Publications by Year

2021

Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations

Front. Phys. (2021) DOI arXiv
R. Vasan, M. P. Rowan, C. T. Lee, G. R. Johnson, P. Rangamani, and M. Holst$ More info →

Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes

Proc. Natl. Acad. Sci. (2021) DOI bioRxiv
T. Hempel, M. J. Razo*, C. T. Lee*, B. C. Taylor*, R. E. Amaro$, and F. Noé$ More info →

Value of Models for Membrane Budding

Curr. Opin. Cell Biol. (2021) DOI
C. T. Lee, M. Akamatsu, and P. Rangamani$ More info →

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2020

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Biophys. J. (2020) DOI arXiv bioRxiv
C. T. Lee$, J. G. Laughlin, J. B. Moody, R. E. Amaro, J. A. McCammon, M. J. Holst, and P. Rangamani$ More info →

3D Mesh Processing Using GAMer 2 to Enable Reaction-Diffusion Simulations in Realistic Cellular Geometries

PLOS Comp. Biol. (2020) DOI arXiv bioRxiv
C. T. Lee*, J. G. Laughlin*, N. La Beaumelle, R. E. Amaro, J. A. McCammon, R. Ramamoorthi, M. J. Holst, and P. Rangamani$ More info →

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2019

Structural Basis for Ligand Modulation of the CCR2 Conformational Landscape

Proc. Natl. Acad. Sci. (2019) DOI bioRxiv
B. C. Taylor, C. T. Lee, and R. E. Amaro$ More info →

The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation

ACM Trans. Math. Softw. (2019) DOI arXiv
C. T. Lee*$, J. B. Moody*, R. E. Amaro, J. A. Mccammon, and M. J. Holst More info →

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2018

Exascale Computing: A New Dawn for Computational Biology

Comput. Sci. Eng. (2018) DOI
C. T. Lee, and R. E. Amaro$ More info →

Quantitative Ranking of β-cyclodextrin Ligand Binding Kinetics With SEEKR, a Hybrid MD/BD/Milestoning Approach

J. Phys. Chem. Lett. (2018) DOI ChemRxiv: ChemRxiv
B. R. Jagger, C. T. Lee, and R. E. Amaro$ More info →

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2016

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

J. Chem. Inf. Model. (2016) DOI
C. T. Lee, J. Comer$, C. Herndon, N. Leung, A. Pavlova, R. V. Swift, C. Tung, C. N. Rowley, R. E. Amaro$, C. Chipot$, Y. Wang$, and J. C. Gumbart$ More info →

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

Chem. Rev. (2016) DOI
J. R. Wagner*, C. T. Lee*, J. D. Durrant, R. D. Malmstrom, V. A. Feher, and R. E. Amaro$ More info →

Two Relations to Estimate Membrane Permeability Using Milestoning

J. Phys. Chem. B (2016) DOI
L. W. Votapka*, C. T. Lee*, and R. E. Amaro$ More info →

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2015

Known Structure, Unknown Function: An Inquiry-Based Undergraduate Biochemistry Laboratory Course

Biochem. Mol. Biol. Educ. (2015) DOI
C. Gray*, C. W. Price*, C. T. Lee, A. H. Dewald, M. A. Cline, C. E. McAnany, L. Columbus$, and C. Mura$ More info →

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2014

Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

J. Chem. Theory Comput. (2014) DOI
R. D. Malmstrom, C. T. Lee, A. T. Van Wart, and R. E. Amaro$ More info →

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