Tbp.2019.000101 |
0.377 |
|
| 2020 |
Aristoff D, Zuckerman DM. Optimizing Weighted Ensemble Sampling of Steady States Multiscale Modeling & Simulation. 18: 646-673. DOI: 10.1137/18M1212100 |
0.317 |
|
| 2020 |
Zuckerman DM. Key biology you should have learned in physics class: Using ideal-gas mixtures to understand biomolecular machines American Journal of Physics. 88: 182-193. DOI: 10.1119/10.0000634 |
0.316 |
|
| 2020 |
Haddad BG, Flores JA, Dolan KA, Myers JB, Yoshioka CC, Zuckerman DM, Reichow SL. Visualization of Protein-Lipid Interactions in Connexin-46/50 Intercellular Channels by Cryo-EM and MD-Simulation Biophysical Journal. 118: 497a. DOI: 10.1016/J.Bpj.2019.11.2748 |
0.334 |
|
| 2020 |
Copperman JT, Zuckerman DM. Accelerated Estimation of Long-timescale Kinetics by Combining Weighted Ensemble Simulation with Markov Model “Microstates” using Non-Markovian Theory Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.1099 |
0.476 |
|
| 2019 |
Bogetti AT, Mostofian B, Dickson A, Pratt AJ, Saglam AS, Harrison PO, Adelman JL, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, Zwier MC, Zuckerman DM, Chong LT. A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]. Living Journal of Computational Molecular Science. 1. PMID 32395705 DOI: 10.33011/livecoms.1.2.10607 |
0.76 |
|
| 2019 |
Copperman J, Aristoff D, Makarov DE, Simpson G, Zuckerman DM. Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture. The Journal of Chemical Physics. 151: 174108. PMID 31703496 DOI: 10.1063/1.5120511 |
0.341 |
|
| 2019 |
Spiriti J, Subramanian SR, Palli R, Wu M, Zuckerman DM. Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α. Plos One. 14: e0215694. PMID 31013302 DOI: 10.1371/Journal.Pone.0215694 |
0.406 |
|
| 2019 |
Mostofian B, Zuckerman DM. Statistical uncertainty analysis for small-sample, high log-variance data: Cautions for bootstrapping and Bayesian bootstrapping. Journal of Chemical Theory and Computation. PMID 31002504 DOI: 10.1021/Acs.Jctc.9B00015 |
0.41 |
|
| 2019 |
Adhikari U, Mostofian B, Copperman J, Subramanian SR, Petersen A, Zuckerman DM. Computational estimation of ms-sec atomistic folding times. Journal of the American Chemical Society. PMID 30892023 DOI: 10.1021/Jacs.8B10735 |
0.432 |
|
| 2019 |
Mostofian B, Zuckerman DM. Error Analysis for Small-Sample, High-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping Biophysical Journal. 116: 140a. DOI: 10.1016/J.Bpj.2018.11.779 |
0.425 |
|
| 2018 |
Grossfield A, Patrone PN, Roe DR, Schultz AJ, Siderius DW, Zuckerman DM. Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 1. PMID 30533602 |
0.659 |
|
| 2018 |
Laio A, Panagiotopoulos AZ, Zuckerman DM. Preface: Special Topic on Enhanced Sampling for Molecular Systems. The Journal of Chemical Physics. 149: 072001. PMID 30134673 DOI: 10.1063/1.5049669 |
0.442 |
|
| 2018 |
Nunes-Alves A, Zuckerman DM, Arantes GM. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. Biophysical Journal. 114: 1058-1066. PMID 29539393 DOI: 10.1016/J.Bpj.2018.01.014 |
0.437 |
|
| 2018 |
Ashwanikumar N, Plaut JS, Mostofian B, Patel S, Kwak P, Sun C, McPhail K, Zuckerman DM, Esener SC, Sahay G. Supramolecular self assembly of nanodrill-like structures for intracellular delivery. Journal of Controlled Release : Official Journal of the Controlled Release Society. PMID 29501722 DOI: 10.1016/J.Jconrel.2018.02.041 |
0.308 |
|
| 2018 |
Pratt A, Zuckerman DM, Chong LT. WESTPA 2.0 Advances in Sampling, Storage, and Analysis of Weighted Ensemble Simulations Biophysical Journal. 114: 677a. DOI: 10.1016/J.Bpj.2017.11.3650 |
0.423 |
|
| 2018 |
Mostofian B, Adhikari U, Zuckerman DM. Statistically Reliable Molecular Dynamics Simulations of Transient Conformational Changes in the Estrogen Receptor Biophysical Journal. 114: 674a. DOI: 10.1016/J.Bpj.2017.11.3635 |
0.394 |
|
| 2018 |
Adhikari U, Mostofian B, Zuckerman DM. Weighted Ensemble Simulation Studies of Millisecond Folder NTL9 Biophysical Journal. 114: 558a. DOI: 10.1016/J.Bpj.2017.11.3048 |
0.39 |
|
| 2017 |
Donovan-Maiye RM, Langmead CJ, Zuckerman DM. Systematic Testing of Belief-Propagation Estimates for Absolute Free Energies in Atomistic Peptides and Proteins. Journal of Chemical Theory and Computation. PMID 29185777 DOI: 10.1021/Acs.Jctc.7B00775 |
0.392 |
|
| 2017 |
Zuckerman DM, Chong LT. Weighted Ensemble Simulation: Review of Methodology, Applications, and Software. Annual Review of Biophysics. PMID 28301772 DOI: 10.1146/Annurev-Biophys-070816-033834 |
