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L. Chong · SciRah

Researcher profile · Semantic Scholar

L. Chong

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L. Chong — researcher profile on SciRah

h-index: 30
Works: 62
Citations: 7,767

Most-cited papers

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
P. Kollman, I. Massova, Carolina M. Reyes, B. Kuhn +11 more
2000Accounts of Chemical Research4,626 citations
Semantic Scholar
Weighted Ensemble Simulation: Review of Methodology, Applications, and Software
D. Zuckerman, L. Chong
2017Annual Review of Biophysics323 citations Open access
Semantic Scholar
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7.
L. Chong, Y. Duan, Lu Wang, I. Massova +1 more
1999Proceedings of the National Academy of Sciences of the United States of America234 citations Open access
Semantic Scholar
A glycan gate controls opening of the SARS-CoV-2 spike protein
Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, L. Casalino +13 more
2021Nature Chemistry228 citations Open access
Semantic Scholar
Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
Karl T. Debiec, D. Cerutti, Lewis R. Baker, A. Gronenborn +2 more
2016Journal of Chemical Theory and Computation186 citations Open access
Semantic Scholar
Reaching biological timescales with all-atom molecular dynamics simulations.
M. Zwier, L. Chong
2010Current opinion in pharmacology (Print)179 citations
Semantic Scholar
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics
L. Casalino, A. Dommer, Zied Gaieb, Emília P. Barros +25 more
2020bioRxiv178 citations Open access
Semantic Scholar
WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis
M. Zwier, Joshua L. Adelman, Joseph W. Kaus, A. Pratt +8 more
2015Journal of Chemical Theory and Computation151 citations Open access
Semantic Scholar
A glycan gate controls opening of the SARS-CoV-2 spike protein
Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, L. Casalino +13 more
2021bioRxiv139 citations Open access
Semantic Scholar
Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields
Karl T. Debiec, A. Gronenborn, L. Chong
2014Journal of Physical Chemistry B112 citations Open access
Semantic Scholar
Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories
Ernesto Suárez, Steven A. Lettieri, M. Zwier, C. Stringer +3 more
2012Journal of Chemical Theory and Computation106 citations Open access
Semantic Scholar
Path-sampling strategies for simulating rare events in biomolecular systems
L. Chong, A. S. Saglam, D. Zuckerman
2016Current Opinion in Structural Biology105 citations Open access
Semantic Scholar
WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications
John D. Russo, She Zhang, Jeremy M. G. Leung, Anthony T. Bogetti +12 more
2021bioRxiv91 citations Open access
Semantic Scholar
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
A. Dommer, L. Casalino, Fiona L. Kearns, Mia Rosenfeld +48 more
2021bioRxiv91 citations Open access
Semantic Scholar
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
M. Zwier, A. Pratt, Joshua L. Adelman, Joseph W. Kaus +2 more
2016Journal of Physical Chemistry Letters88 citations Open access
Semantic Scholar
Computation of electrostatic complements to proteins: A case of charge stabilized binding
L. Chong, Sara E. Dempster, Zachary S. Hendsch, L. Lee +1 more
1998Protein Science76 citations Open access
Semantic Scholar
Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations
A. S. Saglam, L. Chong
2018bioRxiv70 citations Open access
Semantic Scholar
Simulations of the alternating access mechanism of the sodium symporter Mhp1.
Joshua L. Adelman, A. Dale, M. Zwier, Divesh Bhatt +3 more
2011Biophysical Journal63 citations Open access
Semantic Scholar
The Native GCN4 Leucine-Zipper Domain Does Not Uniquely Specify a Dimeric Oligomerization State
Kaylyn M. Oshaben, R. Salari, D. McCaslin, L. Chong +1 more
2012Biochemistry55 citations Open access
Semantic Scholar
Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na(+)/Cl(-), Methane/Benzene, and K(+)/18-Crown-6 Ether.
M. Zwier, Joseph W. Kaus, L. Chong
2011Journal of Chemical Theory and Computation55 citations
Semantic Scholar
Selective, tight-binding inhibitors of integrin alpha4beta1 that inhibit allergic airway responses.
K. Lin, H. Ateeq, S.-H. Hsiung, L. Chong +13 more
1999Journal of Medicinal Chemistry55 citations
Semantic Scholar
A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations
Paul A. Torrillo, Anthony T. Bogetti, L. Chong
2020bioRxiv52 citations Open access
Semantic Scholar
Effect of Interdomain Linker Length on an Antagonistic Folding-Unfolding Equilibrium between Two Protein Domains
T. A. Cutler, B. Mills, D. Lubin, L. Chong +1 more
2008Journal of Molecular Biology44 citations Open access
Semantic Scholar
A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]
Anthony T. Bogetti, Barmak Mostofian, Alex Dickson, AJ Pratt +10 more
2019Living journal of computational molecular science37 citations Open access
Semantic Scholar
Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations.
L. Chong, C. Snow, Young Min Rhee, V. Pande
2005Journal of Molecular Biology37 citations
Semantic Scholar
