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Journal articles on the topic 'Docking inverse'

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Published: 7 July 2024

Last updated: 7 July 2024

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1

Darme, Pierre, Manuel Dauchez, Arnaud Renard, Laurence Voutquenne-Nazabadioko, Dominique Aubert, Sandie Escotte-Binet, Jean-Hugues Renault, Isabelle Villena, Luiz-Angelo Steffenel, and Stéphanie Baud. "AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability." International Journal of Molecular Sciences 22, no. 14 (July 13, 2021): 7489. http://dx.doi.org/10.3390/ijms22147489.

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Molecular docking is widely used in computed drug discovery and biological target identification, but getting fast results can be tedious and often requires supercomputing solutions. AMIDE stands for AutoMated Inverse Docking Engine. It was initially developed in 2014 to perform inverse docking on High Performance Computing. AMIDE version 2 brings substantial speed-up improvement by using AutoDock-GPU and by pulling a total revision of programming workflow, leading to better performances, easier use, bug corrections, parallelization improvements and PC/HPC compatibility. In addition to inverse docking, AMIDE is now an optimized tool capable of high throughput inverse screening. For instance, AMIDE version 2 allows acceleration of the docking up to 12.4 times for 100 runs of AutoDock compared to version 1, without significant changes in docking poses. The reverse docking of a ligand on 87 proteins takes only 23 min on 1 GPU (Graphics Processing Unit), while version 1 required 300 cores to reach the same execution time. Moreover, we have shown an exponential acceleration of the computation time as a function of the number of GPUs used, allowing a significant reduction of the duration of the inverse docking process on large datasets.

2

Kammer, Daniel C., and Adam D. Steltzner. "Structural Identification of Mir Using Inverse System Dynamics and Mir/Shuttle Docking Data." Journal of Vibration and Acoustics 123, no. 2 (December 1, 2000): 230–37. http://dx.doi.org/10.1115/1.1355030.

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The objective of this work was to investigate the use of inverse system identification techniques on Mir/Shuttle docking data to identify Mir vibrational characteristics for ultimate application to damage detection. A time-domain technique called a Remote Sensing System was proposed as an approach. The method uses inverse structural dynamics to identify vibrational characteristics of a structure. The Remote Sensing System method was demonstrated with a numerical simulation of Mir/Shuttle docking assuming that sensors were collocated with the Mir docking location. The method was then applied to the combined set of docking data from Mir/Shuttle missions STS-81, STS-89, and STS-91. Overall, the results produced by this work appear to indicate that Mir was in an undamaged state, at least with respect to docking excitation, at the time of STS-91. The significance of the contribution of the Remote Sensing System approach is that it is not affected by the nonstationarity and nonlinearity associated with the Mir/Shuttle docking interface, and docking forces at the interface do not have to be measured.

3

Kim, Stephanie S., Melanie L. Aprahamian, and Steffen Lindert. "Improving inverse docking target identification with Z ‐score selection." Chemical Biology & Drug Design 93, no. 6 (January 2, 2019): 1105–16. http://dx.doi.org/10.1111/cbdd.13453.

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4

Perez, German, Marcello Mascini, Valentina Lanzone, Manuel Sergi, Michele Del Carlo, Mauro Esposito, and Dario Compagnone. "Peptides Trapping Dioxins: A Docking-Based Inverse Screening Approach." Journal of Chemistry 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/491827.

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A rapid and cost-effective computational methodology for designing and rationalizing the selection of small peptides as receptors for dioxin-like compounds was proposed. The backbone of the dioxin Ah receptor binding site was used to design a series of penta- and hexapeptide libraries, with 1400 elements in total. Peptide flexibility was considered and 10 conformers were found to be a good option to represent peptide conformational space with fair speed-accuracy ratio. Each peptide conformer was treated as a possible receptor, generating a dedicated box and then running a docking process using as ligands a family of 76 dibenzo-p-dioxins and 113 dibenzofurans mono- and polychlorinated. Significant predictions were confirmed by comparing primary structure of top and bottom ranked peptides binding dioxins confirming that scrambled positions of the same amino acids gave completely different predicted binding. The hexapeptide EWFQPW, with the best binding score, was chosen as selective sorbent material in solid-phase extraction. The retention performances were tested using the 2,3,7,8-tetrachlorodibenzo-p-dioxin and two polychlorinated biphenyls in order to verify the hexapeptide specificity. The solid-phase extraction experimental procedure was optimized, and analytical parameters of hexapeptide sorbent material were compared with the resin without hexapeptide and a commercial reversed phase cartridge.

5

Ma, Zhiwei, Xianjin Xu, and Xiaoqin Zou. "MDockServer: An Efficient Docking Platform for Inverse Virtual Screening." Biophysical Journal 114, no. 3 (February 2018): 56a. http://dx.doi.org/10.1016/j.bpj.2017.11.358.

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6

Xu, Xianjin, Marshal Huang, and Xiaoqin Zou. "Docking-based inverse virtual screening: methods, applications, and challenges." Biophysics Reports 4, no. 1 (February 2018): 1–16. http://dx.doi.org/10.1007/s41048-017-0045-8.

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7

Russo, Silvana, and Walter Filgueira De Azevedo. "Advances in the Understanding of the Cannabinoid Receptor 1 – Focusing on the Inverse Agonists Interactions." Current Medicinal Chemistry 26, no. 10 (June 20, 2019): 1908–19. http://dx.doi.org/10.2174/0929867325666180417165247.

