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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 Feb 01 2021
Journal Name
Journal Of Physics: Conference Series
The Fear Effect on a Food Chain Prey-Predator Model Incorporating a Prey Refuge and Harvesting
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Abstract<p>In this paper, we investigate the impact of fear on a food chain mathematical model with prey refuge and harvesting. The prey species reproduces by to the law of logistic growth. The model is adapted from version of the Holling type-II prey-first predator and Lotka-Volterra for first predator-second predator model. The conditions, have been examined that assurance the existence of equilibrium points. Uniqueness and boundedness of the solution of the system have been achieve. The local and global dynamical behaviors are discussed and analyzed. In the end, numerical simulations are confirmed the theoretical results that obtained and to display the effectiveness of varying each parameter</p> ... Show More
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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Assessment of in Vitro Effect of Three Fluoride Releasing Agents on Enamel Demineralization around Orthodontic Brackets
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Publication Date
Wed Oct 08 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Assessment of In Vitro Effect of Three Fluoride Releasing Agents on Enamel Demineralization around Orthodontic Brackets
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Background: White spot lesion considered as irreversible tooth demineralization presenting challenge to orthodontists during treatment schedules, fluoride was the most successfully used measure to overcome this challenge. Materials and method: A total of forty sound human permanent premolars were used in the present study and categorized into four groups, in one group the teeth were bonded with stainless steel brackets using Resin-modified glass ionomer cement (RMGIC) and the other three groups the teeth were bonded with light cured composite Resilience® (Ortho technology Co., USA). Group A; Acidulated phosphate fluoride (APF) topical gel (Mfg by DEEPAK PRODUCTS, INC, USA), fluoride ion 1.23% applied on examine area for four minute. Gro

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Publication Date
Sun Mar 03 2013
Journal Name
Baghdad Science Journal
A Comparison of the Methods for Estimation of Reliability Function for Burr-XII Distribution by Using Simulation.
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This deals with estimation of Reliability function and one shape parameter (?) of two- parameters Burr – XII , when ?(shape parameter is known) (?=0.5,1,1.5) and also the initial values of (?=1), while different sample shze n= 10, 20, 30, 50) bare used. The results depend on empirical study through simulation experiments are applied to compare the four methods of estimation, as well as computing the reliability function . The results of Mean square error indicates that Jacknif estimator is better than other three estimators , for all sample size and parameter values

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Publication Date
Thu May 01 2025
Journal Name
Microbes And Infectious Diseases
Molecular detection and the frequency of a pore-forming toxin in Enterococcus faecalis isolated from urinary tract infections
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Publication Date
Sun Jan 01 2023
Journal Name
Aip Conference Proceedings
Determination of paracetemol in pharmaceutical preparations samples by spectrophotometer using meta phenylenediamine as a chromogenic agent
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Publication Date
Wed Apr 12 2017
Journal Name
Journal Of Engineering
Cultivation of Chlorella Vulgaris Using Airlift Photobioreactor Sparged with 5%CO2-Air as a Biofixing Process
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The present paper addresses cultivation of Chlorella vulgaris microalgae using airlift photobioreactor that sparged with 5% CO2/air. The experimental data were compared with that obtained from bioreactor aerated with air and unsparged bioreactor. The results showed that the concentration of biomass is 0.36 g l-1 in sparged bioreactor with CO2/air, while, the concentration of biomass reached to 0.069 g l-1 in the unsparged bioreactor. They showed also that aerated bioreactor with CO2/air gives more biomass production even the bioreactor was aerated with air. This study proved that application of sparging system for cultivation of Chlorella vulgaris microalgae using either CO2/air mixture or air has a significant growth rate, since the biorea

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Publication Date
Sun Jun 03 2012
Journal Name
Baghdad Science Journal
Batch and Flow-Injection Spectrophotometric Determination of Thymol Using Procaine Hydrochloride as a New Chromogenic Reagent
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New, simple and sensitive batch and Flow-injecton spectrophotometric methods for the determination of Thymol in pure form and in mouth wash preparations have been proposed in this study. These methods were based on a diazotization and coupling reaction between Thymol and diazotized procaine HCl in alkaline medium to form an intense orange-red water-soluble dye that is stable and has a maximum absorption at 474 nm. A graphs of absorbance versus concentration show that Beer’s law is obeyed over the concentration range of 0.4-4.8 and 4-80 µg.ml-1 of Thymol, with detection limits of 0.072 and 1.807 µg.ml-1 of Thymol for batch and FIA methods respectively. The FIA procedure sample throughput was 80 h-1. All different chemical and physical e

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Publication Date
Mon Jan 01 2024
Journal Name
Baghdad Science Journal
A New Approach for Developing Spectrophotometric Determination of Phenylephrine Drug in Pure, Pharmaceutics and Serum Samples Using Sodium Periodate as Oxidizing Agent via a Green Method of CFIA/Merging Zone Technique
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     The research involved a rapid, automated and highly accurate developed CFIA/MZ technique for estimation of phenylephrine hydrochloride (PHE) in pure, dosage forms and biological sample. This method is based on oxidative coupling reaction of 2,4-dinitrophenylhydrazine (DNPH) with PHE in existence of sodium periodate as oxidizing agent in alkaline medium to form a red colored product at ʎmax )520 nm (. A flow rate of 4.3 mL.min-1 using distilled water as a carrier, the method of FIA proved to be as a sensitive and economic analytical tool for estimation of PHE.

Within the concentration range of 5-300 μg.mL-1, a calibration curve was rectilinear, where the detection limit was 3.252 μg.mL

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Publication Date
Fri Sep 02 2022
Journal Name
Military Medical Science Letters
SOLID LIPID NANOPARTICLES AS A PROMISING APPROACH FOR DELIVERY OF ANTICANCER AGENTS: REVIEW ARTICLE
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