0.484 |
|
| 2017 |
Suárez E, Adelman JL, Zuckerman DM. Mechanism Beyond Markov Models: History Information is Needed for Unbiased Pathway Reconstruction of Protein Folding Biophysical Journal. 112: 289a-290a. DOI: 10.1016/J.Bpj.2016.11.1569 |
0.751 |
|
| 2016 |
Chong LT, Saglam AS, Zuckerman DM. Path-sampling strategies for simulating rare events in biomolecular systems. Current Opinion in Structural Biology. 43: 88-94. PMID 27984811 DOI: 10.1016/J.Sbi.2016.11.019 |
0.478 |
|
| 2016 |
Zwier MC, Pratt A, Adelman JL, Kaus JW, Zuckerman DM, Chong LT. 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. The Journal of Physical Chemistry Letters. PMID 27532687 DOI: 10.1021/Acs.Jpclett.6B01502 |
0.744 |
|
| 2016 |
Suárez E, Adelman JL, Zuckerman DM. Accurate estimation of protein folding and unfolding times: Beyond Markov state models. Journal of Chemical Theory and Computation. PMID 27340835 DOI: 10.1021/Acs.Jctc.6B00339 |
0.749 |
|
| 2016 |
Donovan RM, Tapia JJ, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, Zuckerman DM. Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. Plos Computational Biology. 12: e1004611. PMID 26845334 DOI: 10.1371/Journal.Pcbi.1004611 |
0.475 |
|
| 2016 |
Suarez E, Zuckerman DM. Improved Estimation of Long-Time Kinetics using Non-Markovian Analysis of Trajectory Segments: Application to Protein Folding and Unfolding Biophysical Journal. 110: 642a. DOI: 10.1016/J.Bpj.2015.11.3434 |
0.414 |
|
| 2015 |
Spiriti J, Zuckerman DM. Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits. The Journal of Chemical Physics. 143: 243159. PMID 26723644 DOI: 10.1063/1.4938479 |
0.442 |
|
| 2015 |
Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suárez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT. WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis. Journal of Chemical Theory and Computation. 11: 800-809. PMID 26392815 DOI: 10.1021/Ct5010615 |
0.773 |
|
| 2015 |
Suárez E, Pratt AJ, Chong LT, Zuckerman DM. Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. Protein Science : a Publication of the Protein Society. PMID 26131764 DOI: 10.1002/Pro.2738 |
0.446 |
|
| 2015 |
Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suárez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT. WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis Journal of Chemical Theory and Computation. 11: 800-809. DOI: 10.1021/ct5010615 |
0.722 |
|
| 2015 |
Suarez E, Zuckerman DM. Non-Markovian Analyses for Extracting Long-Time Behavior from Molecular Simulation Trajectories Biophysical Journal. 108: 160a. DOI: 10.1016/J.Bpj.2014.11.883 |
0.367 |
|
| 2015 |
Spiriti JM, Zuckerman DM. Energy Tabulation Strategies for Accelerated Monte Carlo Simulation at Multiple Length Scales Biophysical Journal. 108: 472a-473a. DOI: 10.1016/J.Bpj.2014.11.2583 |
0.446 |
|
| 2015 |
Subramanian SR, Zuckerman DM. Docking to the Highly Flexible Estrogen Receptor Ligand Binding Domain via Mixed-Resolution Monte Carlo Biophysical Journal. 108: 319a. DOI: 10.1016/J.Bpj.2014.11.1735 |
0.327 |
|
| 2014 |
Spiriti J, Zuckerman DM. Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations. Journal of Chemical Theory and Computation. 10: 5161-5177. PMID 25400525 DOI: 10.1021/Ct500622Z |
0.476 |
|
| 2014 |
Suárez E, Lettieri S, Zwier MC, Stringer CA, Subramanian SR, Chong LT, Zuckerman DM. Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories. Journal of Chemical Theory and Computation. 10: 2658-2667. PMID 25246856 DOI: 10.1021/Ct401065R |
0.473 |
|
| 2014 |
Palli R, Subramanian SR, Zuckerman DM. Mixed-Resolution Monte Carlo: Application to Flexible Docking of the Estrogen Receptor Biophysical Journal. 106: 475a. DOI: 10.1016/J.Bpj.2013.11.2685 |
0.306 |
|
| 2014 |
Subramanian SR, Palli R, Zuckerman DM. Mixed-Resolution Monte Carlo: A Tool for Sampling Proteins and Ligands Biophysical Journal. 106: 412a. DOI: 10.1016/J.Bpj.2013.11.2320 |
0.369 |
|
| 2014 |
Spiriti JM, Zuckerman DM. A New Strategy for Coarse-Grained Protein Simulations: Smoothed Energy Tables Biophysical Journal. 106: 412a. DOI: 10.1016/J.Bpj.2013.11.2319 |
0.472 |
|
| 2013 |
Donovan RM, Sedgewick AJ, Faeder JR, Zuckerman DM. Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories. The Journal of Chemical Physics. 139: 115105. PMID 24070313 DOI: 10.1063/1.4821167 |
0.47 |
|
| 2013 |
