Identification of AtHsp90. 6 involved in early embryogenesis and its structure prediction by molecular dynamics simulations

A Luo, X Li, X Zhang, H Zhan, H Du… - Royal Society …, 2019 - royalsocietypublishing.org
… key molecular chaperone involved in folding the synthesized protein and controlling protein
quality. Conformational dynamics coupled to ATPase activity … potential analysis revealed the …

[HTML][HTML] Computational driven molecular dynamics simulation of keratinocyte growth factor behavior at different pH conditions

MB Boroujeni, MS Dastjerdeh, MA Shokrgozar… - Informatics in Medicine …, 2021 - Elsevier
… the structure, stability, and function of proteins [[59], [60], [61]]. Our finding revealed that with
… and behavior of rhKGF were also similar to the Sphingosine kinase 1 (SphK1) protein. As it …

Uncovering the structural and binding insights of dual inhibitors simultaneously targeting two distinct sites on EGFR kinase

KK Bhanja, M Sharma, N Patra - The Journal of Physical …, 2023 - ACS Publications
… performed conventional molecular dynamics simulations and … These variations contribute
to irregular kinase activity and … Furthermore, our findings reveal that the typical K745–E762 …

Identification of Novel PI3Kα Inhibitor Against Gastric Cancer: QSAR-, Molecular Docking–, and Molecular Dynamics Simulation–Based Analysis

F Yuan, T Li, X Xu, T Chen, Z Cao - Applied Biochemistry and …, 2024 - Springer
… viable, the thermodynamic and kinetic properties of protein apo … ns in simulated protein ligand
molecular dynamics systems. … its kinase inhibiting activity against cyclin-dependent kinase, …

Searching for natural Aurora a kinase inhibitors from peppers using molecular docking and molecular dynamics

P Siudem, Ł Szeleszczuk, K Paradowska - Pharmaceuticals, 2023 - mdpi.com
… Table 1 shows a list of ligands, the IC50 values determined … desolvation of the ligand is
thermodynamically non-favorable as … hydrogen bonds using molecular dynamics simulations [28]. …

Conformational insight on WT-and mutated-EGFR receptor activation and inhibition by epigallocatechin-3-gallate: Over a rational basis for the design of selective non …

C Minnelli, E Laudadio, G Mobbili… - … journal of molecular …, 2020 - mdpi.com
molecular dynamic simulation (MD), the present study investigated the architectural changes
of wild-type and mutants EGFR’s kinase … MD simulation revealed the formation of little more …

Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics

J Chen, W Wang, H Sun, L Pang, B Yin - … of Computer-Aided Molecular …, 2020 - Springer
… Enthalpy and entropy changes are two significant thermodynamic factors accompanying …
Alignment of two structures falling into the energy basins I and II shows that two loops L2 …

Protein flexibility and dissociation pathway differentiation can explain onset of resistance mutations in kinases

M Shekhar, Z Smith, MA Seeliger… - Angewandte Chemie …, 2022 - Wiley Online Library
… can be explained purely through thermodynamics. However, the more … how all-atom molecular
dynamics simulations using recent … agents for modulating kinase activity has been well …

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

DJ Huggins, PC Biggin, MA Dämgen… - … Molecular Science, 2019 - Wiley Online Library
… , molecular dynamics simulation of the enzyme MalL reveal … artifacts in the activation
mechanism of p38α MAP kinase.105 … key conformational and thermodynamic features, but also to …

Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation

L Chen, WM Marsiglia, H Chen, J Katigbak… - Nature chemical …, 2020 - nature.com
… complex that is thermodynamically disadvantaged because … The structure reveals an
asymmetric complex of two FGFR3K … Consistent with our NMR data, molecular dynamics