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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
Sat Mar 02 2019
Journal Name
Biochem. Cell.arch.
EVALUATION OF PRIMARY IMPLANTS STABILITY IN IMMEDIATE AND DELAYED TREATMENT PROTOCOLS ACCORDING TO BONE DENSITY, JAWS, GENDER AND AGE UTILIZING PERIOTEST M DEVICE
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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
Effect Altsoam and add ammonium chloride and sodium Pkarbinat in some drinking water productivity and physiological traits of male chicken meat thermally stressful
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The use of male mothers fur c meat Fabro to learn Effect concentrations of ammonium chloride NH4CL and Bacarbonnat sodium NaHCO3 in drinking water by heat stress and Altsoam during heat stress on some of the qualities of productivity and Alvesrgih divided animals to 6 transactions, namely: - control without adding NH4CL, NaHCO3 and Altsoam (treatment 1) Altsoam-1200 of 7-4 weeks old chicken meat to heat patrol 25-34-25 .. 7 weeks old Weight was measured gravimetric vivo increase feed consumption

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Publication Date
Sun Mar 04 2012
Journal Name
Baghdad Science Journal
Evaluation of cellular immune response in Golden Hamsters experimentally infected with Leishmania donovani comparing with cellular immune response against chicken Red Blood Cells.
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The Evaluation of the immune response in Golden Hamsters experimentally infected with Leishmania donovani was determined in this study, particularly, the cellular immune response. Follow up has maintained to determine the Delayed Type of Hypersensitivity using skin test both in infected and control lab animals. Chicken red blood cells were used as a parameter to evaluate the immune system; they are dull and have the ability of immunization. Two concentrations of chicken R.B.C were examined to determine which gives the higher titration in Hamsters and those were 1.5 X 109 cell/ml and 3 X 109 cell/ml , the second concentration gave the maximum titration where then used in this work. After sensitization with Chicken R.B.C for both in

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Publication Date
Wed Oct 08 2025
Journal Name
Key Engineering Materials
Improved Performance of Hydrogen Sulfide Gas Sensor Based on Zinc Oxide Nanostructures Thermally Synthesized Doped with Silver Nanoparticles and Multi-Walled Carbon Nanotubes
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The present work reports an approach of hydrothermal growth of ZnO nanorods, which simplifies the production of low cost films with controlled morphology for H2S gas sensor application. The prepared ZnO nanorods exhibit a hexagonal wurtzite phase analyzed by the X-ray diffraction analysis. The FTIR spectra provide information that the band located between 465-570 cm-1 corresponds to the stretching bond of Zn-O, which confirms the creation of ZnO. PL spectroscopic studies showed that the doping of Ag NPs and f-MWCNT in the ZnO matrix leads to the tuning of the bandgap. The SEM analysis showed the morphology of ZnO was the nanorods. The nanocomposites Ag/ZnO and F-MWCNT/ZnO which prepared, sep

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Publication Date
Tue Mar 19 2024
Journal Name
Baghdad Science Journal
Synthesis, Spectroscopic, and Characterization of Novel Nano Sized Mannich Base Complexes with Pt (IV) and Au (III) Ions and Assessing Their Antioxidants Activity
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في هذا البحث تم تحضير المركبات المعدنية النانوية الجديدة لأيونات البلاتين 4+و الذهب 3+ مع ليكاند قاعدة مانخ جديد مشتق من السيبروفلوكساسين بطريقة الموجات فوق الصوتية. تم تشخيص المعقدات النانوية والليكاند الجديد بأستخدام  تقنيات فيزيائية و كيميائية مختلفة مثل أطياف الاشعة تحت الحمراء، حيود الاشعة السينية ، المجهر الالكتروني الماسح ، المجهر الالكتروني النافذ و مجهر القوة الذرية.  تم تحديد نشاط مضادات الأك

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Publication Date
Sun Jun 27 2021
Journal Name
Iraqi National Journal Of Nursing Specialties
Level of Depression and Anxiety among School Age Children with Acute Lymphoblastic Leukemia under Chemotherapy Treatment at Pediatric Teaching Hospitals in Baghdad City
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Objective(s): To assess the level of depression and anxiety among school age children with acute lymphoblastic leukemia under chemotherapy treatment and to find out the relationship between the level of depression and anxiety among the affected children and their demographic characteristics.
Methodology: A cross-sectional study was conducted on school age children both gender having acute lymphoblastic leukemia under chemotherapy treated and their age between 6 years to 12 years. The study started from the period of September, 19th 2020 to March,1st 2021. Non-probability (Purposive) sample of (114) children with acute lymphoblastic leukemia under chemotherapy was selected in attending hospital wards, outpatient and counseling clinics