Subramanian SR, Zuckerman DM. Conformation-Switching in Adenylate Kinase Revisited with a Path-Ensemble Simulation Biophysical Journal. 104: 69a-70a. DOI: 10.1016/J.Bpj.2012.11.421 |
0.45 |
|
| 2013 |
Zuckerman DM. Simultaneous Calculation of Dynamical and Equilibrium Properties of Atomistic Systems using an Ensemble of Weighted Trajectories Biophysical Journal. 104: 496a. DOI: 10.1016/J.Bpj.2012.11.2735 |
0.503 |
|
| 2013 |
Suarez E, Petersen A, Lettieri S, Zuckerman DM. Small Protein Folding using Weighted Ensemble Simulation: A Case Study of Trp-Cage Biophysical Journal. 104: 398a. DOI: 10.1016/J.Bpj.2012.11.2218 |
0.448 |
|
| 2012 |
Mamonov AB, Lettieri S, Ding Y, Sarver JL, Palli R, Cunningham TF, Saxena S, Zuckerman DM. Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units. Journal of Chemical Theory and Computation. 8: 2921-2929. PMID 23162384 DOI: 10.1021/Ct300263Z |
0.395 |
|
| 2012 |
Lettieri S, Zuckerman DM. Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models. Journal of Computational Chemistry. 33: 268-75. PMID 22120971 DOI: 10.1002/Jcc.21970 |
0.418 |
|
| 2012 |
Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, Grabe M. Insight into the Alternating Access Mechanism of the Sodium Symporter Mhp1 using Path Sampling Simulations Biophysical Journal. 102: 661a-662a. DOI: 10.1016/J.Bpj.2011.11.3604 |
0.75 |
|
| 2012 |
Stringer C, Zwier M, Chong L, Zuckerman D. Equilibrium Sampling using a Weighted Ensemble of Dynamical Trajectories Biophysical Journal. 102: 21a. DOI: 10.1016/J.Bpj.2011.11.142 |
0.435 |
|
| 2011 |
Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, Grabe M. Simulations of the alternating access mechanism of the sodium symporter Mhp1. Biophysical Journal. 101: 2399-407. PMID 22098738 DOI: 10.1016/J.Bpj.2011.09.061 |
0.74 |
|
| 2011 |
Bhatt D, Zuckerman DM. Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible? Journal of Chemical Theory and Computation. 7: 2520-2527. PMID 21869866 DOI: 10.1021/Ct200086K |
0.401 |
|
| 2011 |
Lettieri S, Mamonov AB, Zuckerman DM. Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space. Journal of Computational Chemistry. 32: 1135-43. PMID 21387340 DOI: 10.1002/Jcc.21695 |
0.394 |
|
| 2011 |
Zuckerman DM. Equilibrium sampling in biomolecular simulations. Annual Review of Biophysics. 40: 41-62. PMID 21370970 DOI: 10.1146/Annurev-Biophys-042910-155255 |
0.36 |
|
| 2011 |
Cashman DJ, Mamonov AB, Bhatt D, Zuckerman DM. Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled semi-atomistic simulations Current Topics in Medicinal Chemistry. 11: 211-220. PMID 20939787 DOI: 10.1016/J.Bpj.2008.12.3752 |
0.439 |
|
| 2011 |
Mamonov AB, Zhang X, Zuckerman DM. Rapid sampling of all-atom peptides using a library-based polymer-growth approach. Journal of Computational Chemistry. 32: 396-405. PMID 20734315 DOI: 10.1002/Jcc.21626 |
0.405 |
|
| 2011 |
Ding Y, Mamonov AB, Zuckerman DM. Improved Library-Based Monte Carlo, Applied to Multi-Level Sampling Biophysical Journal. 100: 155a. DOI: 10.1016/J.Bpj.2010.12.1057 |
0.473 |
|
| 2010 |
Bhatt D, Zuckerman DM. Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase. Journal of Chemical Theory and Computation. 6: 3527-3539. PMID 21660120 DOI: 10.1021/Ct100406T |
0.429 |
|
| 2010 |
Zhang X, Bhatt D, Zuckerman DM. Automated sampling assessment for molecular simulations using the effective sample size. Journal of Chemical Theory and Computation. 6: 3048-3057. PMID 21221418 DOI: 10.1021/Ct1002384 |
0.483 |
|
| 2010 |
Bhatt D, Zhang BW, Zuckerman DM. Steady-state simulations using weighted ensemble path sampling. The Journal of Chemical Physics. 133: 014110. PMID 20614962 DOI: 10.1063/1.3456985 |
0.402 |
|
| 2010 |
Ding Y, Mamonov AB, Zuckerman DM. Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo. The Journal of Physical Chemistry. B. 114: 5870-7. PMID 20380366 DOI: 10.1021/Jp910112D |
0.433 |
|
| 2010 |
Zhang BW, Jasnow D, Zuckerman DM. The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures. The Journal of Chemical Physics. 132: 054107. PMID 20136305 DOI: 10.1063/1.3306345 |
0.385 |
|
| 2010 |
Mamonov AB, Zuckerman DM. Library-Based Monte Carlo as a Convenient Platform for Variable-Resolution Protein Models Biophysical Journal. 98: 571a. DOI: 10.1016/J.Bpj.2009.12.3101 |
0.391 |
|
| 2010 |
Bhatt D, Petersen AA, Zuckerman DM. Weighted Ensemble Path Sampling for Efficient Calculation of Steady State Properties Biophysical Journal. 98: 392a. DOI: 10.1016/J.Bpj.2009.12.2113 |
0.375 |
|