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Background: Cannabinoid Receptor 1 (CB1) is a membrane protein prevalent in the central nervous system, whose crystallographic structure has recently been solved. Studies will be needed to investigate CB1 complexes with its ligands and its role in the development of new drugs. Objective: Our goal here is to review the studies on CB1, starting with general aspects and focusing on the recent structural studies, with emphasis on the inverse agonists bound structures. Methods: We start with a literature review, and then we describe recent studies on CB 1 crystallographic structure and docking simulations. We use this structural information to depict protein-ligand interactions. We also describe the molecular docking method to obtain complex structures of CB 1 with inverse agonists. Results: Analysis of the crystallographic structure and docking results revealed the residues responsible for the specificity of the inverse agonists for CB 1. Most of the intermolecular interactions involve hydrophobic residues, with the participation of the residues Phe 170 and Leu 359 in all complex structures investigated in the present study. For the complexes with otenabant and taranabant, we observed intermolecular hydrogen bonds involving residues His 178 (otenabant) and Thr 197 and Ser 383 (taranabant). Conclusion: Analysis of the structures involving inverse agonists and CB 1 revealed the pivotal role played by residues Phe 170 and Leu 359 in their interactions and the strong intermolecular hydrogen bonds highlighting the importance of the exploration of intermolecular interactions in the development of novel inverse agonists.

8

Kamal, Ahmed A. M., Lucia Petrera, Jens Eberhard, and Rolf W. Hartmann. "Structure–functionality relationship and pharmacological profiles of Pseudomonas aeruginosa alkylquinolone quorum sensing modulators." Organic & Biomolecular Chemistry 15, no. 21 (2017): 4620–30. http://dx.doi.org/10.1039/c7ob00263g.

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Alkylquinolone derived compounds revealed four pharmacological profiles for PqsR modulation. Molecular docking illuminated the structural requirements. Only inverse agonists were effective pathoblockers inhibiting pyocyanin.

9

Kämper, Andreas, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, and Thomas Lengauer. "Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies." Journal of Chemical Information and Modeling 46, no. 2 (March 2006): 903–11. http://dx.doi.org/10.1021/ci050467z.

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10

Ban, Tomohiro, Masahito Ohue, and Yutaka Akiyama. "Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem." Computational Biology and Chemistry 73 (April 2018): 139–46. http://dx.doi.org/10.1016/j.compbiolchem.2018.02.008.

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11

Hui-fang, Liu, Shen Qing, Zhang Jian, and Fu Wei. "Evaluation of various inverse docking schemes in multiple targets identification." Journal of Molecular Graphics and Modelling 29, no. 3 (November 2010): 326–30. http://dx.doi.org/10.1016/j.jmgm.2010.09.004.

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12

ZHANG, MING, LIQUN WANG, and RONALD GOLDMAN. "BÉZIER SUBDIVISION FOR INVERSE MOLECULAR KINEMATICS." International Journal of Computational Geometry & Applications 16, no. 05n06 (December 2006): 513–32. http://dx.doi.org/10.1142/s0218195906002166.

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Conformational searching is a core task in inverse molecular kinematics. Algorithmic improvements affecting either the speed or quality of conformational searching will have a profound impact on applications including ligand-receptor docking, ab initio prediction of protein structure, and protein folding. In this paper, we investigate a specific geometry-constrained conformational searching problem, where some feature atoms have pre-specified target positions. Using Bézier subdivision, we present a method to locate and approximate the solutions of the equations derived from constraints on the feature atoms. The conformations corresponding to these solutions are all the conformations satisfying the target constraints. Three implementations of the subdivision method taking advantage of the sparsity of the coefficients of the polynomial equations are presented and the results are compared and contrasted.

13

Chen, Shao-Jun, and Ji-Long Ren. "Identification of a Potential Anticancer Target of Danshensu by Inverse Docking." Asian Pacific Journal of Cancer Prevention 15, no. 1 (January 15, 2014): 111–16. http://dx.doi.org/10.7314/apjcp.2014.15.1.111.

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14

Vasseur, Romain, Stéphanie Baud, Luiz Angelo Steffenel, Xavier Vigouroux, Laurent Martiny, Michaël Krajecki, and Manuel Dauchez. "Inverse docking method for new proteins targets identification: A parallel approach." Parallel Computing 42 (February 2015): 48–59. http://dx.doi.org/10.1016/j.parco.2014.09.008.

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15

Zhou, Wanmeng, Hua Wang, Douglas Thomson, Guojin Tang, and Fan Zhang. "Inverse simulation system for evaluating handling qualities during rendezvous and docking." Acta Astronautica 137 (August 2017): 461–71. http://dx.doi.org/10.1016/j.actaastro.2017.05.011.

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16

Grinter, Sam Z., Yayun Liang, Sheng-You Huang, Salman M. Hyder, and Xiaoqin Zou. "An inverse docking approach for identifying new potential anti-cancer targets." Journal of Molecular Graphics and Modelling 29, no. 6 (April 2011): 795–99. http://dx.doi.org/10.1016/j.jmgm.2011.01.002.

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17

Kores, Katarina, Zala Kolenc, Veronika Furlan, and Urban Bren. "Inverse Molecular Docking Elucidating the Anticarcinogenic Potential of the Hop Natural Product Xanthohumol and Its Metabolites." Foods 11, no. 9 (April 26, 2022): 1253. http://dx.doi.org/10.3390/foods11091253.

