Sara Y Cheng
Sara Y Cheng
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Polarizable force fields for biomolecular simulations: Recent advances and applications
Z Jing, C Liu, SY Cheng, R Qi, BD Walker, JP Piquemal, P Ren
Capturing RNA folding free energy with coarse-grained molecular dynamics simulations
DR Bell, SY Cheng, H Salazar, P Ren
Scientific reports 7 (1), 1-14, 2017
Synthetic DNA Melting Probe Enables Differentiation of Four Single-Nucleotide Variants by Melting Temperature
S Cheng, J Obliosca, YA Chen, M Llanos, YL Liu, D Imphean, D Bell, ...
Bulletin of the American Physical Society, 2018
Coarse-grained MD simulations reveal beta-amyloid fibrils of various sizes bind to interfacial liquid-ordered and liquid-disordered regions in phase separated lipid rafts with …
SY Cheng, Y Cao, M Rouzbehani, KH Cheng
Biophysical chemistry 260, 106355, 2020
Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field
JR Abella, SY Cheng, Q Wang, W Yang, P Ren
Journal of chemical theory and computation 10 (7), 2792-2801, 2014
LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature
JM Obliosca, SY Cheng, YA Chen, MF Llanos, YL Liu, DM Imphean, ...
Journal of the American Chemical Society 139 (20), 7110-7116, 2017
Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface
SY Cheng, G Chou, C Buie, MW Vaughn, C Compton, KH Cheng
Chemistry and physics of lipids 196, 33-51, 2016
Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins
M Liu, AK Das, J Lincoff, S Sasmal, SY Cheng, RM Vernon, ...
International Journal of Molecular Sciences 22 (7), 3420, 2021
Lipid insertion domain unfolding regulates protein orientational transition behavior in a lipid bilayer
KH Cheng, L Qiu, SY Cheng, MW Vaughn
Biophysical chemistry 206, 22-39, 2015
Characterization of 3D Voronoi tessellation nearest neighbor lipid shells provides atomistic lipid disruption profile of protein containing lipid membranes
SY Cheng, HV Duong, C Compton, MW Vaughn, H Nguyen, KH Cheng
Biophysical chemistry 198, 22-35, 2015
Convergence of Stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation
D An, SY Cheng, T Head-Gordon, L Lin, J Lu
Journal of Computational Physics 438, 110338, 2021
Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR …
SY Cheng, G Chou, C Buie, MW Vaughn, C Compton, KH Cheng
Data in brief 7, 658-672, 2016
Data showing the lipid conformations and membrane binding behaviors of beta-amyloid fibrils in phase-separated cholesterol-enriched lipid domains with and without glycolipid …
SY Cheng, Y Cao, M Rouzbehani, KH Cheng
Data in brief 30, 105496, 2020
Folded Proteins Inform the Development of Models for Intrinsically Disordered Proteins
SY Cheng, J Lincoff, S Sasmal, R Vernon, J Forman-Kay, T Head-Gordon
arXiv preprint arXiv:2007.06150, 2020
Microsecond Coarse-Grained MD Simulations of Beta-Amyloid Fibrils Binding to Phase Separated Lipid Raft Domains Reveal Diverse Membrane-bounded Conformations and Binding …
K Cheng, S Cheng, Y Cao, M Rouzbehani, R Davenport-Dendy, A Urby, ...
Bulletin of the American Physical Society 65, 2020
Atomistic and Coarse-Grained MD Simulation Studies of the Energetics and Interactions of Regulatory Dib1 Protein Inside a Highly Dynamic Pre-Catalytic Spliceosomal …
R Goldstein, S Cheng, G Orr, C Schreib, C Maeder, K Cheng
Bulletin of the American Physical Society 65, 2020
Energetics and Interfacial Interactions of Spliceosomal Protein Dib1 Predicted with MD Simulations
R Goldstein, S Cheng, G Orr, C Schreib, K Cheng, C Maeder
The FASEB Journal 33 (S1), 627.2-627.2, 2019
Computational and experimental studies of biomolecules
SY Cheng
Role of Transbilayer Distribution of Lipid Molecules on the Structure and Protein-Lipid Interaction of an Amyloidogenic Protein on the Membrane Surface
K Cheng, S Cheng
APS March Meeting Abstracts 2017, B5. 008, 2017
RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations
S Cheng, D Bell, P Ren
APS March Meeting Abstracts 2017, X14. 006, 2017
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