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Ligand docking
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In this research paper we report the detailed synthesis, spectral (1H-NMR, FT-IR, and UV-Vis), crystal structure determination, DFT studies, and molecular modeling of 4-amino-3-mercapto-5-methyl-1,2,4-triazole (L2) Schiff base ligand and its complexes of cadmium as suitable bioactive agents for the treatment of malaria. From the spectroscopic results, the synthesized Schiff base has potentialtridentate coordination with themetal ion via hydroxy naphthalinic-O, azomethine-N and sulphur atom of the thione group.
17p
dianmotminh02
03-05-2024
2
1
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The melting points of the complexes were >350oC, indicating high thermal stability. Cu-Zn-containing complex showed the least binding energy against the three proteins. The bioactivity scores of the complexes were between -0.50 and 0.0. Against A549 Cu-Zn, Co-Zn and Fe-Zn containing complexes showed potential activity. Against MCF-7, Fe-Cu containing complex had IC50 of 53.5 whereas Co-Zn containing complex was active against HepG2. Three complexes were active against S. aureus in the tested range.
18p
dianmotminh02
03-05-2024
2
1
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Ebook "Protein modelling" detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction.
332p
tudohanhtau1006
29-03-2024
2
1
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A molecular docking study of three natural acridones, namely citrusinine-I, 5-hydroxynoracronycin, and paratrimerin C on a target enzyme DNA polymerase μ (Pol μ), was performed. In addition, the hydrogen peroxide anion (HOO─ ), a model radical, and delavirdine, a synthetic drug, are used as ligands for docking on this target protein to investigate the activity of the selected compounds to protect Pol μ protein against their harmful effects.
7p
nhanchienthien
25-07-2023
3
2
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Unsaturated ketone derivatives are known as monoamine oxidase B (MAO-B) inhibitors, a potential drug target for Parkinson’s disease. Here, molecular modeling studies, including 2D-QSAR, ADMET prediction, molecular docking, and MD simulation, were performed on a new series of MAO-B inhibitors. The objective is to identify new MAO-B inhibitors with high inhibitory efficacy. The developed 2D-QSAR model was based on the descriptors of MOE software.
21p
lyhuyenthu
31-01-2023
4
2
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A binding stability order predicting, molecular docking based fast technique was developed for host–guest complexes. Molecular descriptors were applied to ligand molecules to make the binding energy based docking scoring functions more efficient and reach the ±0.50 log K unit theoretical precision for predictions. The goal of this work was to model complexes of cucurbit[7]uril (CB7) as a host molecule with different local anesthetics and choline and phosphonium choline molecules.
17p
tudichquannguyet
29-11-2021
6
0
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The excessive activity of acetylcholinesterase enzyme (AChE) causes different neuronal problems, especially dementia and neuronal cell deaths. Food and Drug Administration (FDA) approved drugs donepezil, rivastigmine, tacrine and galantamine are AChE inhibitors and in the treatment of Alzheimer’s disease (AD) these drugs are currently prescribed. However, these inhibitors have various adverse side effects. Therefore, there is a great need for the novel selective AChE inhibitors with fewer adverse side effects for the effective treatment.
15p
tudichquannguyet
29-11-2021
15
1
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The selectivity and the thermostability of EndoBI-1 and EndoBI-2 suggest that these enzymes may be useful for many scientific and industrial applications. In this study, the growing numbers of homologous sequences in different databases were exploited in a comparative approach to investigate structural properties of EndoBI-1 and EndoBI-2 enzymes. Moreover, the complete and partial homology models of these two enzymes were generated and evaluated.
13p
tudichquannguyet
29-11-2021
8
2
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The molecular features characteristics provided by the 3D-QSAR contour plots were quite useful for designing and improving the activity of acetylcholinesterase of this class. Based on these findings, a new series of 1,2,3-triazole based derivatives were designed, among which compound A1 with the highest predictive activity was subjected to detailed molecular docking and compared to the most active compound.
14p
tudichquannguyet
29-11-2021
10
1
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Antimicrobial resistance (AMR) threatens millions of people around the world and has been declared a global risk by the World Economic Forum. One of the important AMR mechanisms in Enterobacteriaceae is the production of extended-spectrum β-lactamases. The most common ESBL, CTX-M β-lactamases, is spread to the world by CTX-M-15 and CTX-M-14. Sulbactam, clavulanic acid, and tazobactam are first-generation β-lactamase inhibitors and avibactam is a new non-β-lactam β-lactamase inhibitor.
12p
tudichquannguyet
29-11-2021
6
1
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Approximately 20% of MM patients harbor glucocorticoid (GC) resistance and are not responsive to therapeutic effect. Chaperoneheat-shock proteins Hsp90 is needed for ligand docking, The imbalance of Hsp90/GRα (glucocorticoid receptor α) may be an important cause of GC resistance.
7p
vimahuateng
26-11-2021
15
1
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The obtained results indicate that the complexes bind to DNA through intercalation mode, which is further validated by molecular docking studies. The hydrolytic cleavage of the pBR322 DNA from supercoiled to nicked form, by the metal complexes was investigated by gel electrophoresis technique. The metal complexes were also screened for their antioxidant, antiinflammatory and antibacterial activities and the findings have been reported.
12p
nguaconbaynhay11
16-04-2021
9
2
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Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to predict interactions without regard to the underlying structural scaffold that creates the surface.
22p
viwyoming2711
16-12-2020
15
1
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State-of-the-art protein-ligand docking methods are generally limited by the traditionally low accuracy of their scoring functions, which are used to predict binding affinity and thus vital for discriminating between active and inactive compounds.
12p
vikentucky2711
26-11-2020
11
1
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Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested that chemical similarity searching may be driven by the most-similar ligand.
11p
vioklahoma2711
19-11-2020
12
1
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Target identification is necessary for the comprehensive inference of the mechanism of action of a compound. The application of computational methods to predict the targets of bioactive compounds saves cost and time in drug research and development.
11p
viconnecticut2711
28-10-2020
9
1
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Molecular simulations are used to provide insight into protein structure and dynamics, and have the potential to provide important context when predicting the impact of sequence variation on protein function.
8p
vijisoo2711
27-10-2020
9
0
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Protein-ligand docking has emerged as a particularly important tool in drug design and development, and flexible ligand docking is a widely used method for docking simulations. Many docking software packages can simulate flexible ligand docking, and among them, Autodock is widely used.
20p
vicolorado2711
22-10-2020
8
0
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Despite continued efforts using chemical similarity methods in virtual screening, currently developed approaches suffer from time-consuming multistep procedures and low success rates. We recently developed a machine learning-based chemical binding similarity model considering common structural features from molecules binding to the same, or evolutionarily related targets.
18p
vicolorado2711
22-10-2020
14
0
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In this paper, catalpol propionylated analogs (CPs) were designed as drug ligands of glutathione peroxidase (GSH-Px) based on molecular docking (MD) using Surflex-Docking method. The calculated total scores (Total_score) and C log P of CPs are higher than that of catalpol, which show that the CPs maybe served as potential lead compounds as new antiaging drugs.
11p
vijiraiya2711
27-05-2020
15
1
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