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Natural products from plants exert a promising potential to act as antioxidants, antimicrobials, anti-inflammatory, and anticarcinogenic agents. Xanthohumol, a natural compound from hops, is indeed known for its anticarcinogenic properties. Xanthohumol is converted into three metabolites: isoxanthohumol (non-enzymatically) as well as 8- and 6-prenylnaringenin (enzymatically). An inverse molecular docking approach was applied to xanthohumol and its three metabolites to discern their potential protein targets. The aim of our study was to disclose the potential protein targets of xanthohumol and its metabolites in order to expound on the potential anticarcinogenic mechanisms of xanthohumol based on the found target proteins. The investigated compounds were docked into the predicted binding sites of all human protein structures from the Protein Data Bank, and the best docking poses were examined. Top scoring human protein targets with successfully docked compounds were identified, and their experimental connection with the anticarcinogenic function or cancer was investigated. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using retrospective metrics. More than half of the human protein targets of xanthohumol with the highest docking scores have already been connected with the anticarcinogenic function, and four of them (including two important representatives of the matrix metalloproteinase family, MMP-2 and MMP-9) also have a known experimental correlation with xanthohumol. Another important protein target is acyl-protein thioesterase 2, to which xanthohumol, isoxanthohumol, and 6-prenylnaringenin were successfully docked with the lowest docking scores. Moreover, the results for the metabolites show that their most promising protein targets are connected with the anticarcinogenic function as well. We firmly believe that our study can help to elucidate the anticarcinogenic mechanisms of xanthohumol and its metabolites as after consumption, all four compounds can be simultaneously present in the organism.

18

Wilde, Markus, Marco Ciarcià, Alessio Grompone, and Marcello Romano. "Experimental Characterization of Inverse Dynamics Guidance in Docking with a Rotating Target." Journal of Guidance, Control, and Dynamics 39, no. 6 (June 2016): 1173–87. http://dx.doi.org/10.2514/1.g001631.

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19

Kores, Katarina, Samo Lešnik, Urban Bren, Dušanka Janežič, and Janez Konc. "Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking." Journal of Chemical Information and Modeling 59, no. 5 (March 18, 2019): 2467–78. http://dx.doi.org/10.1021/acs.jcim.8b00981.

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20

Mani, Vasudevan, Minhajul Arfeen, Syed Imam Rabbani, Ali Shariq, and Palanisamy Amirthalingam. "Levetiracetam Ameliorates Doxorubicin-Induced Chemobrain by Enhancing Cholinergic Transmission and Reducing Neuroinflammation Using an Experimental Rat Model and Molecular Docking Study." Molecules 27, no. 21 (October 29, 2022): 7364. http://dx.doi.org/10.3390/molecules27217364.

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Cancer chemotherapy-induced cognitive impairment (chemobrain) is a major complication that affects the prognosis of therapy. Our study evaluates the nootropic-like activity of levetiracetam (LEVE) against doxorubicin (DOX)-induced memory defects using in vivo and molecular modelling. Rats were treated with LEVE (100 and 200 mg/kg, 30 days) and chemobrain was induced by four doses of DOX (2 mg/kg, i.p.). Spatial memory parameters were evaluated using an elevated plus maze (EPM) and Y-maze. Additionally, acetylcholinesterase (AChE) and the neuroinflammatory biomarkers cyclooxygenase-2 (COX-2), prostaglandin E2 (PGE2), nuclear factor-κB (NF-κB), and tumor necrosis factor-alpha (TNF-α) were analyzed using brain homogenate. PharmMapper was used for inverse docking and AutoDock Vina was used for molecular docking. LEVE treatment significantly diminished the DOX-induced memory impairment parameters in both the EPM and Y-maze. In addition, the drug treatment significantly reduced AChE, COX-2, PGE2, NF-κB, and TNF-α levels compared to DOX-treated animals. The inverse docking procedures resulted in the identification of AChE as the potential target. Further molecular modelling studies displayed interactions with residues Gly118, Gly119, and Ser200, critical for the hydrolysis of ACh. Analysis of the results suggested that administration of LEVE improved memory-related parameters in DOX-induced animals. The ‘nootropic-like’ activity could be related to diminished AChE and neuroinflammatory mediator levels.

21

Xi, Lin, Huasheng Ni, Buyun Wang, Zengchan Li, and Chenghao Zhang. "Dynamic Synthesis of Three−Point Circle Peripheral Docking Technology Pose." Applied Sciences 13, no. 4 (February 19, 2023): 2685. http://dx.doi.org/10.3390/app13042685.

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Research on space docking technology was first motivated by the application scenario of space station docking in the aviation field. Due to the maturity of this technology, its application field is expanding to other industries. To benefit the intelligent transportation field, this study uses space docking technology to realize combination and reconstruction between car bodies. Different spatial docking methods and structural characteristics are determined by different application scenarios. The docking of the space station is completed in the suspended state of the body in the outer space environment, which requires advanced technology, is high in hardware cost, and involves a small channel diameter. In this study, the docking of the reconstructed vehicle is completed on the ground; thus, it is low in hardware cost and involves a large channel diameter. Based on the above technical requirements, a three−point circular peripheral docking method is designed for the reconstructed vehicle. A visual positioning system is built, the mapping relationship between the camera coordinate system and the landmark coordinate system rotation matrix and translation vector is established, and the adaptive capture behavior is realized by path planning through the inverse pose solution model. Simulation experiments demonstrate that the active and passive vehicle bodies can achieve compliance capture with small collision force under the two conditions of forward collision and oblique collision, and the recovery coefficient after collision and docking is in the range of (0, 0.01). The acceleration decay process under two working conditions is measured in the crash test of a sample vehicle, which verifies the feasibility of the space reconstruction of the vehicle docking mechanism and the ability of this configuration to achieve tasks, providing a constructive idea for space docking technology with a large channel diameter.

22

GLAS-ALBRECHT, RENÉ, BIRGIT KAESBERG, GERD KNOLL, KARL ALLMANN, REGINA PAPE, and HELMUT PLATTNER. "Synchronised Secretory Organelle Docking in Paramecium." Journal of Cell Science 100, no. 1 (September 1, 1991): 45–54. http://dx.doi.org/10.1242/jcs.100.1.45.