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Publication Date
Wed Aug 28 2019
Journal Name
International Journal Of Drug Delivery Technology
Synthesis, Characterization and Screening their Antibactrial Activity of some New Oxazepine and Diazepine Compounds Containing 1,3,4-Oxadiazole Ring Derived from L-Ascorbic Acid
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The search involve the synthesis of some new 1,3-oxazepine and 1,3-diazepine derivatives were synthesized from Schiff base. The Schiff base (VIII) prepared from reaction of aldehyde (IV) derived from L-ascorbic acid with aromatic amine ([2-(4- nitrophenyl)-5-(4-aminophenyl)-1,3,4-oxadiazole] (VII). Oxazepine compounds (IX-XI) were synthesized from the cyclic condensation of Schiff base (VIII) with (maleic, phthalic and 3-nitrophthalic) anhydride, compounds (IX-XI) that were reacted with p-methoxyaniline to give diazepine derivatives (XII-XIV). The structures of the new synthesized compounds have been confirmed by physical properties and spectroscopy measurements such as FTIR, and some of them by 1 H-NMR, 13 CNMR, Mass, and evaluated

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Publication Date
Fri May 01 2015
Journal Name
Journal Of Engineering
Numerical Analysis of Fluid Flow and Heat Transfer by Forced Convection in Channel with one-sided Semicircular Sections and Filled with Porous Media
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This research presents a numerical study to simulate the heat transfer by forced convection as a result of fluid flow inside channel’s with one-sided semicircular sections and fully filled with porous media. The study assumes that the fluid were Laminar , Steady , Incompressible and inlet Temperature was less than Isotherm temperature of a Semicircular sections .Finite difference techniques were used to present the governing equations (Momentum, Energy and Continuity). Elliptical Grid is Generated using Poisson’s equations . The Algebraic equations were solved numerically by using (LSOR (.This research studied the effect of changing the channel shapes on fluid flow and heat transfer  in two cases ,the first: cha

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Publication Date
Thu May 14 2009
Journal Name
Journal Of Kerbala University
Synthesis and Characterization of Novel Macrocyclic ligand and its complexes with (Co(II) ,Ni(II) ,Cu(II) ,Zn(II) , and Cd(II) ) ions.
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A new Macrocyclic Schiff base ligand Bis[4-hydroxy(1,2-ethylene-dioxidebenzylidene) pheylenediamine] [H2L] and its complexes with (Co(II) , Ni(II) , Cu(II) , Zn(II) and Cd(II)) are reported . The ligand was prepared in two steps,in the first step a solution of (o-phenylene diamine) in methanol react under reflux with (2,4-dihydroxybenzylaldeyed) to give an (intermediatecompound) [Bis-1,2 (2,4-dihydroxybenzylediene)pheylinediamine] which react in the second step with (1,2- dichloro ethane) giving the mentioned ligand.Then the complexes were synthesis of adding of corresponding metal salts to the solution of the ligand in methanol under reflux with 1:1 metal to ligand ratio. On the basis of, molar conductance, I.R., UV-Vis, chloride content a

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Publication Date
Sun Dec 10 2017
Journal Name
Research Journal Of Pharmaceutical, Biological And Chemical Sciences
Preparation, Spectral studies and Biological Efficiency of Metal (II) Mixed Ligand Complexes Schiff Base derived from (Benzaldehyde and O-Aminoaniline) with 8-Hydroxyquinoline.
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A novel Schiff base ligand [N1-benzylidenebenezene-1,2-diamine(L) = C20H16N2] was prepared through intensification of benzaldehyde (C6H5CHO) and O- amino aniline O-C6H4(NH2)2 in ethanol with 8-Hydroxyquinoline (8HQ) . Formed compounds were acquired of 1:1:2 molar proportion reactions for metal ions and ligands (L) and 2(8HQ) during reaction for MCl2 .nH2O salt products complexes conformable into the forms [M(L)(8HQ)2] ,where M = Mn(II),Co(II) and Ni(II). Whole the compounds were identified during the basis of their; FT-IR and U.V spectrum, melting point, molar conduct, identify of the percentage from the metal at the complexes via flame (AAS), C, H and N content of the Schiff base (L) and metal complexes were analysis and magnetic susceptib

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