| Polarizable force fields for biomolecular simulations: Recent advances and applications Z Jing, C Liu, SY Cheng, R Qi, BD Walker, JP Piquemal, P Ren | 254* | |
| 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 | 45 | 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 | 32* | 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 | 24 | 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 | 19 | 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 | 17 | 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 | 12 | 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 | 10 | 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 | 9 | 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 | 6 | 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 | 5 | 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 | 3 | 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 | 1 | 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 | | 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 | | 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 | | 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 | | 2019 |
| Computational and experimental studies of biomolecules SY Cheng | | 2018 |
| 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 | | 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 | | 2017 |