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In certain strains (nd) of Paramecium tetraurelia all secretory organelles (trichocysts) can be detached from the cell surface and then reattached synchronously. To account for the lability of microtubules involved in trichocyst docking during the preparation procedures we analysed this process by combining video microscopy, analogue contrast enhancement microscopy, laser scanning fluorescence microscopy (both after fast freezing, freeze-substitution and anti-tubulin antibody fluorescence labelling), and electron microscopy after cryofixation. We found that synchronous trichocyst docking is saltatory, occurring along transiently formed microtubules (not normally recognised in these cells), which emanate from ciliary basal bodies, acting as organising centres. Hence, trichocyst transport proceeds from the plus to the minus end of microtubules (in contrast to gland cells), with the ‘correct’ polarity (trichocyst tips pointing to the cell surface). We then injected chromaffin granules (isolated from bovine adrenal medullae) during the trichocyst detachment phase and analysed cells by electron microscopy during and after synchronised redocking of trichocysts. We used a chromate reaction for chromaffin granule identification on semithin sections by X-ray microanalysis (scanning transmission EM). While chromaffin granules remained intact (as judged by morphology and Cr signals) and although cell function was unimpaired (as judged by complete trichocyst attachment), we determined that heterologous organelle transport was not detectable, probably because of inverse microtubule polarity.

23

Wu, Qinhang, Gang Bao, Yang Pan, Xiaoqi Qian, and Furong Gao. "Discovery of potential targets of Triptolide through inverse docking in ovarian cancer cells." PeerJ 8 (March 18, 2020): e8620. http://dx.doi.org/10.7717/peerj.8620.

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Triptolide (TPL) is proposed as an effective anticancer agent known for its anti-proliferation of a variety of cancer cells including ovarian cancer cells. Although some studies have been conducted, the mechanism by which TPL acts on ovarian cancer remains to be clearly described. Herein, systematic work based on bioinformatics was carried out to discover the potential targets of TPL in SKOV-3 cells. TPL induces the early apoptosis of SKOV-3 cells in a dose- and time-dependent manner with an IC50 = 40 ± 0.89 nM when cells are incubated for 48 h. Moreover, 20 nM TPL significantly promotes early apoptosis at a rate of 40.73%. Using a self-designed inverse molecular docking protocol, we fish the top 19 probable targets of TPL from the target library, which was built on 2,250 proteins extracted from the Protein Data Bank. The 2D-DIGE assay reveals that the expression of eight genes is affected by TPL. The results of western blotting and qRT-PCR assay suggest that 40 nM of TPL up-regulates the level of Annexin A5 (6.34 ± 0.07 fold) and ATP syn thase (4.08 ± 0.08 fold) and down-regulates the level of β-Tubulin (0.11 ± 0.12 fold) and HSP90 (0.21 ± 0.09 fold). More details of TPL affecting on Annexin A5 signaling pathway will be discovered in the future. Our results define some potential targets of TPL, with the hope that this agent could be used as therapy for the preclinical treatment of ovarian cancer.

24

Zhou, Wanmeng, Hua Wang, Dateng Yu, and Fuyu Sun. "Error Analysis and Modification of Inverse Simulation for Manually Controlled Rendezvous and Docking." Journal of Aerospace Engineering 30, no. 1 (January 2017): 04016072. http://dx.doi.org/10.1061/(asce)as.1943-5525.0000662.

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25

Choi, Youngjin. "In silico target identification of biologically active compounds using an inverse docking simulation." TANG [HUMANITAS MEDICINE] 3, no. 2 (May 31, 2013): 12.1–12.4. http://dx.doi.org/10.5667/tang.2013.0008.

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26

Raied, Mustafa Shakir, Abed Saoud Shaimaa, Faruk Hussain Dhuha, Fahad Ali Khalid, Shawqi Algburi Firas, and Salman Jasim Husam. "Synthesis, Antioxidant ability and Docking study for new 4,4'-((2-(Aryl)-1H-benzo[d]imidazole-1,3(2H)-diyl)bis(methylene))diphenol)." Research Journal of Chemistry and Environment 26, no. 10 (September 25, 2022): 28–36. http://dx.doi.org/10.25303/2610rjce028036.

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New series of 4,4'-((2-(Aryl)-1H-benzo[d]imidazole-1,3(2H)-diyl)bis(methylene))Diphenol(3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hydroxyl for the aryl attached position two for benzimidazole decrease the capability of interaction and give less bending and smaller docking score and there is inverse relationship between increasing hindrances around phenolic hydroxyl and DNA polymerase inhibition for these compounds.

27

Furlan, Veronika, Janez Konc, and Urban Bren. "Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin." Molecules 23, no. 12 (December 18, 2018): 3351. http://dx.doi.org/10.3390/molecules23123351.

