Daniel M Zuckerman

Daniel M Zuckerman

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Daniel M Zuckerman

Daniel M Zuckerman

Publications by authors named "Daniel M Zuckerman"

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

J Chem Theory Comput 2019 May 7. Epub 2019 May 7.

Department of Biomedical Engineering, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239-3098 , United States.

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http://dx.doi.org/10.1021/acs.jctc.9b00015DOI Listing
May 2019

Computational Estimation of Microsecond to Second Atomistic Folding Times.

J Am Chem Soc 2019 Apr 12;141(16):6519-6526. Epub 2019 Apr 12.

Department of Biomedical Engineering, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239 , United States.

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http://dx.doi.org/10.1021/jacs.8b10735DOI Listing
April 2019

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

PLoS One 2019 23;14(4):e0215694. Epub 2019 Apr 23.

Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215694PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478315PMC
April 2019

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

Nature 2018 12 12;564(7736):372-377. Epub 2018 Dec 12.

Department of Chemistry, Portland State University, Portland, OR, USA.

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http://dx.doi.org/10.1038/s41586-018-0786-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309215PMC
December 2018

Preface: Special Topic on Enhanced Sampling for Molecular Systems.

J Chem Phys 2018 Aug;149(7):072001

Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97239, USA.

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http://dx.doi.org/10.1063/1.5049669DOI Listing
August 2018

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

J Control Release 2018 07 1;282:76-89. Epub 2018 Mar 1.

Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, United States; Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97201, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jconrel.2018.02.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6008205PMC
July 2018

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

Biophys J 2018 03;114(5):1058-1066

Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883560PMC
March 2018

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

J Chem Theory Comput 2018 Jan 22;14(1):426-443. Epub 2017 Dec 22.

Department of Biomedical Engineering, Oregon Health and Science University , Portland, Oregon 97239, United States.

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http://dx.doi.org/10.1021/acs.jctc.7b00775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933972PMC
January 2018

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

PLoS One 2017 20;12(3):e0173500. Epub 2017 Mar 20.

Dept. of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173500PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358804PMC
August 2017

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

Annu Rev Biophys 2017 05 1;46:43-57. Epub 2017 Mar 1.

Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260; email:

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http://dx.doi.org/10.1146/annurev-biophys-070816-033834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896317PMC
May 2017

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

Curr Opin Struct Biol 2017 04 13;43:88-94. Epub 2016 Dec 13.

OHSU Center for Spatial Systems Biomedicine and Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2016.11.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420491PMC
April 2017

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

J Phys Chem B 2016 12 5;120(49):12420-12431. Epub 2016 Dec 5.

Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.6b08323
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http://dx.doi.org/10.1021/acs.jpcb.6b08323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850897PMC
December 2016

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

Proc Natl Acad Sci U S A 2016 10 19;113(40):11220-11225. Epub 2016 Sep 19.

Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260;

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http://dx.doi.org/10.1073/pnas.1608533113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056049PMC
October 2016

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

J Chem Theory Comput 2016 Aug 11;12(8):3473-81. Epub 2016 Jul 11.

Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States.

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http://dx.doi.org/10.1021/acs.jctc.6b00339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5022777PMC
August 2016

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

PLoS Comput Biol 2016 Feb 4;12(2):e1004611. Epub 2016 Feb 4.

Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4741515PMC
February 2016

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

Protein Sci 2016 Jan 9;25(1):67-78. Epub 2015 Sep 9.

Department of Computational and Systems Biology, University of Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1002/pro.2738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815309PMC
January 2016

Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.

J Chem Phys 2015 Dec;143(24):243159

Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1063/1.4938479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4698120PMC
December 2015

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

Proteins 2015 Aug 1;83(8):1526-38. Epub 2015 Jul 1.

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260.

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http://dx.doi.org/10.1002/prot.24843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509971PMC
August 2015

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

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

Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States.