| 2009 |
Grossfield A, Zuckerman DM. Quantifying uncertainty and sampling quality in biomolecular simulations. Annual Reports in Computational Chemistry. 5: 23-48. PMID 20454547 DOI: 10.1016/S1574-1400(09)00502-7 |
0.646 |
|
| 2009 |
Bhatt D, Zuckerman DM. Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method. The Journal of Chemical Physics. 131: 214110. PMID 19968340 DOI: 10.1063/1.3269674 |
0.335 |
|
| 2009 |
Mamonov AB, Bhatt D, Cashman DJ, Ding Y, Zuckerman DM. General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models. The Journal of Physical Chemistry. B. 113: 10891-904. PMID 19594147 DOI: 10.1021/Jp901322V |
0.452 |
|
| 2009 |
Zhang X, Mamonov AB, Zuckerman DM. Absolute free energies estimated by combining precalculated molecular fragment libraries. Journal of Computational Chemistry. 30: 1680-91. PMID 19504588 DOI: 10.1002/Jcc.21337 |
0.37 |
|
| 2009 |
Lyman E, Zuckerman DM. Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol. The Journal of Chemical Physics. 130: 081102. PMID 19256587 DOI: 10.1063/1.3081626 |
0.616 |
|
| 2009 |
Zhang BW, Zuckerman DM, Jasnow D. The “Weighted Ensemble” Path Sampling Method Can Find Target States Blindly And Automatically Biophysical Journal. 96: 407a. DOI: 10.1016/J.Bpj.2008.12.2077 |
0.443 |
|
| 2009 |
Zhang XQ, Zuckerman DM. Evaluating The Effective Sample Size Of Equilibrium Molecular Simulations Using Automatically Approximated Physical States Biophysical Journal. 96: 407a. DOI: 10.1016/J.Bpj.2008.12.2076 |
0.425 |
|
| 2009 |
Mamonov AB, Zuckerman DM. Improving The Computational Efficiency Of Non-Dynamical Approaches For Equilibrium Sampling Of All-Atom Protein Models Biophysical Journal. 96: 407a. DOI: 10.1016/J.Bpj.2008.12.2075 |
0.433 |
|
| 2008 |
Ytreberg FM, Zuckerman DM. A black-box re-weighting analysis can correct flawed simulation data. Proceedings of the National Academy of Sciences of the United States of America. 105: 7982-7. PMID 18544653 DOI: 10.1073/Pnas.0706063105 |
0.427 |
|
| 2007 |
Ytreberg FM, Aroutiounian SKh, Zuckerman DM. Demonstrated Convergence of the Equilibrium Ensemble for a Fast United-Residue Protein Model. Journal of Chemical Theory and Computation. 3: 1860-6. PMID 26627628 DOI: 10.1021/Ct700076T |
0.43 |
|
| 2007 |
Zhang BW, Jasnow D, Zuckerman DM. Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin. Proceedings of the National Academy of Sciences of the United States of America. 104: 18043-8. PMID 17984047 DOI: 10.1073/Pnas.0706349104 |
0.459 |
|
| 2007 |
Lyman E, Zuckerman DM. On the structural convergence of biomolecular simulations by determination of the effective sample size. The Journal of Physical Chemistry. B. 111: 12876-82. PMID 17935314 DOI: 10.1021/Jp073061T |
0.661 |
|
| 2007 |
Lyman E, Zuckerman DM. Annealed importance sampling of peptides. The Journal of Chemical Physics. 127: 065101. PMID 17705625 DOI: 10.1063/1.2754267 |
0.647 |
|
| 2007 |
Zhang BW, Jasnow D, Zuckerman DM. Transition-event durations in one-dimensional activated processes. The Journal of Chemical Physics. 126: 074504. PMID 17328617 DOI: 10.1063/1.2434966 |
0.352 |
|
| 2006 |
Zuckerman DM, Lyman E. A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]. Journal of Chemical Theory and Computation. 2: 1693. PMID 26627040 DOI: 10.1021/Ct600297Q |
0.611 |
|
| 2006 |
Lyman E, Zuckerman DM. Resolution Exchange Simulation with Incremental Coarsening. Journal of Chemical Theory and Computation. 2: 656-66. PMID 26626672 DOI: 10.1021/Ct050337X |
0.634 |
|
| 2006 |
Zuckerman DM, Lyman E. A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation. Journal of Chemical Theory and Computation. 2: 12001202. PMID 19043602 DOI: 10.1021/Ct0600464 |
0.665 |
|
| 2006 |
Ytreberg FM, Swendsen RH, Zuckerman DM. Comparison of free energy methods for molecular systems. The Journal of Chemical Physics. 125: 184114. PMID 17115745 DOI: 10.1063/1.2378907 |
0.414 |
|
| 2006 |
Lyman E, Zuckerman DM. Ensemble-based convergence analysis of biomolecular trajectories. Biophysical Journal. 91: 164-72. PMID 16617086 DOI: 10.1529/Biophysj.106.082941 |
0.648 |
|
| 2006 |
Ytreberg FM, Zuckerman DM. Simple estimation of absolute free energies for biomolecules. The Journal of Chemical Physics. 124: 104105. PMID 16542066 DOI: 10.1063/1.2174008 |
0.369 |
|
| 2006 |
Lyman E, Ytreberg FM, Zuckerman DM. Resolution exchange simulation. Physical Review Letters. 96: 028105. PMID 16486650 DOI: 10.1103/Physrevlett.96.028105 |
