Daniel M. Zuckerman - Publications

Affiliations: 
University of Pittsburgh, Pittsburgh, PA, United States 
Area:
General Biophysics

59 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
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  0.56
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  0.56
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  0.56
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  0.72
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  0.32
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  0.72
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  0.56
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  0.72
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  0.56
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  0.56
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  0.56
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  0.56
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  0.72
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2011 Zuckerman DM. Equilibrium sampling in biomolecular simulations. Annual Review of Biophysics. 40: 41-62. PMID 21370970 DOI: 10.1146/annurev-biophys-042910-155255  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2007 Lyman E, Zuckerman DM. Annealed importance sampling of peptides. The Journal of Chemical Physics. 127: 065101. PMID 17705625 DOI: 10.1063/1.2754267  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2006 Lyman E, Ytreberg FM, Zuckerman DM. Resolution exchange simulation. Physical Review Letters. 96: 028105. PMID 16486650 DOI: 10.1103/PhysRevLett.96.028105  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2004 Zuckerman DM, Woolf TB. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities Journal of Statistical Physics. 114: 1303-1323.  0.56
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  0.56
2002 Zuckerman DM, Woolf TB. Theory of a systematic computational error in free energy differences. Physical Review Letters. 89: 180602. PMID 12398588  0.56
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  0.56
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  0.56
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  0.56
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  0.56
1999 Zuckerman DM, Woolf TB. Dynamic reaction paths and rates through importance-sampled stochastic dynamics Journal of Chemical Physics. 111: 9475-9484.  0.56
1998 Fisher ME, Zuckerman DM. Exact thermodynamic formulation of chemical association Journal of Chemical Physics. 109: 7961-7981. DOI: 10.1063/1.477444  0.56
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  0.56
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  0.56
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