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http://dx.doi.org/10.1021/ct500622zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230378PMC
November 2014

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

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

Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States.

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http://dx.doi.org/10.1021/ct401065rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168800PMC
July 2014

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

J Chem Phys 2013 Sep;139(11):115105

Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1063/1.4821167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790806PMC
September 2013

Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models.

J Comput Chem 2012 Jan 25;33(3):268-75. Epub 2011 Nov 25.

Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1002/jcc.21970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408236PMC
January 2012

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

Biophys J 2011 Nov 15;101(10):2399-407. Epub 2011 Nov 15.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1016/j.bpj.2011.09.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218348PMC
November 2011

Equilibrium sampling in biomolecular simulations.

Annu Rev Biophys 2011 ;40:41-62

Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1146/annurev-biophys-042910-155255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434601PMC
September 2011

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

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

Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave, Biomedical Sciences Tower 3, Pittsburgh, PA 15260.

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http://dx.doi.org/10.1021/ct200086kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159166PMC
August 2011

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

J Comput Chem 2011 Apr 29;32(6):1135-43. Epub 2010 Nov 29.

Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1002/jcc.21695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390976PMC
April 2011

Rapid sampling of all-atom peptides using a library-based polymer-growth approach.

J Comput Chem 2011 Feb 23;32(3):396-405. Epub 2010 Aug 23.

Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1002/jcc.21626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005036PMC
February 2011

Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase.

J Chem Theory Comput 2010 Oct;6(11):3527-3539

Department of Computational and Systems Biology, University of Pittsburgh.

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http://dx.doi.org/10.1021/ct100406tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108504PMC
October 2010

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

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

Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213.

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http://dx.doi.org/10.1021/ct1002384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017371PMC
September 2010

Steady-state simulations using weighted ensemble path sampling.

J Chem Phys 2010 Jul;133(1):014110

Department of Computational Biology, University of Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1063/1.3456985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912933PMC
July 2010

Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo.

J Phys Chem B 2010 May;114(17):5870-7

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1021/jp910112dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882875PMC
May 2010

The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures.

J Chem Phys 2010 Feb;132(5):054107

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1063/1.3306345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830257PMC
February 2010

Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method.

J Chem Phys 2009 Dec;131(21):214110

Department of Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1063/1.3269674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802520PMC
December 2009

Absolute free energies estimated by combining precalculated molecular fragment libraries.

J Comput Chem 2009 Aug;30(11):1680-91

Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1002/jcc.21337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783641PMC
August 2009

General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models.

J Phys Chem B 2009 Aug;113(31):10891-904

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1021/jp901322vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766542PMC
August 2009

Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol.

J Chem Phys 2009 Feb;130(8):081102

Center for Biophysical Modeling and Simulation, University of Utah, 315 S 1400 E, Rm. 2020, Salt Lake City, Utah 84112-0850, USA.

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http://dx.doi.org/10.1063/1.3081626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671214PMC
February 2009

Quantifying uncertainty and sampling quality in biomolecular simulations.

Annu Rep Comput Chem 2009 Jan;5:23-48

University of Rochester Medical Center, Department of Biochemistry and Biophysics, Box 712, Rochester, N.Y., 14642, USA, 585-276-4193.

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http://dx.doi.org/10.1016/S1574-1400(09)00502-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865156PMC
January 2009

A black-box re-weighting analysis can correct flawed simulation data.

Proc Natl Acad Sci U S A 2008 Jun;105(23):7982-7

Department of Physics, University of Idaho, Moscow, ID 83844-0903, USA.

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http://dx.doi.org/10.1073/pnas.0706063105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786942PMC
June 2008

On the structural convergence of biomolecular simulations by determination of the effective sample size.

J Phys Chem B 2007 Nov 13;111(44):12876-82. Epub 2007 Oct 13.

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1021/jp073061tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538559PMC
November 2007

Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

Proc Natl Acad Sci U S A 2007 Nov 1;104(46):18043-8. Epub 2007 Nov 1.

Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0706349104
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http://dx.doi.org/10.1073/pnas.0706349104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2084293PMC
November 2007

Demonstrated Convergence of the Equilibrium Ensemble for a Fast United-Residue Protein Model.

J Chem Theory Comput 2007 Sep;3(5):1860-6

Department of Physics, University of Idaho, Moscow, Idaho 83844-0903.

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http://dx.doi.org/10.1021/ct700076tDOI Listing
September 2007

Annealed importance sampling of peptides.

J Chem Phys 2007 Aug;127(6):065101

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://aip.scitation.org/doi/10.1063/1.2754267
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http://dx.doi.org/10.1063/1.2754267DOI Listing
August 2007

Transition-event durations in one-dimensional activated processes.

J Chem Phys 2007 Feb;126(7):074504

Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1063/1.2434966DOI Listing
February 2007

Comparison of free energy methods for molecular systems.

J Chem Phys 2006 Nov;125(18):184114

Department of Physics, University of Idaho, Moscow, Idaho 83844-0903, USA.

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http://dx.doi.org/10.1063/1.2378907DOI Listing
November 2006

Ensemble-based convergence analysis of biomolecular trajectories.

Biophys J 2006 Jul 14;91(1):164-72. Epub 2006 Apr 14.

Department of Computational Biology, School of Medicine, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1529/biophysj.106.082941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479051PMC
July 2006

Resolution Exchange Simulation with Incremental Coarsening.

J Chem Theory Comput 2006 May;2(3):656-66

Department of Computational Biology, School of Medicine, and Department of Environmental and Occupational Health, Graduate School of Public Health, BST W1041, 200 Lothrop Street, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.

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http://dx.doi.org/10.1021/ct050337xDOI Listing
May 2006

Simple estimation of absolute free energies for biomolecules.

J Chem Phys 2006 Mar;124(10):104105

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1063/1.2174008DOI Listing
March 2006

Resolution exchange simulation.

Phys Rev Lett 2006 Jan 18;96(2):028105. Epub 2006 Jan 18.

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1103/PhysRevLett.96.028105DOI Listing
January 2006

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.

J Chem Theory Comput 2006 ;2(4):12001202

Department of Computational Biology, School of Medicine, and Department of Environmental & Occupational Health, Graduate School of Public Health, Suite 3064 BST3, 3501 Fifth Avenue, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, ;

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http://dx.doi.org/10.1021/ct0600464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586297PMC
January 2006

Peptide conformational equilibria computed via a single-stage shifting protocol.

J Phys Chem B 2005 May;109(18):9096-103

Department of Computational Biology and the Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, Pennsylvania 15261, USA.

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http://dx.doi.org/10.1021/jp0510692DOI Listing
May 2005

Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems.

J Comput Chem 2004 Nov;25(14):1749-59

Center for Computational Biology and Bioinformatics, University of Pittsburgh, 200 Lothrop St., Pittsburgh, Pennsylvania 15261, USA.

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http://dx.doi.org/10.1002/jcc.20103DOI Listing
November 2004

Single-ensemble nonequilibrium path-sampling estimates of free energy differences.

J Chem Phys 2004 Jun;120(23):10876-9

Center for Computational Biology and Bioinformatics, School of Medicine and Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.

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http://dx.doi.org/10.1063/1.1760511DOI Listing
June 2004

Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics.

J Mol Graph Model 2004 May;22(5):359-68

Department of Physiology, Johns Hopkins University, School of Medicine, Biophysics 206, 725 N. Wolfe Street, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1016/j.jmgm.2003.12.003DOI Listing
May 2004

Theory of a systematic computational error in free energy differences.

Phys Rev Lett 2002 Oct 15;89(18):180602. Epub 2002 Oct 15.

Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1103/PhysRevLett.89.180602DOI Listing
October 2002