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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 May 01 2024
Journal Name
Diamond And Related Materials
A comparative study on the effects of multi-walled carbon nanotubes and graphene nanoplates incorporated for improved thermal conductivity and dielectric properties of polyvinyl chloride
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Publication Date
Thu Jun 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the effect of preheating on micro leakage of Class II composites Restoration (A comparative in vitro study)
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Background: The aim of this in vitro study was to evaluate and compare the effect of preheating microleakage among three different filler size composites which include Filtektm Z250 micro hybrid, Z250xt Nano hybrid and nanocomposite Z350xt.  in Class II cavity preparation .

Materials and methods: sixty maxillary first premolars were prepared with class II cavities. Samples were divided into three groups according to material used    group A (FiltekZ250 micro hybrid). Group B(Z250xt Nano hybrid). Group C (nanocomposite Z350xt)and each group divided into two subgroups of ten teeth according to temperature of  composite:

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Publication Date
Sun Mar 05 2017
Journal Name
Baghdad Science Journal
Study a concentration of Uranium for samples of soil from Falluja City using PM-355
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In this study a concentration of uranium was measured for twenty two samples of soil distributed in many regions (algolan, almoalmeen, alaskary and nasal streets) from Falluja Cityin AL-Anbar Governorate in addition to other region (alandlos street) as a back ground on the Falluja City that there is no military operations happened on it. The uranium concentrations in soil samples measured by using fission tracks registration in (PM-355) track detector that caused by the bombardment of (U) with thermal neutrons from (241Am-Be) neutron source that has flux of (5×103n cm-2 s-1). The concentrations values were calculated by a comparison with standard samples. The results shows that the uranium concentrations algolan street varies from(1.

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Publication Date
Sun Aug 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Relational leadership and its effect on organizational energy (A comparative study in the Rafidain and Rashid banks)
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This research aims to test the relationship between "relational leadership as an independent variable and organizational energy as a dependent variable. The current research variables are among the recent and important variables for the development of organizations, and for the purpose of explaining the relationship and influence between the variables, a set of goals has been formulated, including providing the interested and scientific and theoretical information explaining the nature of the variables The research, and the extent to which its causes are reflected in the research sample to increase the interest of the research organization’s organization and make it more appropriate to the required performance in light of a cha

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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 31 2023
Journal Name
Iraqi Geological Journal
History Matching of Reservoir Simulation Model: a Case Study from the Mishrif Reservoir, Buzurgan Oilfield, Iraq
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In petroleum reservoir engineering, history matching refers to the calibration process in which a reservoir simulation model is validated through matching simulation outputs with the measurement of observed data. A traditional history matching technique is performed manually by engineering in which the most uncertain observed parameters are changed until a satisfactory match is obtained between the generated model and historical information. This study focuses on step by step and trial and error history matching of the Mishrif reservoir to constrain the appropriate simulated model. Up to 1 January 2021, Buzurgan Oilfield, which has eighty-five producers and sixteen injectors and has been under production for 45 years when it started

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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Selection of the initial value of the time series generating the first-order self-regression model in simulation modeAnd their impact on the accuracy of the model
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In this paper, compared eight methods for generating the initial value and the impact of these methods to estimate the parameter of a autoregressive model, as was the use of three of the most popular methods to estimate the model and the most commonly used by researchers MLL method, Barg method  and the least squares method and that using the method of simulation model  first order autoregressive through the design of a number of simulation experiments and the different sizes of the samples.

                  

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Publication Date
Wed Aug 01 2018
Journal Name
Ecotoxicology And Environmental Safety
Biochemical and molecular alterations in freshwater mollusks as biomarkers for petroleum product, domestic heating oil
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Publication Date
Thu Dec 16 2021
Journal Name
Open Access Macedonian Journal Of Medical Sciences
A Comparative Study of Pediatric Fracture Shaft Femur Fixating by Plate and Screws Using Lateral Approach Between Subvastus Lateralis and Transvastus Lateralis Outcome
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BACKGROUND: Femoral shaft fracture is a common fracture in pediatric age group reaching 62% of all fracture shaft femur in children in spite of rapid union rate and successful conservative treatment but some cases need surgical intervention and one of the methods using plate and screw by the lateral approach. AIM: This study aims to compare functional outcome fixation of mid-shaft femur fracture in children by plate and screws between (subvastus lateralis and transvastus lateralis) regarding infection, union, and limitation of knee movement. PATIENT AND METHOD: The study was done on 30 children who had diaphyseal fracture femur in Al-Kindy Teaching Hospital in period (April 2018–April 2020) with 6 months follow-up, and the pa

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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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