Lillian T. Chong, Ph.D. - Publications

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 
 2006- Chemistry University of Pittsburgh, Pittsburgh, PA, United States 
computational biophysics

34 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
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  1
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  0.48
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  1
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  0.48
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  0.48
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  1
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  1
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/  1
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  1
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  0.48
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  1
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  1
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  1
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  1
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  1
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  1
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: 10.1021/jp210172b  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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