Publications
Review and Perspective Articles
AT Bogetti, MF Presti, SN Loh, and LT Chong. “The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics.” J. Phys. Chem. B 2021, 125 (32), 9069–9077. link pdf
DM Zuckerman and LT Chong. “Weighted ensemble simulation: Review of methodology, applications, and software.” Ann. Rev. Biophys. 2017, 46, 43. link pdf
LT Chong, AS Saglam, and DM Zuckerman. “Path-sampling strategies for simulating rare events in biomolecular systems.” Curr. Opin. Struct. Biol. 2017, 43, 88. link pdf
MC Zwier and LT Chong. “Reaching biological timescales with all-atom molecular dynamics simulations.” Curr. Opin. Pharmacol. 2010, 10, 745-752. link pdf
Weighted ensemble methods and software
DT Yang, and LT Chong. “WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.” J. Chem. Inf. Model. 2024. link pdf
AT Bogetti*, JMG Leung*, LT Chong. “LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways.” J. Chem. Inf. Model. 2023. *equal authorship link pdf
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, LT Chong. “WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.” J. Chem. Theory Comput. 2022, 18 (2), 638–649. *equal authorship link pdf
S Zhang, JP Thompson, J Xia, AT Bogetti, F York, AG Skillman, LT Chong, DN LeBard. “Mechanistic Insights into Passive Membrane Permeability of Drug-Like Molecules from a Weighted Ensemble of Trajectories.” J. Chem. Inf. Model 2022. link pdf
AJ DeGrave*, AT Bogetti*, and LT Chong. “The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations.” bioRxiv 2021. *equal authorship link pdf
PA Torrillo*, AT Bogetti*, and LT Chong. “A minimal, adaptive binning scheme for weighted ensemble simulations.” J. Chem. Phys. A 2021, 125: 1642–1649. *equal authorship link pdf
AS Saglam and LT Chong. “Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations.” Chem. Sci. 2019, 10, 2360. link pdf data
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.” Living J. Comput. Mol. Sci. 2019, 1, 10607. *equal authorship link pdf
DM Zuckerman and LT Chong. “Weighted ensemble simulation: Review of methodology, applications, and software.” Ann. Rev. Biophys. 2017, 46, 43. link pdf
LT Chong, AS Saglam, and DM Zuckerman. “Path-sampling strategies for simulating rare events in biomolecular systems.” Curr. Opin. Struct. Biol. 2017, 43, 88. link pdf
E Suárez, AJ Pratt, LT Chong, and DM Zuckerman. “Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.” Prot. Sci. 2016, 25, 67. link pdf
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. 2015,11, 800. link pdf
E Suárez, 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. 2014, 10, 2658. link pdf
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. 2011, 7, 1189. link pdf
Protein binding simulations
AS Saglam and LT Chong. “Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations.” Chem. Sci. 2019, 10, 2360. link pdf data
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 2017, 121, 10046. link pdf
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 2016, 120, 117. link pdf
MC Zwier, AJ Pratt, JL Adelman, JW Kaus, DM Zuckerman, and LT Chong. “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.” J. Phys. Chem. Lett. 2016, 7, 3440. link pdf
MT Panteva*, R Salari*, M Bhattacharjee, and LT Chong. “Direct observations of shifts in the beta-sheet register of a protein-peptide complex using explicit solvent simulations.” Biophys. J. Letters 2011, 100, L50. *equal authorship link pdf
Simulations of protein folding and other large-scale conformational transitions in proteins
JR Santhouse*, JMG Leung*, LT Chong, and WS Horne. “Effects of Altered Backbone Composition on the Folding Kinetics and Mechanism of an Ultrafast-Folding Protein.” Chem. Sci. 2024. *equal authorship link pdf
X Bogetti*, AT Bogetti*, J Casto, GS Rule, LT Chong, and S Saxena. “Direct Observation of Negative Cooperativity in a Detoxification Enzyme at the Atomic Level by Electron Paramagnetic Resonance Spectroscopy and Simulation.” Protein Sci. 2023. *equal authorship link pdf
JR Santhouse*, JMG Leung*, LT Chong, and WS Horne. “Implications of the Unfolded State in the Folding Energetics of Heterogeneous-Backbone Protein Mimetics.” Chem. Sci. 2022. *equal authorship link pdf
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. *co-corresponding authors link pdf
L Casalino, A Dommer, Z Gaieb, EP Barros, T Sztain, S Ahn, A Trifan, A Brace, AT Bogetti, H Ma, H Lee, M Turilli, S Khalid, LT Chong, C Simmerling, DJ Hardy, JDC Maia, JC Phillips, T Kurth, A Stern, L Huang, J McCalpin, M Tatineni, T Gibbs, JE Stone, S Jha, A Ramanathan, and RE Amaro. “AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics.” bioRxiv 2020.
link pdf This paper has been awarded the Gordon Bell Special Prize.
