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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
Mon Nov 01 2021
Journal Name
Journal Of Physics: Conference Series
Neural Network Model for Synthesis of Thermally Sprayed (AI/AI<sub>2</sub>O<sub>3</sub>) Composite Protective Coatings
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Abstract<p>Al<sub>2</sub>O<sub>3</sub> and Al<sub>2</sub>O<sub>3</sub>–Al composite coatings were deposited on steel specimens using Oxy-acetylene gas thermal spray gun. Alumina was mixed with Aluminum in six groups of concentrations (0, 5, 10,12,15 and 20% ) Al2O3, Specimens were tested for corrosion using Potentiodynamic polarization technique. Further tests were conducted for the effect of temperature on polarization curve and the hardness tests for the coated specimens. At first, Modelling was carried out using MINITAB-19, least square method, as a 2nd degree nonlinear model, bad results were achieved because of the high nonlinearity. Better result w</p> ... Show More
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Publication Date
Wed Aug 04 2021
Journal Name
Membranes
Model Based Simulation and Genetic Algorithm Based Optimisation of Spiral Wound Membrane RO Process for Improved Dimethylphenol Rejection from Wastewater
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Reverse Osmosis (RO) has already proved its worth as an efficient treatment method in chemical and environmental engineering applications. Various successful RO attempts for the rejection of organic and highly toxic pollutants from wastewater can be found in the literature over the last decade. Dimethylphenol is classified as a high-toxic organic compound found ubiquitously in wastewater. It poses a real threat to humans and the environment even at low concentration. In this paper, a model based framework was developed for the simulation and optimisation of RO process for the removal of dimethylphenol from wastewater. We incorporated our earlier developed and validated process model into the Species Conserving Genetic Algorithm (SCG

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Publication Date
Mon Apr 01 2019
Journal Name
Biochem. Cell. Arch.
Comparative Histopathological Effects Of Acetamiprid And Its Nanometric Form On Albino Mice
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Formulations based on nanomaterials have the ability to reduce the consuming of hazardous pesticides and theirimpact on human health and environment. The present study focused on a comparative investigation of histological effects of nanocapule acetamiprid (NACMP) in vivoand commercial parental bulk form of acetamiprid (ACMP) on albino mice. Nanoformulations of pesticides have the potential to improve food productivity without compromising with the ecosystem. In the present study, nanocapsules containing acetamiprid were prepared from two natural macromolecules, alginate and chitosan. The characterization of the nanocapsules were investigated by Dynamic Light Scattering(DLS), T ransmission Electron Microscopy (TEM) and Atomic force

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Comparative Bioequivalence Studies of doxysam and doxycycline (Pfizer) by reversed phase HPLC.
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Isocratic high performance liquid chromatography on reversed phase a (150x 4.6 mm I.D), 5 ?m ?-Bondapak RP-8 column (with acidic mobile phase allow the separation of doxcycycline hydrochloride with low detection limit of 0.2 µg/ml detected by UV set at 226 nm. The method was validated for Doxycycline between 0.156- to 5 µg/ml. The concentration of doxycycline was assessed in two single dose randomized crossover studies with intervals of one week between two period. In sera of 20 adults healthy male volunteers with average age of (42 + 10) year, body weight 48-85 kg, body height of (160-185cm) after a single dose of doxycycline hydrochoride 100 mg in form of capsules were orally administrated for both formulations. The blood sa

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Publication Date
Fri Oct 01 2010
Journal Name
Saudi Pharmaceutical Journal
Comparative clinical evaluation of ketotifen and montelukast sodium in asthmatic Iraqi patients
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Publication Date
Tue Apr 01 2014
Journal Name
Structural Science, Crystal Engineering And Materials
Comparison of the structural motifs and packing arrangements of six novel derivatives and one polymorph of 2-(1-phenyl-1H-1,2,3-triazol-4-yl)pyridine
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The crystal structures of a new polymorph and seven new derivatives of 2-(1-phenyl-1H-1,2,3-triazol-4-yl)pyridine have been characterized and examined along with three structures from the literature to identify trends in their intermolecular contact patterns and packing arrangements in order to develop an insight into the crystallization behaviour of this class of compound. Seven unique C-H...X contacts were identified in the structures and three of these are present in four or more structures, indicating that these are reliable supramolecular synthons. Analysis of the packing arrangements of the molecules using XPac identified two closely related supramolecular constructs that are present in eight of the 11 structures; in all cases, the st

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Publication Date
Sun May 24 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of transforming growth factor beta one (TGF-?1) immunohistochemical (IHC) expression profile in the gingival tissue of patients with different forms of periodontal diseases
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Background: This study evaluate the immunohistochemical expression profile of transforming growth factor beta-1 in inflamed gingival tissue of patients with gingivitis and chronic periodontitis compared to healthy subjects and, determine the correlation between this cytokine and the clinical periodontal parameters, intensity of inflammation and chronic periodontitis severity. Materials and methods: Gingival tissue specimens were taken from 23 chronic periodontitis patients, 20 gingivitis patients and 20 periodontally healthy subjects. The periodontal status was evaluated by dichotomous measurements of the clinical periodontal parameters (PLI, GI, BOP, PPD, CAL). The gingival specimens were fixed immediately in 10% formalin and processed ro

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Publication Date
Sun Sep 04 2016
Journal Name
Baghdad Science Journal
Study the Shielding Properties against Gamma-rays for Epoxy Resin Reinforced by Different materials
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In the present work the Buildup factor for gamma rays were studied in shields from epoxy reinforced by lead powder and by aluminum powder, for NaI(Tl) scintillation detector size ( ×? ), using two radioactive sources (Co-60 and Cs-137). The shields which are used (epoxy reinforced by lead powder with concentration (10-60)% and epoxy reinforced by aluminum powder with concentration (10-50)% by thick (6mm) and epoxy reinforced by lead powder with concentration (50%) with thick (2,4,6,8,10)mm. The experimental results show that: The linear absorption factor and Buildup factor increase with increase the concentration for the powders which used in reinforcement and high for aluminum powder than the lead powder and decrease with inc

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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
The Technical Treatment for Pottery Body by (Kintsugi) Technique in Japanese Pottery – Analytic Study
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The aesthetic and technical expertise help  in producing the artistic work and achieving results in aesthetic formulations that reflect the aesthetic and  expressive dimensions and the reflective dimensions of the pottery, surpassing its traditions, asserting  its active presence in life, cherishing it  even when it  breaks  or get damaged   by employing techniques that are originated  from  the Japanese environment.

                       The research problem is to study how ( Kintsugi) technique and similar techniques are used to create  new rebirths of pottery piec

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Publication Date
Fri Mar 10 2023
Journal Name
Indian Journal Of Physics
Describing the differential inelastic inverse mean free path of PMMA polymer with the Mermin–Belkacem-Sigmund model
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