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Research efforts are placing an ever increasing emphasis on identifying signal transduction pathways related to the chemopreventive activity of curcumin. Its anticarcinogenic effects are presumably mediated by the regulation of signaling cascades, including nuclear factor κB (NF-κB), activator protein 1 (AP-1), and mitogen-activated protein kinases (MAPK). By modulating signal transduction pathways, curcumin induces apoptosis in malignant cells, thus inhibiting cancer development and progression. Due to the lack of mechanistic insight in the scientific literature, we developed a novel inverse molecular docking protocol based on the CANDOCK algorithm. For the first time, we performed inverse molecular docking of curcumin into a collection of 13,553 available human protein structures from the Protein Data Bank resulting in prioritized target proteins of curcumin. Our predictions were in agreement with the scientific literature and confirmed that curcumin binds to folate receptor β, DNA (cytosine-5)-methyltransferase 3A, metalloproteinase-2, mitogen-activated protein kinase 9, epidermal growth factor receptor and apoptosis-inducing factor 1. We also identified new potential protein targets of curcumin, namely deoxycytidine kinase, NAD-dependent protein deacetylase sirtuin-1 and -2, ecto-5′-nucleotidase, core histone macro-H2A.1, tyrosine-protein phosphatase non-receptor type 11, macrophage colony-stimulating factor 1 receptor, GTPase HRas, aflatoxin B1 aldehyde reductase member 3, aldo-keto reductase family 1 member C3, amiloride-sensitive amine oxidase, death-associated protein kinase 2 and tryptophan-tRNA ligase, that may all play a crucial role in its observed anticancer effects. Moreover, our inverse docking results showed that curcumin potentially binds also to the proteins cAMP-specific 3′,5′-cyclic phosphodiesterase 4D and 17-β-hydroxysteroid dehydrogenase type 10, which provides a new explanation for its efficiency in the treatment of Alzheimer’s disease. We firmly believe that our computational results will complement and direct future experimental studies on curcumin’s anticancer activity as well as on its therapeutic effects against Alzheimer’s disease.

28

Sun, Deyuan, Junyi Wang, Zhigang Xu, Jianwen Bao, and Han Lu. "Research on Human-Robot Collaboration Method for Parallel Robots Oriented to Segment Docking." Sensors 24, no. 6 (March 8, 2024): 1747. http://dx.doi.org/10.3390/s24061747.

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In the field of aerospace, large and heavy cabin segments present a significant challenge in assembling space engines. The substantial inertial force of cabin segments’ mass often leads to unexpected motion during docking, resulting in segment collisions, making it challenging to ensure the accuracy and quality of engine segment docking. While traditional manual docking leverages workers’ expertise, the intensity of the labor and low productivity are impractical for real-world applications. Human-robot collaboration can effectively integrate the advantages of humans and robots. Parallel robots, known for their high precision and load-bearing capacity, are extensively used in precision assembly under heavy load conditions. Therefore, human-parallel-robot collaboration is an excellent solution for such problems. In this paper, a framework is proposed that is easy to realize in production, using human-parallel-robot collaboration technology for cabin segment docking. A fractional-order variable damping admittance control and an inverse dynamics robust controller are proposed to enhance the robot’s compliance, responsiveness, and trajectory tracking accuracy during collaborative assembly. This allows operators to dynamically adjust the robot’s motion in real-time, counterbalancing inertial forces and preventing collisions between segments. Segment docking assembly experiments are performed using the Stewart platform in this study. The results show that the proposed method allows the robot to swiftly respond to interaction forces, maintaining compliance and stable motion accuracy even under unknown interaction forces.

29

SAKK, ERIC. "ON THE COMPUTATION OF MOLECULAR SURFACE CORRELATIONS FOR PROTEIN DOCKING USING FOURIER TECHNIQUES." Journal of Bioinformatics and Computational Biology 05, no. 04 (August 2007): 915–35. http://dx.doi.org/10.1142/s0219720007002916.

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The computation of surface correlations using a variety of molecular models has been applied to the unbound protein docking problem. Because of the computational complexity involved in examining all possible molecular orientations, the fast Fourier transform (FFT) (a fast numerical implementation of the discrete Fourier transform (DFT)) is generally applied to minimize the number of calculations. This approach is rooted in the convolution theorem which allows one to inverse transform the product of two DFTs in order to perform the correlation calculation. However, such a DFT calculation results in a cyclic or "circular" correlation which, in general, does not lead to the same result as the linear correlation desired for the docking problem. In this work, we provide computational bounds for constructing molecular models used in the molecular surface correlation problem. The derived bounds are then shown to be consistent with various intuitive guidelines previously reported in the protein docking literature. Finally, these bounds are applied to different molecular models in order to investigate their effect on the correlation calculation.

30

Bhardwaj, Prashant, G. P. Biswas, and Biswanath Bhunia. "Docking-based inverse virtual screening strategy for identification of novel protein targets for triclosan." Chemosphere 235 (November 2019): 976–84. http://dx.doi.org/10.1016/j.chemosphere.2019.07.027.

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31

Zhou, Wanmeng, Hua Wang, Guojin Tang, and Shuai Guo. "Inverse simulation system for manual-controlled rendezvous and docking based on artificial neural network." Advances in Space Research 58, no. 6 (September 2016): 938–49. http://dx.doi.org/10.1016/j.asr.2016.05.039.

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32

Zhou, Wanmeng, and Hua Wang. "Researches on inverse simulation’s applications in teleoperation rendezvous and docking based on hyper-ellipsoidal restricted model predictive control for inverse simulation structure." Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering 229, no. 9 (November 4, 2014): 1675–89. http://dx.doi.org/10.1177/0954410014558320.

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33

Ribone, Sergio R., S. Alexis Paz, Cameron F. Abrams, and Marcos A. Villarreal. "Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking." Journal of Computer-Aided Molecular Design 36, no. 1 (November 26, 2021): 25–37. http://dx.doi.org/10.1007/s10822-021-00432-3.

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Lešnik, Samo, and Urban Bren. "Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking." Foods 11, no. 1 (December 28, 2021): 67. http://dx.doi.org/10.3390/foods11010067.

