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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Sun Dec 31 2023
Journal Name
Iraqi Geological Journal
A Comparative Reservoir Study of Zubair and Nahr Umr Formations in Subba Oilfield, Southern Iraq
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The lower Cretaceous sandstones of Zubair and Nahr Umr formations are the main producing reservoirs in Subba oilfield in southern Iraq. Key differences in their petrophysical and depositional attributes exist affecting their reservoir characteristics. The evaluation of well logs and core porosity-permeability data show better reservoir properties in Nahr Formation. The Litho-saturation logs indicate greater thickness of oil-saturated reservoir units for Nahr Unr Formation associated with lower values of shale volume, and higher values of effective porosity. In addition, higher values of permeability for Nahr Umr Formation is suggested by applying porosity-irreducible water saturation cross plot. The reducing reservoir quality of Zub

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Publication Date
Sun Oct 31 2021
Journal Name
International Journal Of Sustainable Development And Planning
The Crossing as a New Approach for the Urban Transformation of Traditional Cities Towards the Sustainability
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The topic of urban transformations has attracted the attention of researchers as it is one of the basic issues through which cities can be transformed towards sustainability. A specific level of transformation levels according to a philosophical concept known as a crossing. This article has relied on a specific methodology that aims to find a new approach for urban transformation based on the crossing concept. This concept derives from philosophical entrances based on the concepts of (being, process, becoming, and integration). Four levels have been for the crossing are (normal, ascending, leap, and descending). Each of these levels includes specific characteristics that distinguish it. The results showed that there is no descending

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Publication Date
Wed Feb 20 2019
Journal Name
Iraqi Journal Of Physics
Preparation of polyaniline polymer and using it as a Vapor sensor of acids
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 Polyaniline organic Semiconductor polymer was prepared by oxidation polymerization by adding hydrochloric acid concentration of 0.1M and potassium per sulfate concentration of 0.2M to 0.1M of aniline at room temperature, the polymer was deposited at glass substrate, the structural and optical properties were studies through UV-VIS, IR, XRD measurements, films have been operated as a sensor of vapor  H2SO4 and HCl  acids.

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Publication Date
Fri Mar 26 2021
Journal Name
Chemical Papers
DFT, anticancer, antioxidant and molecular docking investigations of some ternary Ni(II) complexes with 2‑[(E)‑[4‑(dimethylamino) phenyl]methyleneamino]phenol
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The biological activities of some ternary nickel complexes with a Schiff base obtained from 4-dimethylaminobenzaldehyde and 2-aminophenol have been reported. The Schiff base ( HL1) acts as a primary ligand whereas, anthranilic acid ( HL2), 2-nitroaniline ( HL3), alanine ( HL4) and histidine ( HL5) act as secondary ligand or co-ligand. The anticancer activity of these compounds was studied against human colon carcinoma (HCT-116), human hepatocellular liver carcinoma (HEPG-2) and human breast carcinoma (MCF-7) cell lines. As per the results, the compounds were active against the cell lines. The antioxidant activity of the same compounds was evaluated using DPPH (1,1-diphenyl-2-picryl-hydrazyl) radical scavenging and compared with ascorbic aci

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Publication Date
Thu Aug 31 2017
Journal Name
Journal Of Engineering
Reactive Adsorption Desulfurization by Nanocrystalline ZnO/Zeolite A Molecular Sieves
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      Nanocrystalline ZnO/Zeolite type A composite was prepared by simple method of operation by . the precipitation of zinc oxide and loading on zeolite 5A in one step. Characterization was made by X-ray diffraction (XRD), X-ray fluorescence(XRF), N2  adsorption- desorption for BET surface area, and Atomic force microscopy (AFM). Results showed that zinc oxide was loaded on zeolite as noticed by the characteristic peaks and was of nano scale having an average diameter of 88.57nm. The percentage loading of ZnO on zeolite A was 28.37% and the surface area was 222m2/g. The activity of the prepared catalyst was examined in the desulfurization of double hydrogenated diesel fuel. The process was investigated in a

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Publication Date
Sun Nov 01 2015
Journal Name
Iosr Journal Of Dental And Medical Sciences (iosr-jdms)
Acanthosis Nigricans as a Cause of Facial M Elanosis (Clinical Andhistopathological Study
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PKE Sharquie MD, PDPAA Noaimi MD, DDV, FDSM Al-Ogaily MD, IOSR Journal of Dental and Medical Sciences (IOSR-JDMS), 2015

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Publication Date
Sat Apr 01 2023
Journal Name
Journal Of Applied Hematology
Molecular Alterations in IDH 1/2 Genes among Iraqi Adult Acute Myeloid Leukemia Patients
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BACKGROUND:

The recurrent somatic variations in IDH1/2 genes in AML play imperative roles in epigenetic dysregulation and the pathogenesis of AML, which could be useful prognostic markers for risk stratification.

AIM:

The aim of the study was to detect the frequency of R132 mutations in the IDH1 gene and R140Q mutation in the IDH2 gene with their treatment outcomes.

PATIENTS
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Publication Date
Mon Feb 01 2021
Journal Name
Https://www.researchgate.net/journal/university-of-baghdad-engineering-journal-1726-4073
Electrical Conductivity as a General Predictor of Multiple Parameters in Tigris River Based on Statistical Regression Model
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Surface water samples from different locations within Tigris River's boundaries in Baghdad city have been analyzed for drinking purposes. Correlation coefficients among different parameters were determined. An attempt has been made to develop linear regression equations to predict the concentration of water quality constituents having significant correlation coefficients with electrical conductivity (EC). This study aims to find five regression models produced and validated using electrical conductivity as a predictor to predict total hardness (TH), calcium (Ca), chloride (Cl), sulfate (SO4), and total dissolved solids (TDS). The five models showed good/excellent prediction ability of the parameters mentioned above, which is a very

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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Engineering
Electrical Conductivity as a General Predictor of Multiple Parameters in Tigris River Based on Statistical Regression Model
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Surface water samples from different locations within Tigris River's boundaries in Baghdad city have been analyzed for drinking purposes. Correlation coefficients among different parameters were determined. An attempt has been made to develop linear regression equations to predict the concentration of water quality constituents having significant correlation coefficients with electrical conductivity (EC). This study aims to find five regression models produced and validated using electrical conductivity as a predictor to predict total hardness (TH), calcium (Ca), chloride (Cl), sulfate (SO4), and total dissolved solids (TDS). The five models showed good/excellent prediction ability of the parameters mentioned

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Publication Date
Sat Nov 01 2014
Journal Name
International Journal Of Basic And Applied Sciences
A reliable iterative method for solving the epidemic model and the prey and predator problems
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In the present article, we implement the new iterative method proposed by Daftardar-Gejji and Jafari (NIM) [V. Daftardar-Gejji, H. Jafari, An iterative method for solving nonlinear functional equations, J. Math. Anal. Appl. 316 (2006) 753-763] to solve two problems; the first one is the problem of spread of a non-fatal disease in a population which is assumed to have constant size over the period of the epidemic, and the other one is the problem of the prey and predator. The results demonstrate that the method has many merits such as being derivative-free, overcome the difficulty arising in calculating Adomian polynomials to handle the nonlinear terms in Adomian Decomposition Method (ADM), does not require to calculate Lagrange multiplier a

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