User profiles for Ruxi Qi
Ruxi QiUniversity of California Irvine Verified email at uci.edu Cited by 9352 |
Recent developments and applications of the MMPBSA method
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been
widely applied as an efficient and reliable free energy simulation method to model …
widely applied as an efficient and reliable free energy simulation method to model …
[BOOK][B] Amber 2023
Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …
dynamics simulations, particularly on biomolecules. None of the individual programs carries …
AmberTools
AmberTools is a free and open-source collection of programs used to set up, run, and
analyze molecular simulations. The newer features contained within AmberTools23 are …
analyze molecular simulations. The newer features contained within AmberTools23 are …
Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d–containing cyanobacterium
L Shen, Y Gao, K Tang, R Qi, L Fu, JH Chen… - Science …, 2024 - science.org
Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d) as its major
pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina …
pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina …
Identification of a highly conserved neutralizing epitope within the RBD region of diverse SARS-CoV-2 variants
…, Z Jiang, Y Gao, M Rao, J Feng, Z Zhang, R Qi… - Nature …, 2024 - nature.com
The constant emergence of SARS-CoV-2 variants continues to impair the efficacy of existing
neutralizing antibodies, especially XBB.1.5 and EG.5, which showed exceptional immune …
neutralizing antibodies, especially XBB.1.5 and EG.5, which showed exceptional immune …
Replica exchange molecular dynamics: a practical application protocol with solutions to common problems and a peptide aggregation and self-assembly example
Protein aggregation is associated with many human diseases such as Alzheimer’s disease (AD),
Parkinson’s disease (PD), and type II diabetes (T2D). Understanding the molecular …
Parkinson’s disease (PD), and type II diabetes (T2D). Understanding the molecular …
Expanding the nanoarchitectural diversity through aromatic di-and tri-peptide coassembly: Nanostructures and molecular mechanisms
Molecular self-assembly is pivotal for the formation of ordered nanostructures, yet the structural
diversity obtained by the use of a single type of building block is limited. Multicomponent …
diversity obtained by the use of a single type of building block is limited. Multicomponent …
Regulation of the Hippo pathway by phosphatidic acid-mediated lipid-protein interaction
The Hippo pathway plays a crucial role in organ size control and tumor suppression, but its
precise regulation is not fully understood. In this study, we discovered that phosphatidic acid (…
precise regulation is not fully understood. In this study, we discovered that phosphatidic acid (…
Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer
Experiments suggested that the fibrillation of the 11–25 fragment (hIAPP(11–25)) of human
islet amyloid polypeptide (hIAPP or amylin) involves the formation of transient α-helical …
islet amyloid polypeptide (hIAPP or amylin) involves the formation of transient α-helical …
The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1
Heavy metals are both integral parts of cells and environmental toxicants, and their deregulation
is associated with severe cellular dysfunction and various diseases. Here we show that …
is associated with severe cellular dysfunction and various diseases. Here we show that …