0.645 |
|
| 2005 |
Ytreberg FM, Zuckerman DM. Peptide conformational equilibria computed via a single-stage shifting protocol. The Journal of Physical Chemistry. B. 109: 9096-103. PMID 16852082 DOI: 10.1021/Jp0510692 |
0.408 |
|
| 2004 |
Ytreberg FM, Zuckerman DM. Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. Journal of Computational Chemistry. 25: 1749-59. PMID 15362132 DOI: 10.1002/Jcc.20103 |
0.406 |
|
| 2004 |
Ytreberg FM, Zuckerman DM. Single-ensemble nonequilibrium path-sampling estimates of free energy differences. The Journal of Chemical Physics. 120: 10876-9. PMID 15268117 DOI: 10.1063/1.1760511 |
0.37 |
|
| 2004 |
Woolf TB, Zuckerman DM, Lu N, Jang H. Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics. Journal of Molecular Graphics & Modelling. 22: 359-68. PMID 15099832 DOI: 10.1016/J.Jmgm.2003.12.003 |
0.607 |
|
| 2004 |
Setty AK, Zuckerman DM. Fast Simulation Protocol for Protein Structural Transitions: Modeling of the Relationship of Structure and Function Mrs Proceedings. 826. DOI: 10.1557/Proc-826-V3.5 |
0.389 |
|
| 2004 |
Ytreberg FM, Zuckerman DM. Erratum: “Single-ensemble nonequilibrium path-sampling estimates of free energy differences” [J. Chem. Phys. 120, 10876 (2004)] The Journal of Chemical Physics. 121: 5022-5023. DOI: 10.1063/1.1783252 |
0.323 |
|
| 2004 |
Zuckerman DM, Woolf TB. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities Journal of Statistical Physics. 114: 1303-1323. DOI: 10.1023/B:Joss.0000013961.84860.5B |
0.57 |
|
| 2004 |
Zuckerman DM. Simulation of an Ensemble of Conformational Transitions in a United-Residue Model of Calmodulin The Journal of Physical Chemistry B. 108: 5127-5137. DOI: 10.1021/Jp0370730 |
0.47 |
|
| 2003 |
Sachs JN, Petrache HI, Zuckerman DM, Woolf TB. Molecular dynamics simulations of ionic concentration gradients across model bilayers Journal of Chemical Physics. 118: 1957-1969. DOI: 10.1063/1.1531589 |
0.601 |
|
| 2002 |
Zuckerman DM, Woolf TB. Theory of a systematic computational error in free energy differences. Physical Review Letters. 89: 180602. PMID 12398588 DOI: 10.1103/Physrevlett.89.180602 |
0.576 |
|
| 2002 |
Zuckerman DM, Woolf TB. Transition events in butane simulations: Similarities across models Journal of Chemical Physics. 116: 2586-2591. DOI: 10.1063/1.1433501 |
0.594 |
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| 2002 |
Petrache HI, Zuckerman DM, Sachs JN, Antoinette Killian J, Koeppe RE, Woolf TB. Hydrophobic matching mechanism investigated by molecular dynamics simulations Langmuir. 18: 1340-1351. DOI: 10.1021/La011338P |
0.607 |
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| 2002 |
Zuckerman DM, Woolf TB. Overcoming finite-sampling errors in fast-switching free-energy estimates: Extrapolative analysis of a molecular system Chemical Physics Letters. 351: 445-453. DOI: 10.1016/S0009-2614(01)01397-5 |
0.57 |
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| 2001 |
Zuckerman DM, Woolf TB. Efficient dynamic importance sampling of rare events in one dimension. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 016702. PMID 11304388 DOI: 10.1103/Physreve.63.016702 |
0.624 |
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| 1999 |
Zuckerman DM, Woolf TB. Dynamic reaction paths and rates through importance-sampled stochastic dynamics Journal of Chemical Physics. 111: 9475-9484. DOI: 10.1063/1.480278 |
0.601 |
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| Low-probability matches (unlikely to be authored by this person) |
| 2016 |
Anandakrishnan R, Zhang Z, Donovan-Maiye R, Zuckerman DM. Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process. Proceedings of the National Academy of Sciences of the United States of America. PMID 27647911 DOI: 10.1016/J.Bpj.2016.11.1507 |
0.3 |
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| 1998 |
Zuckerman DM, Bruinsma RF. Vesicle-vesicle adhesion by mobile lock-and-key molecules: Debye-Hückel theory and Monte Carlo simulation Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 57: 964-977. DOI: 10.1103/Physreve.57.964 |
0.3 |
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| 2016 |
Zhang Z, Anandakrishnan R, Donovan R, Zuckerman D. ATP Synthase: Advantages of the Rotary Mechanism under Diverse Conditions Biophysical Journal. 110: 312a-313a. DOI: 10.1016/J.Bpj.2015.11.1678 |
0.298 |
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| 2001 |
