Yi He
A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
A Liwo, M Baranowski, C Czaplewski, E Gołaś, Y He, D Jagieła, P Krupa, ...
Journal of molecular modeling 20, 1-15, 2014
Mean-field interactions between nucleic-acid-base dipoles can drive the formation of the double helix
Y He, M Maciejczyk, S Ołdziej, HA Scheraga, A Liwo
Physical Review Letters 110 (9), 098101, 2013
Coarse-grained force field: general folding theory
A Liwo, Y He, HA Scheraga
Physical Chemistry Chemical Physics 13 (38), 16890-16901, 2011
WeFold: a coopetition for protein structure prediction
GA Khoury, A Liwo, F Khatib, H Zhou, G Chopra, J Bacardit, LO Bortot, ...
Proteins: Structure, Function, and Bioinformatics 82 (9), 1850-1868, 2014
Conformational rearrangements in the pro-apoptotic protein, Bax, as it inserts into mitochondria: a cellular death switch
RF Gahl, Y He, S Yu, N Tjandra
Journal of Biological Chemistry 289 (47), 32871-32882, 2014
Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field
Y He, Y Xiao, A Liwo, HA Scheraga
Journal of computational chemistry 30 (13), 2127-2135, 2009
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
Y He, MA Mozolewska, P Krupa, AK Sieradzan, TK Wirecki, A Liwo, ...
Proceedings of the National Academy of Sciences 110 (37), 14936-14941, 2013
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
P Krupa, MA Mozolewska, M Wiśniewska, Y Yin, Y He, AK Sieradzan, ...
Bioinformatics 32 (21), 3270-3278, 2016
PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics
Y He, A Liwo, H Weinstein, HA Scheraga
Journal of molecular biology, 2010
AlphaFold illuminates half of the dark human proteins
JL Binder, J Berendzen, AO Stevens, Y He, J Wang, NV Dokholyan, ...
Current opinion in structural biology 74, 102372, 2022
Benchmarking the accuracy of AlphaFold 2 in loop structure prediction
AO Stevens, Y He
Biomolecules 12 (7), 985, 2022
Folding mechanism of beta-hairpin trpzip2: Heterogeneity, transition state and folding pathways
Y Xiao, C Chen, Y He
International journal of molecular sciences 10 (6), 2838-2848, 2009
High cell density production of Deinococcus radiodurans under optimized conditions
Y He
Journal of Industrial Microbiology and Biotechnology 36 (4), 539-546, 2009
Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach
Y He, A Liwo, HA Scheraga
The Journal of Chemical Physics 143 (24), 2015
A polymer electrolyte with high cationic transport number for safe and stable solid Li-metal batteries
X Shan, M Morey, Z Li, S Zhao, S Song, Z Xiao, H Feng, S Gao, G Li, ...
ACS Energy Letters 7 (12), 4342-4351, 2022
Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins
Y He, GG Maisuradze, Y Yin, K Kachlishvili, S Rackovsky, HA Scheraga
Proceedings of the National Academy of Sciences 114 (7), 1578-1583, 2017
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
C Keasar, LJ McGuffin, B Wallner, G Chopra, B Adhikari, D Bhattacharya, ...
Scientific reports 8 (1), 9939, 2018
Unraveling the role of neutral units for single-ion conducting polymer electrolytes
S Zhao, S Song, Y Wang, J Keum, J Zhu, Y He, AP Sokolov, PF Cao
ACS Applied Materials & Interfaces 13 (43), 51525-51534, 2021
A new protein nucleic‐acid coarse‐grained force field based on the UNRES and NARES‐2P force fields
AK Sieradzan, A Giełdoń, Y Yin, Y He, HA Scheraga, A Liwo
Journal of computational chemistry 39 (28), 2360-2370, 2018
Physics-based potentials for coarse-grained modeling of protein–DNA interactions
Y Yin, AK Sieradzan, A Liwo, Y He, HA Scheraga
Journal of chemical theory and computation 11 (4), 1792-1808, 2015
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