Zobrazeno 1 - 10
of 15
pro vyhledávání: '"Sian Xiao"'
Publikováno v:
Viruses, Vol 15, Iss 10, p 2073 (2023)
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterizat
Externí odkaz:
https://doaj.org/article/8da08ab04ca04659858eb93a2da3c667
Publikováno v:
Frontiers in Molecular Biosciences, Vol 9 (2022)
Allostery is a fundamental process in regulating protein activities. The discovery, design, and development of allosteric drugs demand better identification of allosteric sites. Several computational methods have been developed previously to predict
Externí odkaz:
https://doaj.org/article/539aad29409347beac286dbcf1493e61
Publikováno v:
Frontiers in Molecular Biosciences, Vol 8 (2021)
Molecular dynamics (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time.
Externí odkaz:
https://doaj.org/article/0dd63e9213564b10acf17ca8968be3b0
Publikováno v:
The Journal of Physical Chemistry B. 127:3596-3605
Predicting the viscosity of polymer nanocomposites (PNCs) is of critical importance as it governs a dominant role in PNCs processing and application. Machine learning (ML) algorithms, enabled by pre-existing experimental and computational data, have
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b6e31573ecb821108c38e6704a4304a5
https://doi.org/10.1021/acs.jpcb.3c01697
https://doi.org/10.1021/acs.jpcb.3c01697
Publikováno v:
Journal of Computational Biophysics and Chemistry. 22:489-501
Molecular dynamics (MD) simulations have been extensively used to study protein dynamics and subsequently functions. However, they are unable to sufficiently explore the conformational space within equilibrium timescales. The purpose of this study is
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04d1a99d23e4288022b63081d4a3e069
https://doi.org/10.1142/s2737416523500217
https://doi.org/10.1142/s2737416523500217
Publikováno v:
Journal of Chemical Information and Modeling. 63:67-75
Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most of the computational time is sp
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a1d4dc80b335260306316fe722aa3738
https://doi.org/10.1021/acs.jcim.2c01213
https://doi.org/10.1021/acs.jcim.2c01213
Publikováno v:
bioRxiv
In the current study, we combine multiple microsecond MD simulations and Markov state models (MSM) to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 S RBD-ACE2 complexes for the recently emerged XBB.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a13662d53b4a9027dec7d4af41f8c1fe
https://doi.org/10.1101/2023.05.20.541592
https://doi.org/10.1101/2023.05.20.541592
Publikováno v:
bioRxiv
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-base
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e6463a5521d9e3f2e5420c20cac2a79a
Publikováno v:
Nucleic Acids Research.
Allostery refers to the biological process by which an effector modulator binds to a protein at a site distant from the active site, known as allosteric site. Identifying allosteric sites is essential for discovering allosteric process and is conside
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::38673e8c25ddb1808748c62718e569b9
https://doi.org/10.1093/nar/gkad303
https://doi.org/10.1093/nar/gkad303
Publikováno v:
Trends in biochemical sciences.
The fundamental biological importance and complexity of allosterically regulated proteins stem from their central role in signal transduction and cellular processes. Recently, machine-learning approaches have been developed and actively deployed to f
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e36dc4b75342bb9f8f59b9e8574f7409
https://pubmed.ncbi.nlm.nih.gov/36564251
https://pubmed.ncbi.nlm.nih.gov/36564251