Zuckerman DM, Fisher ME, Bekiranov S. Asymmetric primitive-model electrolytes: Debye-Hückel theory, criticality, and energy bounds. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 64: 011206. PMID 11461239 DOI: 10.1103/Physreve.64.011206 |
0.297 |
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| 2018 |
Myers JB, Haddad BG, O'Neill SE, Chorev DS, Yoshioka CC, Robinson CV, Zuckerman DM, Reichow SL. Structure of native lens connexin 46/50 intercellular channels by cryo-EM. Nature. 564: 372-377. PMID 30542154 DOI: 10.1038/S41586-018-0786-7 |
0.291 |
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| 2016 |
Karki I, Christen MT, Spiriti J, Slack RL, Oda M, Kanaori K, Zuckerman DM, Ishima R. Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg(2+) Titration Analysis for HIV-1 Ribonuclease H Domain. The Journal of Physical Chemistry. B. 120: 12420-12431. PMID 27973819 DOI: 10.1021/Acs.Jpcb.6B08323 |
0.29 |
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| 2019 |
Braun E, Gilmer J, Mayes HB, Mobley DL, Monroe JI, Prasad S, Zuckerman DM. Best Practices for Foundations in Molecular Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 1. PMID 31788666 DOI: 10.33011/livecoms.1.1.5957 |
0.288 |
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| 2015 |
Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R. Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase. Proteins. 83: 1526-38. PMID 26061827 DOI: 10.1002/Prot.24843 |
0.286 |
|
| 1998 |
Fisher ME, Zuckerman DM. Chemical association via exact thermodynamic formulations Chemical Physics Letters. 293: 461-468. DOI: 10.1016/S0009-2614(98)00786-6 |
0.282 |
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| 2014 |
Zuckerman D. “A Physical Lens on the Cell”: Beginnings of a Free Online Book on Sub-Cellular Biophysical Processes for Students from Heterogeneous Backgrounds Biophysical Journal. 106: 217a. DOI: 10.1016/J.Bpj.2013.11.1270 |
0.279 |
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| 2017 |
Anandakrishnan R, Zuckerman DM. Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio. Plos One. 12: e0173500. PMID 28319179 DOI: 10.1371/Journal.Pone.0173500 |
0.277 |
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| 1995 |
Zuckerman D, Bruinsma R. Statistical mechanics of membrane adhesion by reversible molecular bonds. Physical Review Letters. 74: 3900-3903. PMID 10058325 DOI: 10.1103/Physrevlett.74.3900 |
0.273 |
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| 1998 |
Fisher ME, Zuckerman DM. Exact thermodynamic formulation of chemical association Journal of Chemical Physics. 109: 7961-7981. DOI: 10.1063/1.477444 |
0.268 |
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| 2021 |
Zuckerman DM, Russo JD. A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications. American Journal of Physics. 89: 1048-1061. PMID 35530173 DOI: 10.1119/10.0005603 |
0.26 |
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| 2019 |
Copperman JT, Aristoff D, Zuckerman DM. Exploring Optimal Resource Allocation for Weighted Ensemble Resampling of Rare Events Biophysical Journal. 116: 141a. DOI: 10.1016/J.Bpj.2018.11.785 |
0.251 |
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| 2019 |
Flores JA, Dolan KA, Haddad BG, Myers JB, Yoshioka CC, Zuckerman DM, Reichow SL. Visualization of Protein-Lipid Interactions in Connexin-46/50 Intercellular Communication Channels at 2.1 Å Resolution Microscopy and Microanalysis. 25: 1216-1217. DOI: 10.1017/S1431927619006810 |
0.25 |
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| 2017 |
Nunes-Alves A, Zuckerman DM, Arantes GM. Weighted Ensemble of Pathways for Ligand Unbinding from T4 Lysozyme Biophysical Journal. 112: 339a. DOI: 10.1016/J.Bpj.2016.11.1834 |
0.249 |
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| 2019 |
Lee Y, Phelps C, Huang T, Mostofian B, Wu L, Zhang Y, Tao K, Chang YH, Stork PJ, Gray JW, Zuckerman DM, Nan X. High-throughput single-particle tracking reveals nested membrane domains that dictate KRas diffusion and trafficking. Elife. 8. PMID 31674905 DOI: 10.7554/Elife.46393 |
0.248 |
|
| 1997 |
Zuckerman DM, Fisher ME, Lee BP. Critique of primitive model electrolyte theories Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 56: 6569-6580. DOI: 10.1103/Physreve.56.6569 |
0.244 |
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| 2019 |
