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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
Wed Dec 01 2021
Journal Name
Baghdad Science Journal
Antimicrobial Effect of Eco- Friendly Silver Nanoparticles Synthesis by Iraqi Date Palm (Phoenix dactylifera) on Gram-Negative Biofilm-Forming Bacteria
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Date palm silver nanoparticles are a green synthesis method used as antibacterial agents. Today,
there is a considerable interest in it because it is safe, nontoxic, low costly and ecofriendly. Biofilm bacteria
existing in marketed local milk is at highly risk on population health and may be life-threatening as most
biofilm-forming bacteria are multidrug resistance. The goal of current study is to eradicate biofilm-forming
bacteria by alternative treatment green synthesis silver nanoparticles. The biofilm formation by bacterial
isolates was detected by Congo red method. The silver nanoparticles were prepared from date palm
(khestawy) fruit extract. The formed nanoparticles were characterized with UV-Vis

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Publication Date
Tue Jun 15 2010
Journal Name
International Journal Of Poultry Science
Effect of n-3 and n-6 Fatty Acid Supplemented Diets on Semen Quality in Japanese Quail (Coturnix coturnix japonica)
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Publication Date
Thu Jun 01 2023
Journal Name
Baghdad Science Journal
Green synthesis of nano binary oxide SiO2/V2O5 NPs integrated ointment cream application on wound dressings and skin cancer cells
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Green synthesis is depending on preparation of nano composited SiO2/V2O5 by using the modified sol-gel method depending on rice husk ash as a source for the extraction of silica gel and the product powder of nano composited SiO2/V2O5 characterization by many techniques such as X-ray diffraction spectroscopy (XRD), field emission scanning electron microscopy (FESEM), and N2 adsorptions/desorption isotherms (BET). This study also includs the biological effectiveness of SiO2/V2O5 and its effect on inhibiting bacterial growth after the prepared nanomaterial was applied to wound dressings, which gave a promising result for its use as

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Publication Date
Tue Oct 30 2018
Journal Name
Acs Omega
Catalytic Hydrogenation of <i>p</i>-Chloronitrobenzene to <i>p</i>-Chloroaniline Mediated by γ-Mo<sub>2</sub>N
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Promoting the production of industrially important aromatic chloroamines over transition-metal nitrides catalysts has emerged as a prominent theme in catalysis. This contribution provides an insight into the reduction mechanism of p-chloronitrobenzene (p-CNB) to p-chloroaniline (p-CAN) over the γ-Mo2N(111) surface by means of density functional theory calculations. The adsorption energies of various molecularly adsorbed modes of p-CNB were computed. Our findings display that, p-CNB prefers to be adsorbed over two distinct adsorption sites, namely, Mo-hollow face-centered cubic (fcc) and N-hollow hexagonal close-packed (hcp) sites with adsorption energies of −32.1 and −38.5 kcal/mol, respectively. We establish that the activation of nit

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Publication Date
Fri Jan 24 2020
Journal Name
Iraqi Journal Of Agricultural Sciences
RESPONSE OF ABELMOSCHUS ESCULENTUS L. FORINOCULATION WITH MYCORRHIZAE AND FOLAIR APPLICATION WITH BIO-STIMULATORS AND EFFECT ON VEGETATIVE GROWTH CHARACTERS
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The current study  was carried out at the Fields belongs of Horticulture  Department, Collage of Agricultural Engineering Science, University of  Baghdad, Al-Jadiriyah for the spring season 2016 -2017 to study the effect for  inoculation mycorrhizae and  folair application  with bio stimulators and their interaction in the growth characters of  (local okra  ptera). A factorial experiment  (2  in randomized complete block design (RCBD), the experiment included (12) treatment  Distributed  in three  replicates. The three factors used in this experiment included . The inoculation with control (C) Mycorrhizae  ( M ) , Biozyme  (B ) ( B1 2cm3.L-1), ( B2 4cm1-.L-1) , Phosphalas (P) (P 2cm3.L-1),  ( M + B1), ( M + B2), (P +

