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Understand Functional Conformational Changes of Large Biomolecules - - PowerPoint PPT Presentation
Understand Functional Conformational Changes of Large Biomolecules - - PowerPoint PPT Presentation
Understand Functional Conformational Changes of Large Biomolecules with Computer Tools Siqin CAO On behalf of Xuhui Huang's group 2503, July 10, Summer Camp 2019 Central Dogma of Molecular Biology RNA polymerase and transcription cycle Cell
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Central Dogma of Molecular Biology
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RNA polymerase and transcription cycle
Cell 127, 941, (2006); Cell 149, 1431, (2012)
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Backtracking observed from computer simulations
Da, Pardo, Xu, Zhang, Gao,Wang, Huang, Nature Communications 7, 11244, (2016)
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Backtracking observed from computer simulations
Da, Pardo, Xu, Zhang, Gao,Wang, Huang, Nature Communications 7, 11244, (2016)
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Computer simulations for biomolecules
Levitt, M., Nature Structural Biology 8, 392-393 (2001); Bioinfomatics 5, 2015
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Kinetic Model
- Chodera. Noé. Pande, Hummer, Shuttle, Levy....
C(x1, x2, . . . xN, t) = e ̂
ℒtC(x1, x2, . . . xN,0)
C1(x1, x2, . . . xN, t) C2(x1, x2, . . . xN, t) C3(x1, x2, . . . xN, t) C4(x1, x2, . . . xN, t) C5(x1, x2, . . . xN, t)
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Markov State Model
Clustering (splitting) Conformations Microstate Model Macrostate Model Kinetic Lumping
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Clustering and state decomposition
Fu Kit Sheong etc, JCTC 11, 17 (2015); Liu Song etc, JCC 38, 152 (2017)
K-Centers APM
(Automatic State Partitioning for Multibody Systems)
APLoD
(Adaptive Partitioning by Local Density- Peaks)
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Paths and dominant paths
- F. Noé etc, PNAS 106, 19011 (2009); L. Meng, etc. JCP 147, 044112 (2017); L. Zhu etc. JCP 150, 124105 (2019)
TPT
(Transition path theory)
TAPS
(Traveling-salesman Based Automated Path Searching Method)
Path lumping
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Self-assembly
- Phys. Chem. Chem. Phys. 18, 23494-23499, (2016); J. Phys. Chem. Lett. 8, 1798–1803, (2017)
Block Copolymer Amphiphilic molecule PYR PYN
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