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Lillian T. Chong, Ph.D. - Publications

Affiliations: 
1997-2002 Graduate Group in Biophysics University of California, San Francisco, San Francisco, CA 
 2002-2006 Chemistry Stanford University, Palo Alto, CA 
 2005-2006 IBM Almaden Research Center, San Jose, CA, United States 
 2006- Chemistry University of Pittsburgh, Pittsburgh, PA, United States 
Area:
computational biophysics
Website:
http://www.chem.pitt.edu/people/faculty
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49 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
2024 Yang DT, Chong LT. WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data. Biorxiv : the Preprint Server For Biology. PMID 38826259 DOI: 10.1101/2024.05.18.594829  0.387
2024 Bogetti AT, Zwier MC, Chong LT. Revisiting Textbook Azide-Clock Reactions: A "Propeller-Crawling" Mechanism Explains Differences in Rates. Journal of the American Chemical Society. 146: 12828-12835. PMID 38687173 DOI: 10.1021/jacs.4c03360  0.765
2023 Santhouse JR, Leung JMG, Chong LT, Horne WS. Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein. Chemical Science. 15: 675-682. PMID 38179541 DOI: 10.1039/d3sc03976e  0.324
2023 Bogetti X, Bogetti A, Casto J, Rule G, Chong L, Saxena S. Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by EPR and simulation. Protein Science : a Publication of the Protein Society. e4770. PMID 37632831 DOI: 10.1002/pro.4770  0.31
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, ... ... Chong LT, 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  0.816
2022 Yang DT, Gronenborn AM, Chong LT. Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field. The Journal of Physical Chemistry. A. 126: 2286-2297. PMID 35352936 DOI: 10.1021/acs.jpca.2c00255  0.339
2022 Bogetti AT, Piston HE, Leung JMG, Cabalteja CC, Yang DT, DeGrave AJ, Debiec KT, Cerutti DS, Case DA, Horne WS, Chong LT. A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics. The Journal of Chemical Physics. 153: 064101. PMID 35287464 DOI: 10.1063/5.0019054  0.795
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, ... Chong LT, 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  0.809
2021 DeGrave AJ, Bogetti AT, Chong LT. The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations. The Journal of Chemical Physics. 154: 114111. PMID 33752378 DOI: 10.1063/5.0041278  0.337
2020 Bogetti AT, Piston HE, Leung JMG, Cabalteja CC, Yang DT, DeGrave AJ, Debiec KT, Cerutti DS, Case DA, Horne WS, Chong LT. A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics The Journal of Chemical Physics. 153: 064101. DOI: 10.1063/5.0019054  0.795
2020 Chong L. Weighted Ensemble Simulation: Tackling the Challenges of Long-Timescale Kinetics Biophysical Journal. 118: 352a. DOI: 10.1016/J.Bpj.2019.11.2030  0.425
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  0.794
2019 Debiec KT, Gronenborn AM, Chong LT. Correction to "Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields". The Journal of Physical Chemistry. B. PMID 31042394 DOI: 10.1021/Acs.Jpcb.9B03732  0.758
2019 Saglam AS, Chong LT. Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations. Chemical Science. 10: 2360-2372. PMID 30881664 DOI: 10.1039/C8Sc04811H  0.795
2018 DeGrave AJ, Ha JH, Loh SN, Chong LT. Large enhancement of response times of a protein conformational switch by computational design. Nature Communications. 9: 1013. PMID 29523842 DOI: 10.1038/S41467-018-03228-6  0.356
2018 Debiec KT, Whitley MJ, Koharudin LMI, Chong LT, Gronenborn AM. Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein. Biophysical Journal. 114: 839-855. PMID 29490245 DOI: 10.1016/J.Bpj.2018.01.001  0.799
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  0.803
2017 Cerutti DS, Debiec KT, Case DA, Chong LT. Links between the charge model and bonded parameter force constants in biomolecular force fields. The Journal of Chemical Physics. 147: 161730. PMID 29096508 DOI: 10.1063/1.4985866  0.793
2017 Saglam AS, Wang D, Zwier MC, Chong LT. Flexibility vs. Preorganization: Direct Comparison of Binding Kinetics for a Disordered Peptide and Its Exact Preorganized Analogues. The Journal of Physical Chemistry. B. PMID 28992700 DOI: 10.1021/Acs.Jpcb.7B08486  0.788
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  0.518
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  0.806
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  0.796
2016 Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. Journal of Chemical Theory and Computation. PMID 27399642 DOI: 10.1021/Acs.Jctc.6B00567  0.801
