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Publications

The WESTPA Papers:

  1. MC Zwier, JL Adelman, JW Kaus, AJ Pratt, KF Wong, NB Rego, E Suárez, S Lettieri, DW Wang, M Grabe, DM Zuckerman, and LT Chong. “WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis”. J. Chem. Theory Comput., 11: 800-809 (2015).
  2. JD Russo*, S Zhang*, JMG Leung*, AT Bogetti*, JP Thompson, AJ DeGrave, PA Torrillo, AJ Pratt, KF Wong, J Xia, J Copperman, JL Adelman, MC Zwier, DN LeBard, DM Zuckerman, and LT Chong. "WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications". J. Chem. Theory Comput, 18 (2), 638–649 (2022) *equal authorship.

A Review of the WE Strategy:

  1. DM Zuckerman and LT Chong. “Weighted ensemble simulation: Review of methodology, applications, and software”. Annu. Rev. Biophys. 2017, 46: 43–57 (2017).

WESTPA Tutorials:

  1. AT Bogetti*, B Mostofian*, A Dickson*, AJ Pratt*, AS Saglam*, PO Harrison*, JL Adelman, M Dudek, PA Torrillo, AJ DeGrave, U Adhikari, MC Zwier, DM Zuckerman, and LT Chong. "A suite of tutorials for the WESTPA rare-events sampling software [Article v1.0]." Living Journal of Computational Molecular Science, 1: 10607 (2019) *equal authorship.
  2. AT Bogetti*, JMG Leung*, JD Russo*, S Zhang*, JP Thompson*, AS Saglam*, D Ray*, B Mostofian, A Dickson, AJ Pratt, PO Harrison, M Dudek, PA Torrillo, AJ DeGrave, U Adhikari, JR Faeder, I Andricioaei, JL Adelman, MC Zwier, DN LeBard, DM Zuckerman, and LT Chong. "A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]." Living Journal of Computational Molecular Science (2023) *equal authorship.

Made with WESTPA:

