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Relevant bibliographies by topics / Molecuar dynamics and docking simulation

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Journal articles

Academic literature on the topic 'Molecuar dynamics and docking simulation'

Author: Grafiati

Published: 14 March 2023

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Journal articles on the topic "Molecuar dynamics and docking simulation"

1

Naqvi, Ahmad Abu Turab, Taj Mohammad, Gulam Mustafa Hasan, and Md Imtaiyaz Hassan. "Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships." Current Topics in Medicinal Chemistry 18, no. 20 (2018): 1755–68. http://dx.doi.org/10.2174/1568026618666181025114157.

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Protein-ligand interaction is an imperative subject in structure-based drug design and protein function prediction process. Molecular docking is a computational method which predicts the binding of a ligand molecule to the particular receptor. It predicts the binding pose, strength and binding affinity of the molecules using various scoring functions. Molecular docking and molecular dynamics simulations are widely used in combination to predict the binding modes, binding affinities and stability of different protein-ligand systems. With advancements in algorithms and computational power, molec

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2

李, 博. "Progress in Molecular Docking and Molecular Dynamics Simulation." Journal of Comparative Chemistry 03, no. 01 (2019): 1–10. http://dx.doi.org/10.12677/cc.2019.31001.

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3

Miyagawa, Hiroh, and Kunihiro Kitamura. "1P565 Molecular dynamics simulations of association and docking between an inhibitor and an enzyme.(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S288. http://dx.doi.org/10.2142/biophys.46.s288_1.

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4

Meng, Fancui. "Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds." Journal of Theoretical Chemistry 2013 (December 4, 2013): 1–7. http://dx.doi.org/10.1155/2013/739574.

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The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-

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5

Bathelt, Christine, Rolf Schmid, and Jürgen Pleiss. "Regioselectivity of CYP2B6: homology modeling, molecular dynamics simulation, docking." Journal of Molecular Modeling 8, no. 11 (2002): 327–35. http://dx.doi.org/10.1007/s00894-002-0104-y.

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Kurniawan, Isman, Muhammad Salman Fareza, and Ponco Iswanto. "CoMFA, Molecular Docking and Molecular Dynamics Studies on Cycloguanil Analogues as Potent Antimalarial Agents." Indonesian Journal of Chemistry 21, no. 1 (2020): 66. http://dx.doi.org/10.22146/ijc.52388.

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Malaria is a disease that commonly infects humans in many tropical areas. This disease becomes a serious problem because of the high resistance of Plasmodium parasite against the well-established antimalarial agents, such as Artemisinin. Hence, new potent compounds are urgently needed to resolve this resistance problem. In the present study, we investigated cycloguanil analogues as a potent antimalarial agent by utilizing several studies, i.e., comparative of molecular field analysis (CoMFA), molecular docking and molecular dynamics (MD) simulation. A CoMFA model with five partial least square

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7

Khare, Noopur, Sanjiv Kumar Maheshwari, Syed Mohd Danish Rizvi, et al. "Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease." Brain Sciences 12, no. 6 (2022): 770. http://dx.doi.org/10.3390/brainsci12060770.

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Calcium homeostasis modulator 1 (CALHM1) is a protein responsible for causing Alzheimer’s disease. In the absence of an experimentally designed protein molecule, homology modelling was performed. Through homology modelling, different CALHM1 models were generated and validated through Rampage. To carry out further in silico studies, through molecular docking and molecular dynamics simulation experiments, various flavonoids and alkaloids from Bauhinia variegata were utilised as inhibitors to target the protein (CALHM1). The sequence of CALHM1 was retrieved from UniProt and the secondary structur

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8

Zaki, Magdi E. A., Sami A. Al-Hussain, Vijay H. Masand, et al. "Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis." Pharmaceuticals 14, no. 4 (2021): 357. http://dx.doi.org/10.3390/ph14040357.

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Due to the genetic similarity between SARS-CoV-2 and SARS-CoV, the present work endeavored to derive a balanced Quantitative Structure−Activity Relationship (QSAR) model, molecular docking, and molecular dynamics (MD) simulation studies to identify novel molecules having inhibitory potential against the main protease (Mpro) of SARS-CoV-2. The QSAR analysis developed on multivariate GA–MLR (Genetic Algorithm–Multilinear Regression) model with acceptable statistical performance (R2 = 0.898, Q2loo = 0.859, etc.). QSAR analysis attributed the good correlation with different types of atoms like non

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9

De Paris, Renata, Christian V. Quevedo, Duncan D. Ruiz, Osmar Norberto de Souza, and Rodrigo C. Barros. "Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments." Computational Intelligence and Neuroscience 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/916240.

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Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we d

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10

Luo, Lianxiang, Ai Zhong, Qu Wang, and Tongyu Zheng. "Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, ADMET, and Molecular Dynamics (MD) Simulation of Potential Inhibitors of PD-L1 from the Library of Marine Natural Products." Marine Drugs 20, no. 1 (2021): 29. http://dx.doi.org/10.3390/md20010029.

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Background: In the past decade, several antibodies directed against the PD-1/PD-L1 interaction have been approved. However, therapeutic antibodies also exhibit some shortcomings. Using small molecules to regulate the PD-1/PD-L1 pathway may be another way to mobilize the immune system to fight cancer. Method: 52,765 marine natural products were screened against PD-L1(PDBID: 6R3K). To identify natural compounds, a structure-based pharmacophore model was generated, following by virtual screening and molecular docking. Then, the absorption, distribution, metabolism, and excretion (ADME) test was c

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