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Rosemary (Rosmarinus officinalis L.) represents a medicinal plant known for its various health-promoting properties. Its extracts and essential oils exhibit antioxidative, anti-inflammatory, anticarcinogenic, and antimicrobial activities. The main compounds responsible for these effects are the diterpenes carnosic acid, carnosol, and rosmanol, as well as the phenolic acid ester rosmarinic acid. However, surprisingly little is known about the molecular mechanisms responsible for the pharmacological activities of rosemary and its compounds. To discern these mechanisms, we performed a large-scale inverse molecular docking study to identify their potential protein targets. Listed compounds were separately docked into predicted binding sites of all non-redundant holo proteins from the Protein Data Bank and those with the top scores were further examined. We focused on proteins directly related to human health, including human and mammalian proteins as well as proteins from pathogenic bacteria, viruses, and parasites. The observed interactions of rosemary compounds indeed confirm the beforementioned activities, whereas we also identified their potential for anticoagulant and antiparasitic actions. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using both redocking procedures and retrospective metrics.

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Negi, Arvind, Nitisha Bhandari, Bharti Rajesh Kumar Shyamlal, and Sandeep Chaudhary. "Inverse docking based screening and identification of protein targets for Cassiarin alkaloids against Plasmodium falciparum." Saudi Pharmaceutical Journal 26, no. 4 (May 2018): 546–67. http://dx.doi.org/10.1016/j.jsps.2018.01.017.

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Saenz-Méndez, Patricia, Martin Eriksson, and Leif A. Eriksson. "Ligand Selectivity between the ADP-Ribosylating Toxins: An Inverse-Docking Study for Multitarget Drug Discovery." ACS Omega 2, no. 4 (April 28, 2017): 1710–19. http://dx.doi.org/10.1021/acsomega.7b00010.

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Deng, Qian, Shuliang Zou, Hongbin Chen, and Weixiong Duan. "Research on the Trajectory Planning of Demolition Robot Attachment Changing." Sensors 20, no. 16 (August 12, 2020): 4502. http://dx.doi.org/10.3390/s20164502.

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The process of changing the attachment of a demolition robot is a complex operation and requires a high docking accuracy, so it is hard for operators to control this process remotely through the camera’s perspective. To solve this problem, this paper studies trajectory planning for changing a demolition robot attachment. This paper establishes a link parameter model of the demolition robot; the position and attitude of the attachment are obtained through a camera, the optimal docking point is calculated to minimize the distance error during angle alignment for attachment change, the inverse kinemics of the demolition robot are solved, the trajectory planning algorithm and visualization program are programmed, and then the trajectory planning for the demolition robot attachment changing method is proposed. The results of calculations and experiments show that the method in this paper can meet the accuracy, efficiency, and safety requirements of demolition robot attachment changing, and it has promising application prospects in the decommissioning and dismantling of nuclear facilities and other radioactive environments.

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Paasche, Mathias Thoresen, Øystein Kaarstad Helgesen, and Edmund Førland Brekke. "Real-time 360 degrees view for the operator of milliAmpere 2." Journal of Physics: Conference Series 2618, no. 1 (October 1, 2023): 012009. http://dx.doi.org/10.1088/1742-6596/2618/1/012009.

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Abstract In the evolving domain of autonomous marine operations, accurate perception and representation of the surrounding environment are crucial for safe and effective execution. This paper addresses this issue by developing and testing a near real-time 360-degree bird’s eye view system for the situations where the ferry, milliAmpere 2, has to be manually controlled by a local operator onboard. The goal was to aid the operator during the critical phase of docking, by displaying the surrounding area of the ferry from a bird’s eye view. The bird’s eye view was made by using inverse perspective mapping on the undistorted images from the 8 cameras onboard. The system was implemented in Python, and aimed to reach a run-time of less than 200ms. This goal was reached during the initial phase of the work. However, during live testing, only near real-time performance was achieved. Despite some shortcomings, the operators found the system to be a “useful additional assistance” during the docking process.

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Kores, Katarina, Janez Konc, and Urban Bren. "Mechanistic Insights into Side Effects of Troglitazone and Rosiglitazone Using a Novel Inverse Molecular Docking Protocol." Pharmaceutics 13, no. 3 (February 28, 2021): 315. http://dx.doi.org/10.3390/pharmaceutics13030315.

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Thiazolidinediones form drugs that treat insulin resistance in type 2 diabetes mellitus. Troglitazone represents the first drug from this family, which was removed from use by the FDA due to its hepatotoxicity. As an alternative, rosiglitazone was developed, but it was under the careful watch of FDA for a long time due to suspicion, that it causes cardiovascular diseases, such as heart failure and stroke. We applied a novel inverse molecular docking protocol to discern the potential protein targets of both drugs. Troglitazone and rosiglitazone were docked into predicted binding sites of >67,000 protein structures from the Protein Data Bank and examined. Several new potential protein targets with successfully docked troglitazone and rosiglitazone were identified. The focus was devoted to human proteins so that existing or new potential side effects could be explained or proposed. Certain targets of troglitazone such as 3-oxo-5-beta-steroid 4-dehydrogenase, neutrophil collagenase, stromelysin-1, and VLCAD were pinpointed, which could explain its hepatoxicity, with additional ones indicating that its application could lead to the treatment/development of cancer. Results for rosiglitazone discerned its interaction with members of the matrix metalloproteinase family, which could lead to cancer and neurodegenerative disorders. The concerning cardiovascular side effects of rosiglitazone could also be explained. We firmly believe that our results deepen the mechanistic understanding of the side effects of both drugs, and potentially with further development and research maybe even help to minimize them. On the other hand, the novel inverse molecular docking protocol on the other hand carries the potential to develop into a standard tool to predict possible cross-interactions of drug candidates potentially leading to adverse side effects.

