Molecular modeling and docking characterization of Dectin-1 (PAMP) receptor of Bubalus bubalis

Yadav, Brijesh Singh; Tripathi, Vijay; Kumar, Abdhesh; Khan, Faheem Ahmed; Barate, Abhijit Kashinath; Kumar, Ajay; Sharma, Bhaskar

doi:10.1016/j.yexmp.2011.09.018

Cited by 16 publications

(16 citation statements)

References 15 publications

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“…It was obligatory to elucidate the protein level study in buffalo. Previously, docking study was undertaken on BG:Dectin-1 complex but detail structural features were not taken into consideration [9]. The recognition of fungal BG by Dectin-1 helps in a variety of cellular responses, like host protection, such as fungal uptake and killing, and the production of inflammatory cytokines and chemokines.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore docked BG:Dectin-1 complex was considered from our previous research work [9], was subjected directly for MD simulation. Study was carried out by three steps, first was to perform MD simulation of BG:Dectin-1 complex.…”

Section: Data and Molecular Dockingmentioning

confidence: 99%

“…On the other hand, the polar surface consists of permanent dipoles and is related with the charge distribution of the solute. On our MM-PBSA calculation, the ionic strength was adjusted by the addition of 0.150 M of NaCl, the number of grid points per A 2 was set to 10, and the number of iterations for linear PB solver was set as a maximum of 50,000. solution but with an activating first ligand, BG; this complex was retrieved from our recent study [9]; however detailed structural insights are needed to be studied, which were conducted through MD approach. (iii) Dectin-1 loaded with second activating ligand, MT.…”

Section: δGsolvation = δGpolar + δGnonpolarmentioning

confidence: 99%

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The effect of β-glucan and its potential analog on the structure of Dectin-1 receptor

Chaturvedi

Yadav

Pandey

et al. 2017

Journal of Molecular Graphics and Modelling

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Section: Discussionmentioning

confidence: 99%

Section: Data and Molecular Dockingmentioning

confidence: 99%

Section: δGsolvation = δGpolar + δGnonpolarmentioning

confidence: 99%

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The effect of β-glucan and its potential analog on the structure of Dectin-1 receptor

Chaturvedi

Yadav

Pandey

et al. 2017

Journal of Molecular Graphics and Modelling

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“…The interaction of this ligand with modeled protein was performed. The Lamarckian genetic algorithm was used in Autodock to perform the automated molecular dockings [33] and default parameters were used. In the process a large grid map was created by AutoGrid to cover the whole surface of protein.…”

Section: Resultsmentioning

confidence: 99%

The Interaction Pattern between a Homology Model of 40S Ribosomal S9 Protein ofRhizoctonia solaniand 1-Hydroxyphenaize by Docking Study

Dharni

Sanchita

Samad

et al. 2014

BioMed Research International

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1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani. In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein. Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

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“…Our preanalyzed suggested templates from the NCBI-PDB database, Phyre2, 3DJIGSAW v.3.0, and Swiss Model were subjected to comparative modeling using the Modeller 9.13 software as described [19,20] and applied previously [21][22][23][24][25][26][27][28][29][30][31][32][33]. Additionally, the best suggested templates from RaptorX were also applied to the comparative modeling analysis using Modeller 9.13 software.…”

Section: Fam72a Reference Sequencementioning

confidence: 99%

Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17)

2014

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FAM72A (p17) is a novel neuronal protein that has been linked to tumorigenic effects in non-neuronal tissue. Using state of the art in silico physicochemical analyses (e.g., I-TASSER, RaptorX, and Modeller), we determined the three-dimensional (3D) protein structure of FAM72A and further identified potential ligand-protein interactions. Our data indicate a Zn(2+)/Fe(3+)-containing 3D protein structure, based on a 3GA3_A model template, which potentially interacts with the organic molecule RSM ((2s)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl] butanamide). The discovery of RSM may serve as potential lead for further anti-FAM72A drug screening tests in the pharmaceutical industry because interference with FAM72A's activities via RSM-related molecules might be a novel option to influence the tumor suppressor protein p53 signaling pathways for the treatment of various types of cancers.

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Molecular modeling and docking characterization of Dectin-1 (PAMP) receptor of Bubalus bubalis

Cited by 16 publications

References 15 publications

The effect of β-glucan and its potential analog on the structure of Dectin-1 receptor

The effect of β-glucan and its potential analog on the structure of Dectin-1 receptor

The Interaction Pattern between a Homology Model of 40S Ribosomal S9 Protein ofRhizoctonia solaniand 1-Hydroxyphenaize by Docking Study

Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17)

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