  1. MC Zwier, JW Kaus, and LT Chong. “Efficient explicit-solvent molecular dynamics simulations of molecular associations: Methane/methane, Na+/Cl-, methane/benzene, and K+/18-crown-6 ether.” J. Chem. Theory Comput., 7: 1189-1197 (2011).
  2. JL Adelman, A Scarbrough, MC Zwier, D Bhatt, LT Chong, DM Zuckerman, and M Grabe. “Simulations of the alternating access mechanism of the sodium symporter Mhp1.” Biophys. J., 101: 2399-2407 (2011).
  3. JL Adelman and M Grabe. “Simulating rare events using a weighted ensemble-based string method.” J. Chem. Phys., 138: 044105 (2013).
  4. RM Donovan, AJ Sedgewick, JR Faeder and DM Zuckerman. “Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.” J. Chem. Phys., 139: 115105 (2013).
  5. E Suarez, S Lettieri, MC Zwier, CA Stringer, SR Subramanian, LT Chong and DM Zuckerman. “Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories.” J. Chem. Theory Comput. 10: 2658-2667 (2014).
  6. JL Adelman and M Grabe. “Simulating current–voltage relationships for a narrow ion channel using the weighted ensemble method” J. Chem. Theory Comput., 11: 1907-1918 (2015).
  7. AS Saglam and LT Chong. “Highly efficient computation of the basal kon using direct simulation of protein-protein association with flexible molecular models” J. Phys. Chem. B (2015).
  8. J Spiriti and DM Zuckerman. “Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits” J. Chem. Phys., 143: 243159 (2015).
  9. E Suarez, AJ Pratt, and LT Chong. “Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses” Prot. Sci., 1: 67-78 (2016).
  10. RM Donovan, JJ Tapia, DP Sullivan, JR Faeder, RF Murphy, M Dittrich, and DM Zuckerman. “Unbiased rare event sampling in spatial stochastic systems biology models using a weighted ensemble of trajectories” PLoS Comput. Biol., 12: e1004611 (2016).
  11. MC Zwier, AJ Pratt, JL Adelman, JW Kaus, DM Zuckerman and LT Chong. “Efficient atomistic simulation of pathways and calculation of rate constants for protein-peptide binding process: Application to the MDM2 protein and an intrinsically disordered p53 peptide” J. Chem. Phys. Lett., 17: 3440-3445 (2016).
  12. AS Saglam, DW Wang, MC Zwier, and LT Chong. “Flexibility vs preorganization: Direct comparison of binding kinetics for a disordered peptide and its exact preorganized analogues” J. Phys. Chem. B, 121: 10046-10054 (2017).
  13. AJ DeGrave, JH Ha, SN Loh, and LT Chong. “Large enhancements of response times of a protein conformational switch by computational design” Nat. Commun., 9: 1013 (2018).
  14. A Nunes-Alves, DM Zuckerman, and GM Arantes. “Escape of a small molecule from inside T4 lysozyme by multiple pathways” Biophys. J., 114: 1058-1066 (2018).
  15. AS Saglam and LT Chong. "Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations." Chem. Sci., (2019).
  16. U Adhikari, B Mostofian, J Copperman, SR Subramanian, AA Petersen, and DM Zuckerman. "Computational estimation of microsecond to second atomistic folding times." J. Am. Chem. Soc., 141: 6519-6526 (2019).
  17. B Mostofian and DM Zuckerman. "Statistical uncertainty analysis for small-sample, high log-variance data: cautions for bootstrapping and Bayesian bootstrapping." J. Chem. Theory. Comput., 15: 3499-3509 (2019).
  18. D Aristoff and DM Zuckerman. "Optimizing weighted ensemble sampling of steady states." Multiscale Model. Sim. (2020).
  19. J Copperman and DM Zuckerman. "Accelerated estimation of long-timescale kinetics from weighted ensemble simulation via non-Markovian “microbin” analysis." J. Chem. Theory Comput., 16: 6763–6775 (2020).
  20. DM Zuckerman and JD Russo. "A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications." arXiv (2020).
  21. T Sztain, S Ahn, AT Bogetti, L Casalino, JA Goldsmith, E Seitz, RS McCool, FL Kearns, F Acosta-Reyes, S Maji, G Mashayekhi, JA McCammon, A Ourmazd, J Frankm, JS McLellan, LT Chong, and RE Amaro. "A glycan gate controls opening of the SARS-CoV-2 spike protein." Nat. Chem. (2021).
  22. S Choe. "Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method." Membranes (2021).
  23. S Zhang, JP Thompson, J Xia, AT Bogetti, F York, AG Skillman, LT Chong, and DN LeBard "Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories." J. Chem. Inf. Model. (2022).
  24. M Beasley, N Frazee, S Groover, SJ Valentine, B Mertz, and J Legleiter "Physicochemical Properties Altered by the Tail Group of Lipid Membranes Influence Huntingtin Aggregation and Lipid Binding." J. Phys. Chem. B (2022).
  25. S Sur and A Grossfield "Effects of cholesterol on the mechanism of fengycin, a biofungicide." Biophys. J. (2022).
  26. JR Santhouse, JMG Leung, LT Chong, WS Horne "Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics." Chem. Sci. (2022).
  27. D Aristoff, J Copperman, G Simpson, RJ Webber, and DM Zuckerman. "Weighted ensemble: Recent mathematical developments " J. Chem. Phys. 158, 014108 (2023).
  28. S Choe "Translocation of a single Arg9 peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method " Sci Rep 13, 1168 (2023).
  29. AA Ojha, S Thakur, S Ahn, RE Amaro "DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling" J. Chem. Theory Comput. (2023).
  30. EE Brossard, SA Corcelli "Molecular Mechanism of Ligand Binding to the Minor Groove of DNA" J. Phys. Chem. Lett. (2023).
  31. E Hellemann, JD Durrant "Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling" J. Chem. Theory Comput. (2023).
  32. X Bogetti, AT Bogetti, J Castro, GS Rule, LT Chong, S Saxena "Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by EPR and simulation" Protein Science (2023).
  33. AJ Poruthoor, A Sharma, A Grossfield "Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics" Biophys. J. (2023).
  34. AT Bogetti, JMG Leung, LT Chong "LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways." J. Chem. Inf. Model. (2023).
  35. JR Santhouse, JMG Leung, LT Chong, WS Horne "Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein." Chem. Sci. (2024).
  36. AT Bogetti, MC Zweir, LT Chong "Revisiting Textbook Azide-Clock Reactions: A “Propeller-Crawling” Mechanism Explains Differences in Rates" J. Am. Chem. Soc. (2024).
  37. DT Yang, LT Chong "WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data" J. Chem. Inf. Model. (2024).
  38. D Plotnikov, SH Ahn "Optimization of the resampling method in the weighted ensemble simulation toolkit with parallelization and analysis" J. Chem. Phys. (2024).