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Wang, Fangfang, Wei Yang, and Xiaojun Hu. "Discovery of High Affinity Receptors for Dityrosine through Inverse Virtual Screening and Docking and Molecular Dynamics." International Journal of Molecular Sciences 20, no. 1 (December 29, 2018): 115. http://dx.doi.org/10.3390/ijms20010115.

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Dityrosine is the product of oxidation that has been linked to a number of serious pathological conditions. Evidence indicates that high amounts of dityrosine exist in oxidized milk powders and some milk related foodstuffs, further reducing the nutritional value of oxidized proteins. Therefore, we hypothesize that some receptors related to special diseases would be targets for dityrosine. However, the mechanisms of the interaction of dityrosine with probable targets are still unknown. In the present work, an inverse virtual screening approach was performed to screen possible novel targets for dityrosine. Molecular docking studies were performed on a panel of targets extracted from the potential drug target database (PDTD) to optimize and validate the screening results. Firstly, two different conformations cis- and trans- were found for dityrosine during minimization. Moreover, Tubulin (αT) (−11.0 kcal/mol) was identified as a target for cis-dityrosine (CDT), targets including αT (−11.2 kcal/mol) and thyroid hormone receptor beta-1 (−10.7 kcal/mol) presented high binding affinities for trans-dityrosine (TDT). Furthermore, in order to provide binding complexes with higher precision, the three docked systems were further refined by performing thermo dynamic simulations. A series of techniques for searching for the most stable binding pose and the calculation of binding free energy are elaborately provided in this work. The major interactions between these targets and dityrosine were hydrophobic, electrostatic and hydrogen bonding. The application of inverse virtual screening method may facilitate the prediction of unknown targets for known ligands, and direct future experimental assays.

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Virgili-Llop, Josep, Costantinos Zagaris, Hyeongjun Park, Richard Zappulla, and Marcello Romano. "Experimental evaluation of model predictive control and inverse dynamics control for spacecraft proximity and docking maneuvers." CEAS Space Journal 10, no. 1 (May 22, 2017): 37–49. http://dx.doi.org/10.1007/s12567-017-0155-7.

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Efeoglu, Cagla, Sena Taskin, Ozge Selcuk, Begum Celik, Ece Tumkaya, Abdulilah Ece, Hayati Sari, Zeynel Seferoglu, Furkan Ayaz, and Yahya Nural. "Synthesis, anti-inflammatory activity, inverse molecular docking, and acid dissociation constants of new naphthoquinone-thiazole hybrids." Bioorganic & Medicinal Chemistry 95 (November 2023): 117510. http://dx.doi.org/10.1016/j.bmc.2023.117510.

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Acharya, Pratap, Ranju Bansal, and Prashant Kharkar. "Hybrids of Steroid and Nitrogen Mustard as Antiproliferative Agents: Synthesis, In Vitro Evaluation and In Silico Inverse Screening." Drug Research 68, no. 02 (September 26, 2017): 100–103. http://dx.doi.org/10.1055/s-0043-118538.

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AbstractHybrids of 16E-arylidene steroids and nitrogen mustard have been synthesized and evaluated for their in vitro cytotoxic activity to develop tissue specific antineoplastic agents from steroids. These hybrids displayed specificity towards leukemia cell lines, however somewhat reduced potency was observed in comparison with the earlier reported 16E-arylidene steroids. The in silico reverse screening experiments were employed to find out the probable pharmacological mechanism of these hybrids. Molecular docking studies suggested glucocorticoid receptors as a probable target for the antileukemic action of these steroid-nitrogen mustard hybrids.

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Isawi, Israa H., Paula Morales, Noori Sotudeh, Dow P. Hurst, Diane L. Lynch, and Patricia H. Reggio. "GPR6 Structural Insights: Homology Model Construction and Docking Studies." Molecules 25, no. 3 (February 7, 2020): 725. http://dx.doi.org/10.3390/molecules25030725.

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GPR6 is an orphan G protein-coupled receptor that has been associated with the cannabinoid family because of its recognition of a sub-set of cannabinoid ligands. The high abundance of GPR6 in the central nervous system, along with high constitutive activity and a link to several neurodegenerative diseases make GPR6 a promising biological target. In fact, diverse research groups have demonstrated that GPR6 represents a possible target for the treatment of neurodegenerative disorders such as Parkinson’s disease, Alzheimer’s disease, and Huntington’s disease. Several patents have claimed the use of a wide range of pyrazine derivatives as GPR6 inverse agonists for the treatment of Parkinson’s disease symptoms and other dyskinesia syndromes. However, the full pharmacological importance of GPR6 has not yet been fully explored due to the lack of high potency, readily available ligands targeting GPR6. The long-term goal of the present study is to develop such ligands. In this paper, we describe our initial steps towards this goal. A human GPR6 homology model was constructed using a suite of computational techniques. This model permitted the identification of unique GPR6 structural features and the exploration of the GPR6 binding crevice. A subset of patented pyrazine analogs were docked in the resultant GPR6 inactive state model to validate the model, rationalize the structure-activity relationships from the reported patents and identify the key residues in the binding crevice for ligand recognition. We will take this structural knowledge into the next phase of GPR6 project, in which scaffold hopping will be used to design new GPR6 ligands.

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Vieira, Graziela, Juliana Cavalli, Elaine C. D. Gonçalves, Saulo F. P. Braga, Rafaela S. Ferreira, Adair R. S. Santos, Maíra Cola, Nádia R. B. Raposo, Raffaele Capasso, and Rafael C. Dutra. "Antidepressant-Like Effect of Terpineol in an Inflammatory Model of Depression: Involvement of the Cannabinoid System and D2 Dopamine Receptor." Biomolecules 10, no. 5 (May 20, 2020): 792. http://dx.doi.org/10.3390/biom10050792.

