Ruxi Qi
Ruxi Qi
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Recent developments and applications of the MMPBSA method
C Wang, DA Greene, L Xiao, R Qi, R Luo
Frontiers in molecular biosciences 4, 87, 2018
Amber 2021
DA Case, HM Aktulga, K Belfon, IY Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California Press, 2021
Expanding the nanoarchitectural diversity through aromatic di-and tri-peptide coassembly: Nanostructures and molecular mechanisms
C Guo, ZA Arnon, R Qi, Q Zhang, L Adler-Abramovich, E Gazit, G Wei
ACS nano 10 (9), 8316-8324, 2016
Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer
R Qi, Y Luo, B Ma, R Nussinov, G Wei
Biomacromolecules 15 (1), 122-131, 2014
Amber 2021: Reference Manual
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, D Cerutti, ...
AMBER 2018; 2018
DA Case, IY Ben-Shalom, SR Brozell, DS Cerutti, TE Cheatham III, ...
University of California, San Francisco, 2018
Regulation of the Hippo pathway by phosphatidic acid-mediated lipid-protein interaction
H Han, R Qi, JJ Zhou, AP Ta, B Yang, HJ Nakaoka, G Seo, KL Guan, ...
Molecular cell 72 (2), 328-340. e8, 2018
Aβ “stretching-and-packing” cross-seeding mechanism can trigger tau protein aggregation
R Qi, Y Luo, G Wei, R Nussinov, B Ma
The Journal of Physical Chemistry Letters 6 (16), 3276-3282, 2015
AMBER 2016 (University of California)
DA Case, D Cerutti, T Cheatham, T Darden, R Duke, T Giese, H Gohlke, ...
San Francisco, 2016
AMBER 2018
TA Darden, RE Duke, D Ghoreishi, MK Gilson, H Gohlke, AW Goetz, ...
University of California, San Francisco, 2018
AMBER 2018, Univ
DA Case, IY Ben-Shalom, SR Brozell, DS Cerutti, TE Cheatham III, ...
California, San Fr, 2018
Replica exchange molecular dynamics: a practical application protocol with solutions to common problems and a peptide aggregation and self-Assembly example
R Qi, G Wei, B Ma, R Nussinov
Methods in molecular biology (Clifton, NJ) 1777, 101, 2018
Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant
J Lei, R Qi, G Wei, R Nussinov, B Ma
Physical Chemistry Chemical Physics 18 (11), 8098-8107, 2016
Conformational stability and dynamics of the cancer‐associated isoform Δ133p53β are modulated by p53 peptides and p53‐specific DNA
J Lei, R Qi, Y Tang, W Wang, G Wei, R Nussinov, B Ma
The FASEB Journal 33 (3), 4225-4235, 2019
Interaction Dynamics in inhibiting the aggregation of Aβ peptides by SWCNTs: a combined experimental and coarse-grained molecular dynamic simulation study
D Lin, R Qi, S Li, R He, P Li, G Wei, X Yang
ACS chemical neuroscience 7 (9), 1232-1240, 2016
Dynamics of the conformational transitions during the dimerization of an intrinsically disordered peptide: a case study on the human islet amyloid polypeptide fragment
Q Qiao, R Qi, G Wei, X Huang
Physical Chemistry Chemical Physics 18 (43), 29892-29904, 2016
Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization
C Zhan, R Qi, G Wei, E Guven-Maiorov, R Nussinov, B Ma
Protein Engineering, Design and Selection 29 (9), 347-354, 2016
AMBER 18; 2018
D Case, I Ben-Shalom, S Brozell, D Cerutti, T Cheatham III, V Cruzeiro, ...
University of California, San Francisco, 0
AMBER 2017, 2017
D Case, D Cerutti, TE Cheatham III, TA Darden, RE Duke, TJ Giese, ...
San Francisco: University of California, 0
Heterogeneous dielectric implicit membrane model for the calculation of MMPBSA binding free energies
DA Greene, R Qi, R Nguyen, T Qiu, R Luo
Journal of chemical information and modeling 59 (6), 3041-3056, 2019
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