2015 Saglam AS, Chong LT. Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models. The Journal of Physical Chemistry. B. PMID 26673903 DOI: 10.1021/Acs.Jpcb.5B10747  0.804
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  0.8
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  0.807
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  0.775
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  0.809
2014 Debiec KT, Gronenborn AM, Chong LT. Evaluating the strength of salt bridges: a comparison of current biomolecular force fields. The Journal of Physical Chemistry. B. 118: 6561-9. PMID 24702709 DOI: 10.1021/Jp500958R  0.789
2012 Oshaben KM, Salari R, McCaslin DR, Chong LT, Horne WS. The native GCN4 leucine-zipper domain does not uniquely specify a dimeric oligomerization state. Biochemistry. 51: 9581-91. PMID 23116373 DOI: 10.1021/Bi301132K  0.743
2012 Salari R, Chong LT. Effects of high temperature on desolvation costs of salt bridges across protein binding interfaces: similarities and differences between implicit and explicit solvent models. The Journal of Physical Chemistry. B. 116: 2561-7. PMID 22300130 DOI: 10.1016/J.Bpj.2012.11.2794  0.734
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  0.793
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  0.787
2011 Zwier MC, Kaus JW, Chong LT. Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na(+)/Cl(-), Methane/Benzene, and K(+)/18-Crown-6 Ether. Journal of Chemical Theory and Computation. 7: 1189-1197. PMID 26606365 DOI: 10.1021/Ct100626X  0.799
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  0.786
2011 Panteva MT, Salari R, Bhattacharjee M, Chong LT. Direct observations of shifts in the β-sheet register of a protein-peptide complex using explicit solvent simulations. Biophysical Journal. 100: L50-2. PMID 21539773 DOI: 10.1016/J.Bpj.2011.03.035  0.761
2011 Xiong K, Zwier MC, Myshakina NS, Burger VM, Asher SA, Chong LT. Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations. The Journal of Physical Chemistry. A. 115: 9520-7. PMID 21528875 DOI: 10.1021/Jp112235D  0.787
2011 Mills BM, Chong LT. Molecular simulations of mutually exclusive folding in a two-domain protein switch. Biophysical Journal. 100: 756-64. PMID 21281591 DOI: 10.1016/J.Bpj.2010.12.3710  0.446
2010 Salari R, Chong LT. Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models. The Journal of Physical Chemistry Letters. 1: 2844-2848. PMID 24920993 DOI: 10.1021/Jz1010863  0.739
2010 Zwier MC, Chong LT. Reaching biological timescales with all-atom molecular dynamics simulations. Current Opinion in Pharmacology. 10: 745-52. PMID 20934381 DOI: 10.1016/J.Coph.2010.09.008  0.814
2009 Chong LT, Pitera JW, Swope WC, Pande VS. Comparison of computational approaches for predicting the effects of missense mutations on p53 function. Journal of Molecular Graphics & Modelling. 27: 978-82. PMID 19168381 DOI: 10.1016/J.Jmgm.2008.12.006  0.771
2009 Cutler TA, Mills BM, Lubin DJ, Chong LT, Loh SN. Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains. Journal of Molecular Biology. 386: 854-68. PMID 19038264 DOI: 10.1016/J.Jmb.2008.10.090  0.379
2006 Chong LT, Swope WC, Pitera JW, Pande VS. Kinetic computational alanine scanning: application to p53 oligomerization. Journal of Molecular Biology. 357: 1039-49. PMID 16457841 DOI: 10.1016/J.Jmb.2005.12.083  0.781
2005 Chong LT, Snow CD, Rhee YM, Pande VS. Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. Journal of Molecular Biology. 345: 869-78. PMID 15588832 DOI: 10.1016/J.Jmb.2004.10.083  0.82
2003 Chong LT, Bandyopadhyay P, Scanlan TS, Kuntz ID, Kollman PA. Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. Journal of Computational Chemistry. 24: 1371-7. PMID 12868101 DOI: 10.1002/Jcc.10293  0.647
2001 Lee TS, Chong LT, Chodera JD, Kollman PA. An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. Journal of the American Chemical Society. 123: 12837-48. PMID 11749542 DOI: 10.1021/Ja011096F  0.689
2000 Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research. 33: 889-97. PMID 11123888 DOI: 10.1021/Ar000033J  0.81
1999 Chong LT, Duan Y, Wang L, Massova I, Kollman PA. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proceedings of the National Academy of Sciences of the United States of America. 96: 14330-5. PMID 10588705 DOI: 10.1073/Pnas.96.25.14330  0.512
1998 Chong LT, Dempster SE, Hendsch ZS, Lee LP, Tidor B. Computation of electrostatic complements to proteins: a case of charge stabilized binding. Protein Science : a Publication of the Protein Society. 7: 206-10. PMID 9514276 DOI: 10.1002/Pro.5560070122  0.564
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