George A, Grabe M, Rosenberg JM, Zuckerman DM. What is Your Machine Really Doing? Systematic Exploration of Alternative Mechanisms as Applied to Transport Biophysical Journal. 116: 127a-128a. DOI: 10.1016/J.Bpj.2018.11.708 |
0.236 |
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| 2024 |
George A, Zuckerman DM. From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis. The Journal of Physical Chemistry. B. PMID 38373358 DOI: 10.1021/acs.jpcb.3c07025 |
0.231 |
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| 1997 |
Martin JI, Wang Z, Zuckerman D, Bruinsma R, Pincus P. Forces between Surfaces with Weakly End-Adsorbed Polymers Journal De Physique Ii. 7: 1111-1121. DOI: 10.1051/Jp2:1997175 |
0.231 |
|
| 1998 |
Zuckerman DM, Bruinsma RF. Vesicle-vesicle adhesion by mobile lock-and-key molecules: Debye-Hückel theory and Monte Carlo simulation Physical Review E. 57: 964-977. DOI: 10.1103/PhysRevE.57.964 |
0.231 |
|
| 1991 |
Fee MS, Mills AP, Shaw ED, Chichester RJ, Zuckerman DM, Chu S, Danzmann K. Sensitive detection of Doppler-free two-photon-excited 2S positronium by spatially separated photoionization. Physical Review. A. 44: R5-R8. PMID 9905741 DOI: 10.1103/Physreva.44.R5 |
0.228 |
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| 2019 |
Lee Y, Phelps C, Huang T, Mostofian B, Wu L, Zhang Y, Tao K, Chang YH, Stork PJ, Gray JW, Zuckerman DM, Nan X. Author response: High-throughput, single-particle tracking reveals nested membrane domains that dictate KRasG12D diffusion and trafficking Elife. DOI: 10.7554/Elife.46393.Sa2 |
0.225 |
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| 2020 |
Grabe M, Zuckerman DM, Rosenberg JM. EmrE reminds us to expect the unexpected in membrane transport. The Journal of General Physiology. 152. PMID 31816640 DOI: 10.1085/Jgp.201912467 |
0.219 |
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| 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, ... ... Zuckerman DM, 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 |
0.218 |
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| 2022 |
Mostofian B, McFarland R, Estelle A, Howe J, Barbar E, Reichow SL, Zuckerman DM. Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM. Journal of Molecular Biology. 434: 167520. PMID 35245498 DOI: 10.1016/j.jmb.2022.167520 |
0.218 |
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| 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, ... ... Zuckerman D, 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 |
0.218 |
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| 2019 |
Spiriti JM, Conway JF, Zuckerman DM. Should Virus Capsids Assemble Perfectly? A Simple Equilibrium Model for Defects Biophysical Journal. 116: 62a. DOI: 10.1016/J.Bpj.2018.11.381 |
0.216 |
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| 2024 |
Copperman J, Mclean IC, Gross SM, Chang YH, Zuckerman DM, Heiser LM. Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. Biorxiv : the Preprint Server For Biology. PMID 38293173 DOI: 10.1101/2024.01.18.576248 |
0.208 |
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| 2019 |
Lee Y, Phelps C, Huang T, Mostofian B, Zuckerman D, Nan X. Probing Membrane Nanodomain Organization with Single Particle Tracking via Photoactivated Localization Microscopy (spt-PALM) Microscopy and Microanalysis. 25: 1248-1249. DOI: 10.1017/S1431927619006974 |
0.205 |
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| 2020 |
Mostofian B, McFarland R, Barbar EJ, Reichow SL, Zuckerman DM. Automated Identification of Flexible Multivalent IDP-Bound Assemblies in Electron Micrographs Biophysical Journal. 118: 295a-296a. DOI: 10.1016/J.Bpj.2019.11.1676 |
0.204 |
|
| 1992 |
Brandes GR, Mills AP, Voris SS, Zuckerman DM. Solid Neon Moderator with a Large Activity Source Materials Science Forum. 1359-1362. DOI: 10.4028/Www.Scientific.Net/Msf.105-110.1359 |
0.204 |
|
| 2018 |
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, et al. Clinically Observed Estrogen Receptor Alpha Mutations within the Ligand-Binding Domain Confer Distinguishable Phenotypes. Oncology. 94: 176-189. PMID 29306943 DOI: 10.1159/000485510 |
0.202 |
|
| 2020 |
Aristoff D, Zuckerman DM. OPTIMIZING WEIGHTED ENSEMBLE SAMPLING OF STEADY STATES. Multiscale Modeling & Simulation : a Siam Interdisciplinary Journal. 18: 646-673. PMID 34421402 DOI: 10.1137/18m1212100 |
0.198 |
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| 2021 |