Related Weighted Ensemble Publications:

  1. GA Huber and S Kim. "Weighted-ensemble Brownian dynamics simulations for protein association reactions." Biophys. J., 70: 97–110 (1996).
  2. A Rojnuckarin, S Kim, and S Subramaniam. "Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond." Proc. Nat. Acad. Sci. USA, 95: 4288–4292 (1998).
  3. A Rojnuckarin, DR Livesay, and S Subramaniam. "Bimolecular reaction simulation using weighted ensemble Brownian dynamics and the University of Houston Brownian dynamics program." Biophys. J., 79: 686-693 (2000).
  4. BW Zhang, D Jasnow, and DM Zuckerman. "Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin." Proc. Nat. Acad. Sci. USA, 104: 18043-18048 (2007).
  5. BW Zhang, D Jasnow, and DM Zuckerman. "The ”weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures." J. Chem. Phys., 132: 054107 (2010).
  6. D Bhatt, BW Zhang, and DM Zuckerman. "Steady state via weighted ensemble path sampling" J. Chem. Phys., 133: 014110 (2010).
  7. D Bhatt and DM Zuckerman. "Heterogeneous path ensembles for conformational transitions in semiatomistic models of adenylate kinase." J. Chem. Theory Comput., 6: 3527–3539 (2010).
  8. MC Zwier and LT Chong. “Reaching biological timescales with all-atom molecular dynamics simulations.” Curr. Opin. Pharmacol., 10: 745-752 (2010).
  9. D Bhatt and DM Zuckerman. "Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?" J. Chem. Theory Comput., 7: 2520-2527 (2011).
  10. D Bhatt and I Bahar. "An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates." J. Chem. Phys., 137: 104101 (2012). 
  11. E Darve and E Ryu. "Computing reaction rates in bio-molecular systems using discrete macro-states." Innovations in Biomolecular Modeling and Simulations. Royal Society of Chemistry, 1: 138-206 (2012).
  12. BW Zhang, D Jasnow, and DM Zuckerman. "Weighted ensemble path sampling for multiple reaction channels." arXiv:0902.2772. 
  13. A Dickson and CL Brooks, III. "WExplore: Hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm." J. Phys. Chem. B, 138: 3532-3542 (2014). 
  14. B Abdul-Wahid, H Feng, D Rajan, R Costaouec, E Darve, D Thain, and JA Izaguirre. "AWE-WQ: Fast-forwarding molecular dynamics using the accelerated weighted ensemble." J. Chem. Inf. Model., 54: 3033-3043 (2014). 
  15. H Feng, R Costaouec, E Darve and JA Izaguirre. "A comparison of weighted ensemble and Markov state model methodologies." J. Chem. Phys., 142: 214113 (2015). 
  16. A Dickson, AM Mustoe, L Salmon and CL Brooks, III. "Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore." Nucl. Acids Res., 42: 12126-12137 (2014).
  17. MJ Tse, BK Chu, M Roy and EL Read. "DNA-binding kinetics determines the mechanism of noise-induced switching in gene networks." Biophy. J., 109: 1746-1757 (2015).
  18. E Suarez, JL Adelman and DM Zuckerman. "Accurate estimation of protein folding and unfolding times: Beyond Markov state models." J. Chem. Theory Comput., 12: 3473-3481 (2016).
  19. LT Chong, AS Saglam and DM Zuckerman. "Path-sampling strategies for simulating rare events in biomolecular systems.." Curr. Opin. Struc. Biol., 43: 88-94 (2017).
  20. A Dickson and SD Lotz. "Multiple ligand unbinding pathways and ligand-induced destabilization revealed by WExplore.." Biophys. J., 112: 620-629 (2017).
  21. A Dickson and SD Lotz. "Ligand release pathways obtained with WExplore: Residence times and mechanisms.." J. Phys. Chem. B, 120: 5377-5385 (2017).
  22. SD Lotz and A Dickson. "Unbiased molecular dynamics of 11 min timescale drug unbinding reveals transition state stabilizing interactions.." J. Am. Chem. Soc., 140: 618-628 (2018).
  23. D Aristoff. "Analysis and optimization of weighted ensemble sampling." ESAIM:M2AN., 52: 1219-1238 (2018).
  24. N Donyapour, NM Rousey and A Dickson. "REVO: Resampling of ensembles byvariation optimization." J. Chem. Phys., 150: 244112 (2019).
  25. K Liu, B Chu, J Newby, EL Read, J Lowengrub and J Allard. "Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length." PLOS Comput. Biol., 15: e1006352 (2019).
  26. D Ray and I Andricioaei. "Weighted ensemble milestoning (WEM): A combined approach for rare event simulations." J. Chem. Phys., 152, 234114 (2020).
  27. S Lotz and A Dickson. "Wepy: A flexible software framework for simulating rare events with weighted ensemble resampling." ChemRXiv (2020).
  28. NM Roussey and A Dickson. "Enhanced Jarzynski free energy calculations using weighted ensemble." J. Chem. Phys. 153, 134116 (2020).
  29. K Moritsugu, N Yamamoto, Y Yonezawa, S Tate, and H Fujisaki. "Path ensembles for pin1-catalyzed cis–trans isomerization of a substrate calculated by weighted ensemble simulations." J. Chem. Theory Comput. 17, 2522-2529 (2021).
  30. R Taylor, J Allard, and EL Read. "Simulation of receptor triggering by kinetic segregation shows role of oligomers and close contacts." Biophys. J. 121, 1660-1675 (2022).