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Cited by 32 publications
(29 citation statements)
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References 62 publications
(95 reference statements)
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“…Recent decades have witnessed the upsurge in biophysical advances especially in crystallographic technologies that can retrieve increasing amounts of structural data for allosteric proteins, sites, and modulators, and constitute solid bases for computational allosteric research. Consequently, various theoretical allosteric models, such as the "conformational selection and population shift" theory, 44,45 the "ensemble allosteric" model, [46][47][48] and the "reversed allostery" model, 15,[49][50][51] have been proposed. They all supply insightful guidance for the development of allosteric tools for drug design.…”
Section: Introductionmentioning
confidence: 99%
“…Recent decades have witnessed the upsurge in biophysical advances especially in crystallographic technologies that can retrieve increasing amounts of structural data for allosteric proteins, sites, and modulators, and constitute solid bases for computational allosteric research. Consequently, various theoretical allosteric models, such as the "conformational selection and population shift" theory, 44,45 the "ensemble allosteric" model, [46][47][48] and the "reversed allostery" model, 15,[49][50][51] have been proposed. They all supply insightful guidance for the development of allosteric tools for drug design.…”
Section: Introductionmentioning
confidence: 99%
“…The gilteritinib was extracted from the 4JQR structure, and we then employed molecular docking method to dock gilteritinib into the ALK active site using the crystal structure of ALK–lorlatinib complex (PDB ID: 4CLI) ( Johnson et al, 2014 ). Molecular docking method has been widely used to model previously unknown protein kinase/enzyme–ligand interactions such as epidermal growth factor receptor (EFGR)–osimertinib ( Qiu et al, 2021 ), angiotension-converting 2 (ACE2)–puerarin/quercetin ( Pan et al, 2020 ), proliferator activated receptor γ (PPARγ)–bavachinin ( Feng et al, 2021 ), and sirtuin 6 (SIRT6)–JYQ-42 interactions ( Zhang et al, 2021 ).…”
Section: Results and Discssionmentioning
confidence: 99%
“…Two rounds of minimizations of the three simulated systems were performed, including the steepest descent and conjugate gradient algorithms. This simulation protocol has also been employed in recent studies of protein conformational dynamics ( Lu et al, 2019c ; An et al, 2021 ; Liu et al, 2021 ; Zhang et al, 2022b ). Then, each system was heated up from 0 to 300 K within 1 ns of MD simulations in the canonical ensemble (NVT), imposing position restraints of 100 kcal/mol·A 2 on the solute atoms.…”
Section: Methodsmentioning
confidence: 99%