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   Articles with "gaussian accelerated" as a keyword



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Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis

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recommendations! Published in 2021 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.0c01470

Abstract: Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and SW2, in K-Ras, which is considered as an important target of anticancer drug design. To unveil a molecular mechanism with regard… read more here.

Keywords: sw1 sw2; gaussian accelerated; gtp; gdp gtp ... See more keywords

Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations

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recommendations! Published in 2022 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.2c00961

Abstract: S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation of bacterial gene expression at the level of transcription attenuation or translation inhibition. In this study, multiple independent Gaussian-accelerated molecular dynamics simulations were performed to… read more here.

Keywords: independent gaussian; sam; multiple independent; identification ... See more keywords

Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems.

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recommendations! Published in 2024 at "Journal of chemical theory and computation"

DOI: 10.1021/acs.jctc.4c00501

Abstract: This study introduces a novel method named multiple parameter replica exchange Gaussian accelerated molecular dynamics (MP-Rex-GaMD), building on the Gaussian accelerated molecular dynamics (GaMD) algorithm. GaMD enhances sampling and retrieves free energy information for biomolecular… read more here.

Keywords: energy; gaussian accelerated; free energy; molecular dynamics ... See more keywords

Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes

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recommendations! Published in 2022 at "RSC Advances"

DOI: 10.1039/d1ra07936k

Abstract: Understanding the molecular mechanism of the GTP-KRAS binding is significant for improving the target roles of KRAS in cancer treatment. In this work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations were applied to decode… read more here.

Keywords: gtp kras; switch; molecular dynamics; free energy ... See more keywords

Investigating the binding mechanism of AML inhibitors based on panobinostat with HDAC3 proteins using Gaussian accelerated molecular dynamics

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recommendations! Published in 2025 at "RSC Advances"

DOI: 10.1039/d5ra01129a

Abstract: Class I histone deacetylases (HDACs) play a crucial role in the transformation and survival of myeloid and lymphoid malignancies, with HDAC1, 2, and 3 (Class I HDACs) being potential molecular targets for acute myelogenous leukemia… read more here.

Keywords: panobinostat hdac3; gaussian accelerated; molecular dynamics; investigating binding ... See more keywords

Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations.

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recommendations! Published in 2023 at "Journal of enzyme inhibition and medicinal chemistry"

DOI: 10.1080/14756366.2023.2195995

Abstract: Mutations highly affect the structural flexibility of two switch domains in M-RAS considered an important target of anticancer drug design. Gaussian accelerated molecular dynamics (GaMD) simulations were applied to probe the effect of mutations P40D,… read more here.

Keywords: molecular dynamics; gaussian accelerated; accelerated molecular; gtp ras ... See more keywords

Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides

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recommendations! Published in 2022 at "Foods"

DOI: 10.3390/foods11030327

Abstract: Angiotensin-converting enzyme (ACE)-inhibitory peptides extracted from food proteins can lower blood pressure by inhibiting ACE activity. A recent study showed that the inhibitory activity of IY (Ile-Tyr, a dipeptide derived from soybean protein) against ACE… read more here.

Keywords: converting enzyme; enzyme ace; gaussian accelerated; ace ... See more keywords

Study on the Mechanism of Interaction between Dipeptidyl Peptidase 4 and Inhibitory Peptides Based on Gaussian Accelerated Molecular Dynamic Simulation

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recommendations! Published in 2024 at "International Journal of Molecular Sciences"

DOI: 10.3390/ijms25020839

Abstract: Dipeptidyl peptidase 4 (DPP4) inhibitors can effectively inhibit the activity of DPP4, increasing the concentrations of glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), which allows for them to effectively contribute to the reduction of… read more here.

Keywords: gaussian accelerated; peptide; dipeptidyl peptidase; dpp4 ... See more keywords

Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations

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recommendations! Published in 2023 at "Molecules"

DOI: 10.3390/molecules28072886

Abstract: G12 mutations heavily affect conformational transformation and activity of KRAS. In this study, Gaussian accelerated molecular dynamics (GaMD) simulations were performed on the GDP-bound wild-type (WT), G12A, G12D, and G12R KRAS to probe mutation-mediated impacts… read more here.

Keywords: g12 mutations; molecular dynamics; gaussian accelerated; conformational alterations ... See more keywords

Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics

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recommendations! Published in 2024 at "Molecules"

DOI: 10.3390/molecules29030645

Abstract: The HRAS protein is considered a critical target for drug development in cancers. It is vital for effective drug development to understand the effects of mutations on the binding of GTP and GDP to HRAS.… read more here.

Keywords: conformational states; gaussian accelerated; switch domains; molecular dynamics ... See more keywords