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Depression has a multifactorial etiology that arises from environmental, psychological, genetic, and biological factors. Environmental stress and genetic factors acting through immunological and endocrine responses generate structural and functional changes in the brain, inducing neurogenesis and neurotransmission dysfunction. Terpineol, monoterpenoid alcohol, has shown immunomodulatory and neuroprotective effects, but there is no report about its antidepressant potential. Herein, we used a single lipopolysaccharide (LPS) injection to induce a depressive-like effect in the tail suspension test (TST) and the splash test (ST) for a preventive and therapeutic experimental schedule. Furthermore, we investigated the antidepressant-like mechanism of action of terpineol while using molecular and pharmacological approaches. Terpineol showed a coherent predicted binding mode mainly against CB1 and CB2 receptors and also against the D2 receptor during docking modeling analyses. The acute administration of terpineol produced the antidepressant-like effect, since it significantly reduced the immobility time in TST (100–200 mg/kg, p.o.) as compared to the control group. Moreover, terpineol showed an antidepressant-like effect in the preventive treatment that was blocked by a nonselective dopaminergic receptor antagonist (haloperidol), a selective dopamine D2 receptor antagonist (sulpiride), a selective CB1 cannabinoid receptor antagonist/inverse agonist (AM281), and a potent and selective CB2 cannabinoid receptor inverse agonist (AM630), but it was not blocked by a nonselective adenosine receptor antagonist (caffeine) or a β-adrenoceptor antagonist (propranolol). In summary, molecular docking suggests that CB1 and CB2 receptors are the most promising targets of terpineol action. Our data showed terpineol antidepressant-like modulation by CB1 and CB2 cannabinoid receptors and D2-dopaminergic receptors to further corroborate our molecular evidence.

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CHEN, Y. Z., Z. R. LI, and C. Y. UNG. "COMPUTATIONAL METHOD FOR DRUG TARGET SEARCH AND APPLICATION IN DRUG DISCOVERY." Journal of Theoretical and Computational Chemistry 01, no. 01 (July 2002): 213–24. http://dx.doi.org/10.1142/s0219633602000166.

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Ligand-protein inverse docking has recently been introduced as a computer method for identification of potential protein targets of a drug. A protein structure database is searched to find proteins to which a drug can bind or weakly bind. Examples of potential applications of this method in facilitating drug discovery include: (1) identification of unknown and secondary therapeutic targets of a drug, (2) prediction of potential toxicity and side effect of an investigative drug, and (3) probing molecular mechanism of bioactive herbal compounds such as those extracted from plants used in traditional medicines. This method and recent results on its applications in solving various drug discovery problems are reviewed.

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Chen, Shao-Jun. "A Potential Target of Tanshinone IIA for Acute Promyelocytic Leukemia Revealed by Inverse Docking and Drug Repurposing." Asian Pacific Journal of Cancer Prevention 15, no. 10 (May 30, 2014): 4301–5. http://dx.doi.org/10.7314/apjcp.2014.15.10.4301.

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Yanai, Toshihiro, Aya Kurosawa, Yoshiaki Nikaido, Nozomi Nakajima, Tamio Saito, Hiroyuki Osada, Ayumu Konno, Hirokazu Hirai, and Shigeki Takeda. "Identification and molecular docking studies for novel inverse agonists of SREB, super conserved receptor expressed in brain." Genes to Cells 21, no. 7 (May 17, 2016): 717–27. http://dx.doi.org/10.1111/gtc.12378.

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Rauhamäki, Sanna, Pekka A. Postila, Sakari Lätti, Sanna Niinivehmas, Elina Multamäki, Klaus R. Liedl, and Olli T. Pentikäinen. "Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening." ACS Omega 3, no. 6 (June 11, 2018): 6259–66. http://dx.doi.org/10.1021/acsomega.8b00603.

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Khattib, Ali, Sanaa Musa, Majdi Halabi, Tony Hayek, and Soliman Khatib. "Lyso-DGTS Lipid Derivatives Enhance PON1 Activities and Prevent Oxidation of LDL: A Structure–Activity Relationship Study." Antioxidants 11, no. 10 (October 19, 2022): 2058. http://dx.doi.org/10.3390/antiox11102058.

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Paraoxonase 1 (PON1) plays a role in regulating reverse cholesterol transport and has antioxidative, anti-inflammatory, antiapoptotic, vasodilative, and antithrombotic activities. Scientists are currently focused on the modulation of PON1 expression using different pharmacological, nutritional, and lifestyle approaches. We previously isolated a novel active compound from Nannochloropsis microalgae—lyso-diacylglyceryltrimethylhomoserine (lyso-DGTS)—which increased PON1 activity, HDL-cholesterol efflux, and endothelial nitric oxide release. Here, to explore this important lipid moiety’s effect on PON1 activities, we examined the effect of synthesized lipid derivatives and endogenous analogs of lyso-DGTS on PON1 lactonase and arylesterase activities and LDL oxidation using structure–activity relationship (SAR) methods. Six lipids significantly elevated recombinant PON1 (rePON1) lactonase activity in a dose-dependent manner, and four lipids significantly increased rePON1 arylesterase activity. Using tryptophan fluorescence-quenching assay and a molecular docking method, lipid–PON1 interactions were characterized. An inverse correlation was obtained between the lactonase activity of PON1 and the docking energy of the lipid–PON1 complex. Furthermore, five of the lipids increased the LDL oxidation lag time and inhibited its propagation. Our findings suggest a beneficial effect of lyso-DGTS or lyso-DGTS derivatives through increased PON1 activity and prevention of LDL oxidation.