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Publication Date
Mon Dec 15 2025
Journal Name
Bionatura Journal: Ibero-american Journal Of Biotechnology And Life Sciences
Fourteen Years of Organic Amendments Enhance Soil Organic Carbon in Semiarid Iraqi Soils: FTIR Spectroscopy, PLS Modelling and RothC Simulations
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Long-term organic amendments are a key strategy to build soil organic carbon (SOC) stocks in semiarid agroecosystems, where low biomass inputs and calcareous parent material constrain carbon accumulation. This 14-year field experiment in central Iraq (2000–2014) evaluated how a gradient of organic matter (OM) additions (0, 1, 2.5, 5, 10, and 20%) affects SOC dynamics, nutrient availability, and soil organic matter composition in clay-dominated, semiarid soils. Surface and subsurface samples (0–30, 30–60, and 60–90 cm) were analysed for SOC, nutrients, and mid-infrared Fourier transform infrared (FTIR) spectra, which were then integrated with Partial Least Squares (PLS) regression and RothC simulations. Moderate OM inputs (5

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Publication Date
Sat Dec 11 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Association of Age, Parity and Body mass Index with Hemoglobin and Serum Ferritin Levels in Pregnant Women in Baghdad City
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Hemogloin (Hb) and serum ferritin levels are used to assess anemia in pregnancy. Some studies referred to the influence of maternal age, body mass index (BMI) and parity on Hb and serum ferritin levels. The study aimed to examine the possible association of maternal Hb and serum ferritin with maternal age, parity, and BMI in a sample of pregnant women in Baghdad.

 Ninety healthy pregnant women, grouped in three equal groups according to the pregnancy trimester, and thirty apparently healthy non-pregnant women from Baghdad were enrolled in this observational study.  Blood and serum samples were obtained for the estimation of Hb and serum ferritin levels.

The pooled data of participants showed a n

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Publication Date
Wed Jun 10 2026
Journal Name
Applied Physics A
Annealing-temperature-dependent structural, optical, and NO2 gas-sensing properties of Ag-doped NiO thin films prepared by dip coating
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Ag-doped NiO thin films were fabricated by dip coating and subsequently annealed at 373, 473, 573, and 673 K to elucidate the influence of annealing temperature on their structural, morphological, optical, and NO2-sensing characteristics. X-ray diffraction confirmed the formation of polycrystalline Ag/NiO films, with progressively improved crystallinity and larger crystallite size at elevated annealing temperatures. Atomic force microscopy revealed a homogeneous surface morphology with grain growth, with the average grain diameter increasing from 26.40 to 34.2 nm. Optical analysis showed high visible-region transmittance (65–70%) and a gradual reduction in the optical band gap from 2.75 to 2.07 eV with increasing annealing temperature. Ga

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Publication Date
Fri Jul 01 2022
Journal Name
Operative Dentistry
Interfacial Bond Strength and Morphology of Sound and Caries-affected Dentin Surfaces Bonded to Two Resin-modified Glass Ionomer Cements
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SUMMARY<sec> <title>Objective

To evaluate the shear bond strength and interfacial morphology of sound and caries-affected dentin (CAD) bonded to two resin-modified glass ionomer cements (RMGICs) after 24 hours and two months of storage in simulated body fluid at 37°C.

Methods and Materials

Sixty-four permanent human mandibular first molars (32 sound and 32 with occlusal caries, following the International Caries Detection and Assessment System) were selected. Each prepared substrate (sound and CAD) was co

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Publication Date
Mon Jul 01 2024
Journal Name
Journal Of Food Process Engineering
Artificial intelligence‐based modeling of novel non‐thermal milk pasteurization to achieve desirable color and predict quality parameters during storage
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Abstract<sec><label></label><p>This study proposed using color components as artificial intelligence (AI) input to predict milk moisture and fat contents. In this sense, an adaptive neuro‐fuzzy inference system (ANFIS) was applied to milk processed by moderate electrical field‐based non‐thermal (NP) and conventional pasteurization (CP). The differences between predicted and experimental data were not significant (<italic>p</italic> > 0.05) for lightness (<italic>L</italic>*), redness‐greenness (<italic>a</italic>*), yellowness‐blueness (<italic>b</italic>*), total color differences (∆<italic>E</italic>), hue angle (<italic>h</italic></p></sec> ... Show More
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