Highly Efficient Computation of the Basal kon using Direct Simulation of Protein–Protein Association with Flexible Molecular Models
A. S. Saglam, L. Chong
2015Journal of Physical Chemistry B34 citations Open access
Semantic Scholar
Comparison of computational approaches for predicting the effects of missense mutations on p53 function.
L. Chong, J. Pitera, William Swope, V. Pande
2009Journal of Molecular Graphics and Modelling34 citations
Semantic Scholar
An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.
Tai-Sung Lee, L. Chong, J. Chodera, Peter A. Kollman
2001Journal of the American Chemical Society33 citations
Semantic Scholar
Large enhancement of response times of a protein conformational switch by computational design
A. DeGrave, J. Ha, Stewart N. Loh, L. Chong
2018Nature Communications32 citations Open access
Semantic Scholar
Estimating first‐passage time distributions from weighted ensemble simulations and non‐Markovian analyses
Ernesto Suárez, A. Pratt, L. Chong, D. Zuckerman
2016Protein Science30 citations Open access
Semantic Scholar
Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations
Kan Xiong, M. Zwier, Nataliya S. Myshakina, Virginia M. Burger +2 more
2011Journal of Physical Chemistry A20 citations Open access
Semantic Scholar
A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.
Anthony T. Bogetti, Hannah E. Piston, Jeremy M. G. Leung, C. Cabalteja +7 more
2020Journal of Chemical Physics19 citations Open access
Semantic Scholar
Kinetic computational alanine scanning: application to p53 oligomerization.
L. Chong, William Swope, J. Pitera, V. Pande
2006Journal of Molecular Biology18 citations
Semantic Scholar
Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.
Karl T. Debiec, M. J. Whitley, Leonardus M. I. Koharudin, L. Chong +1 more
2018Biophysical Journal17 citations Open access
Semantic Scholar
Molecular simulations of mutually exclusive folding in a two-domain protein switch.
B. Mills, L. Chong
2011Biophysical Journal16 citations Open access
Semantic Scholar
Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models
R. Salari, L. Chong
2010Journal of Physical Chemistry Letters16 citations Open access
Semantic Scholar
The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations.
A. DeGrave, Anthony T. Bogetti, L. Chong
2021Journal of Chemical Physics15 citations Open access
Semantic Scholar
Direct observations of shifts in the β-sheet register of a protein-peptide complex using explicit solvent simulations.
Maria T. Panteva, R. Salari, Monica Bhattacharjee, L. Chong
2011Biophysical Journal15 citations Open access
Semantic Scholar
Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation
Xiaowei Bogetti, Anthony Bogetti, Joshua Casto, G. Rule +2 more
2023Protein Science13 citations Open access
Semantic Scholar
Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9
L. Chong, P. Bandyopadhyay, T. Scanlan, I. Kuntz +1 more
2003Journal of Computational Chemistry12 citations
Semantic Scholar
A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]
Anthony T. Bogetti, Jeremy M. G. Leung, John D. Russo, She Zhang +18 more
2023Living journal of computational molecular science11 citations Open access
Semantic Scholar
Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field
D. Yang, A. Gronenborn, L. Chong
2022Journal of Physical Chemistry A11 citations Open access
Semantic Scholar
Effects of high temperature on desolvation costs of salt bridges across protein binding interfaces: similarities and differences between implicit and explicit solvent models.
R. Salari, L. Chong
201210 citations Open access
Semantic Scholar
Effects of high temperature on desolvation costs of salt bridges across protein binding interfaces: similarities and differences between implicit and explicit solvent models.
R. Salari, L. Chong
2012Journal of Physical Chemistry B8 citations
Semantic Scholar
A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0.1]
Anthony T. Bogetti, Jeremy M. G. Leung, John D. Russo, She Zhang +11 more
2022bioRxiv7 citations Open access
Semantic Scholar
The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics
Anthony T. Bogetti, Maria F. Presti, Stewart N. Loh, L. Chong
2021Journal of Physical Chemistry B7 citations Open access
Semantic Scholar
Extensive Evaluation of Weighted Ensemble Strategies for Calculating Rate Constants and Binding Affinities of Molecular Association/Dissociation Processes
A. Pratt, Ernesto Suárez, D. Zuckerman, L. Chong
2019bioRxiv5 citations Open access
Semantic Scholar
Links between the charge model and bonded parameter force constants in biomolecular force fields.
D. Cerutti, Karl T. Debiec, D. Case, L. Chong
2017Journal of Chemical Physics4 citations Open access
Semantic Scholar
Reducing the impact of transient effects in rate-constant estimation using the weighted ensemble strategy
A. DeGrave, Anthony T. Bogetti, L. Chong
2018bioRxiv2 citations Open access
Semantic Scholar
LPATH: A semi-automated Python tool for clustering molecular pathways
Anthony T. Bogetti, Jeremy M. G. Leung, L. Chong
2023bioRxiv1 citations Open access
Semantic Scholar

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