Yue B, Haddad BG, Khan U, Chen H, Atalla M, Zhang Z, Zuckerman DM, Reichow SL, Bai D. Connexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains. The Journal of Physiology. PMID 33876426 DOI: 10.1113/JP281339 |
0.193 |
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| 1993 |
Fee MS, Mills AP, Chu S, Shaw ED, Danzmann K, Chichester RJ, Zuckerman DM. Measurement of the positronium 1(3)S1-2(3)S1 interval by continuous-wave two-photon excitation. Physical Review Letters. 70: 1397-1400. PMID 10053282 DOI: 10.1103/Physrevlett.70.1397 |
0.184 |
|
| 1992 |
Mills AP, Brandes GR, Zuckerman DM, Liu W, Berko S. Positron Mobility in Natural Diamond Materials Science Forum. 763-766. DOI: 10.4028/Www.Scientific.Net/Msf.105-110.763 |
0.181 |
|
| 1992 |
Mills AP, Shaw ED, Chu S, Danzmann K, Chichester RJ, Zuckerman DM. Evidence for CW 1S-2S Excitation of Positronium Materials Science Forum. 533-538. DOI: 10.4028/Www.Scientific.Net/Msf.105-110.533 |
0.179 |
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| 2023 |
Estelle AB, George A, Barbar EJ, Zuckerman DM. Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. Plos Computational Biology. 19: e1011059. PMID 37083599 DOI: 10.1371/journal.pcbi.1011059 |
0.175 |
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| 1992 |
Brandes GR, Mills AP, Zuckerman DM. Positron Workfunction of Diamond C(100) Surfaces Materials Science Forum. 1363-1366. DOI: 10.4028/Www.Scientific.Net/Msf.105-110.1363 |
0.171 |
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| 2021 |
Sung MW, Yang Z, Driggers CM, Patton BL, Mostofian B, Russo JD, Zuckerman DM, Shyng SL. Vascular K channel structural dynamics reveal regulatory mechanism by Mg-nucleotides. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34711681 DOI: 10.1073/pnas.2109441118 |
0.167 |
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| 2021 |
Adhikari U, Mostofian B, Copperman J, Subramanian SR, Petersen AA, Zuckerman DM. Correction to "Computational Estimation of Microsecond to Second Atomistic Folding Times". Journal of the American Chemical Society. 143: 7588. PMID 33961428 DOI: 10.1021/jacs.0c02854 |
0.161 |
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| 2023 |
Copperman J, Gross SM, Chang YH, Heiser LM, Zuckerman DM. Morphodynamical cell state description via live-cell imaging trajectory embedding. Communications Biology. 6: 484. PMID 37142678 DOI: 10.1038/s42003-023-04837-8 |
0.161 |
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| 2017 |
Mobley D, Shirts M, Zuckerman D. Why We Need the Living Journal of Computational Molecular Science Living Journal of Computational Molecular Science. 1. DOI: 10.33011/livecoms.1.1.2031 |
0.157 |
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| 2022 |
Woo Sung M, Driggers CM, Mostofian B, Russo JD, Patton BL, Zuckerman DM, Shyng SL. Ligand-mediated structural dynamics of a mammalian pancreatic K channel. Journal of Molecular Biology. 167789. PMID 35964676 DOI: 10.1016/j.jmb.2022.167789 |
0.155 |
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| 2020 |
Spiriti J, Conway JF, Zuckerman DM. Should Virus Capsids Assemble Perfectly? Theory and Observation of Defects. Biophysical Journal. 119: 1781-1790. PMID 33113349 DOI: 10.1016/j.bpj.2020.09.021 |
0.119 |
|
| 1998 |
Fisher ME, Zuckerman DM. Chemical association via exact thermodynamic formulations Chemical Physics Letters. 293: 461-468. DOI: 10.1016/S0009-2614(98)00786-6 |
0.099 |
|
| 1992 |
Mills AP, Karl N, Zuckerman DM, Passner J, Hensel J, Beling CD. Positron mobility in anthracene Applied Physics a Solids and Surfaces. 54: 22-25. DOI: 10.1007/BF00348124 |
0.094 |
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| 1997 |
Zuckerman D, Fisher M, Lee B. Critique of primitive model electrolyte theories Physical Review E. 56: 6569-6580. DOI: 10.1103/PhysRevE.56.6569 |
0.052 |
|
| 2015 |
Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R. Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase Proteins: Structure, Function and Bioinformatics. DOI: 10.1002/prot.24843 |
0.033 |
|
| 1985 |
Rickards LD, Zuckerman DM, West PR. Alzheimer's disease: Current congressional response. American Psychologist. 40: 1256-1261. DOI: 10.1037/0003-066x.40.11.1256 |
0.012 |
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| 1999 |
Zuckerman DM. Postdoc Advice Science. 286: 411c-411c. DOI: 10.1126/science.286.5439.411c |
0.01 |
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| Hide low-probability matches. |