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. 2011, 101, 2399. link pdf
Rational design of protein switches
AT Bogetti, MF Presti, SN Loh, and LT Chong. “The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics.” J. Phys. Chem. B 2021, 125 (32), 9069–9077. link pdf
AJ DeGrave, JH Ha, SN Loh, and LT Chong. “Large enhancement of response times of a protein conformational switch by computational design.” Nat. Commun. 2018, 9, 1013. link pdf
BM Mills and LT Chong. “Molecular simulations of mutually exclusive folding in a two-domain protein switch.” Biophys. J. 2011, 100, 756. link pdf
TA Cutler, BM Mills, DJ Lubin, LT Chong, and SN Loh. “Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains.” J. Mol. Biol. 2009, 386, 854. link pdf
Force fields for proteins and protein mimetics
DT Yang, AM Gronenborn, and LT Chong. “Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field” J. Phys. Chem. A 2022, 126, 2286-2297. link pdf code
AT Bogetti*, HE Piston*, JMG Leung*, CC Cabalteja, DT Yang, AJ DeGrave, KT Debiec, DS Cerutti, DA Case, WS Horne, and LT Chong. “A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.” J. Chem. Phys. 2020, 153(6), 064101. *equal authorship link pdf
DS Cerutti, KT Debiec, DA Case, and LT Chong. “Links between the charge model and bonded parameter force constants in biomolecular force constants.” J. Chem. Phys. 2017, 147, 161730. link pdf
KT Debiec, DS Cerutti, LR Baker, AM Gronenborn, DA Case, and LT Chong. “Further along the road less traveled: AMBER ff15ipq, an original protein force field built on a self-consistent physical model.” J. Chem. Theory Comput. 2016, 12, 3926. link pdf
KT Debiec, AM Gronenborn, and LT Chong. “Evaluating the strength of salt bridges - a comparison of current biomolecular force fields.” J. Phys. Chem. B 2014, 118, 6561. link pdf
R Salari and LT Chong. “Effects of increasing temperature on desolvation costs of salt bridges across protein binding interfaces: Similarities and differences between implicit and explicit solvent models.” J. Phys. Chem. B 2012, 116, 2561. link pdf
R Salari and LT Chong. “Desolvation costs of salt bridges across protein binding interfaces: Similarities and differences between implicit and explicit solvent models.” J. Phys. Chem. Lett. 2010, 1, 2844. link pdf
Integrative structural biology
X Xu, JD Closson, LP Marcelino, DC Favaro, ML Silvestrini, R Solazzo, LT Chong, and KH Gardner. “Identification of small-molecule ligand-binding sites on and in the ARNT PAS-B domain.” J. Biol. Chem. 2024. link pdf
X Bogetti*, AT Bogetti*, J Casto, GS Rule, LT Chong, and S Saxena. “Direct Observation of Negative Cooperativity in a Detoxification Enzyme at the Atomic Level by Electron Paramagnetic Resonance Spectroscopy and Simulation.” Protein Sci. 2023. *equal authorship link pdf
JR Santhouse*, JMG Leung*, LT Chong, and WS Horne. “Implications of the Unfolded State in the Folding Energetics of Heterogeneous-Backbone Protein Mimetics.” Chem. Sci. 2022. *equal authorship link pdf
KT Debiec, MJ Whitley, LMI Koharudin, LT Chong, and AM Gronenborn. “Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.” Biophys. J. 2018, 114, 839. link pdf
KM Oshaben, R Salari, DR McCaslin, LT Chong, and WS Horne. “The native GCN4 leucine-zipper domain does not uniquely specify a dimeric oligomerization state.” Biochemistry 2012, 51, 9581. link pdf
K Xiong, MC Zwier, NS Myshakina, VM Burger, SA Asher, and LT Chong. “Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations.” J. Phys. Chem. A 2011, 115, 9520. link pdf
Chemical Reactions
AT Bogetti, MC Zwier, and LT Chong. “Revisiting Textbook Azide-Clock Reactions: A “Propeller-Crawling” Mechanism Explains Differences in Rates” J. Am. Chem. Soc. 2024. link pdf