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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
Tue Oct 01 2024
Journal Name
Journal Of Engineering
A Comprehensive Review for Integrating Petrophysical Properties, Rock Typing, and Geological Modeling for Enhanced Reservoir Characterization
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Reservoir characterization is an important component of hydrocarbon exploration and production, which requires the integration of different disciplines for accurate subsurface modeling. This comprehensive research paper delves into the complex interplay of rock materials, rock formation techniques, and geological modeling techniques for improving reservoir quality. The research plays an important role dominated by petrophysical factors such as porosity, shale volume, water content, and permeability—as important indicators of reservoir properties, fluid behavior, and hydrocarbon potential. It examines various rock cataloging techniques, focusing on rock aggregation techniques and self-organizing maps (SOMs) to identify specific and

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Publication Date
Thu Nov 19 2020
Journal Name
Indonesian Journal Of Chemistry
Determination of Eugenol in Personal-Care Products by Dispersive Liquid-Liquid Microextraction Followed by Spectrophotometry Using <i>p</i>-Amino-<i>N,N</i>-dimethylaniline as a Derivatizing Agent
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Two simple methods for the determination of eugenol were developed. The first depends on the oxidative coupling of eugenol with p-amino-N,N-dimethylaniline (PADA) in the presence of K3[Fe(CN)6]. A linear regression calibration plot for eugenol was constructed at 600 nm, within a concentration range of 0.25-2.50 μg.mL–1 and a correlation coefficient (r) value of 0.9988. The limits of detection (LOD) and quantitation (LOQ) were 0.086 and 0.284 μg.mL–1, respectively. The second method is based on the dispersive liquid-liquid microextraction of the derivatized oxidative coupling product of eugenol with PADA. Under the optimized extraction procedure, the extracted colored product was determined spectrophotometrically at 618 nm. A l

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Physics: Conference Series
Practical Study for the Properties of Hueckel Edge Detection Operator
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Publication Date
Wed Feb 20 2019
Journal Name
Iraqi Journal Of Physics
Study the atomic properties of 2s shell for some atoms
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Ground state energies and other properties of 2S shell for some atoms as Be(Z=4), B(Z=5), C(Z=6) and N(Z=7) were calculated by using Hartree-Fock wave function. We found the values of potential energies in hartree unit (3.8369, 6.78565, 10.18852 and 14.41089) respectively and the other proprieties like expectation values of the position < r1m >  were in agreement with the published results. All the studied atomic properties were normalized. 

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Publication Date
Tue Oct 25 2022
Journal Name
Chalcogenide Letters
Study the properties of Cu2Se thin films for optoelectronic applications
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Copper selenide (Cu2Se) thin films were prepared by thermal evaporation at RT with thickness 500 nm. The heat-treating for (400 &500) K for the absorber layer has been investigated. This research includes, studying the structural properties of X-ray diffraction (XRD) that show the Cu2Se thin film (Cubic) and has a polycrystalline orientation prevalent (220). Moreover, studying the effect of annealing on their surface morphology properties by using Atomic Force Microscopy AFM. Optical properties were considered using the transmittance and absorbance spectra had been recorded when wavelength range (400 - 1000) nm in order to study the absorption coefficient and energy gap. It was found that these films had allowed direct transitio

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The role of the green human resources management practices in a achieving requirements of environmental citizenship- Field research at the General Company for Vegetable Oils.
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The research aims to determine the role of the practices of green human resources management in achieving requirements of environmental citizenship in the workplace, the General Company for Vegetable Oils was chosen for the application of field-side of research which represent one of the important industrial companies in Iraq, which suffers from poor Green human resources management applications, which reflected negatively on the development Environmental citizenship among Employees. The questionnaire use as a tool to collect data and information as well as field presence of the researcher, The research sample included (30) managers of departments and Division ,and through using statistical program (SPSS) the data has been analys

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Publication Date
Mon Apr 01 2013
Journal Name
Journal Of Drugs In Dermatology (jdd)
The Therapeutic Role of Isotretinoin in the Management of Behçet&#039;s Disease: A Single-Blinded, Controlled Therapeutic Study - JDDonline - Journal of Drugs in Dermatology
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AbstractOBJECTIVES: To evaluate the long-term remission efficacy and safety of isotretinoin in the treatment of Behcet's disease (BD). PATIENTS and METHODS: This single-blind, controlled therapeutic study was conducted in the Department of Dermatology and Venereology at Baghdad Teaching Hospital from February 2011 to January 2012. Thirty patients with BD were included in this work. Each patient received isotretinoin 20 mg orally once daily for 3 months. They were assessed at week 2 and then monthly depending on the Clinical Manifestation Index (CMI) and to record any side effects. At week 12, isotretinoin was stopped and patients were given placebo therapy in a form of glucose capsules for another 3 months. RESULTS: Thirty patients were tre

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Publication Date
Fri Mar 01 2024
Journal Name
Medicine Advances
Quality of life, adherence and knowledge of epileptic patients and the impact of a pharmacist‐led educational intervention: A review
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Around 65 million individuals suffer from epilepsy worldwide, and when it is not properly treated, it is linked to higher rates of physical harm and mortality. Due to the requirement for long‐term therapy and the side effects of many medications, medication compliance is a significant issue. The purpose of this review was to summarize the findings of previous studies examining the quality of life (QOL), adherence, patient education, and medication knowledge, as well as the impact of a pharmacist‐led educational intervention. Additionally, to find out if these studies benefit epileptic patients, to find the appropriate method used to help them in all aspects of their lives, and to use these in future studies. A systematic and comprehensi

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Bayesian Tobit Quantile Regression Model Using Double Adaptive elastic net and Adaptive Ridge Regression
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     Recently Tobit  Quantile Regression(TQR) has emerged as an important tool in statistical analysis . in order to improve the parameter estimation in (TQR) we proposed Bayesian hierarchical model with double adaptive elastic net technique  and Bayesian hierarchical model with adaptive ridge regression technique .

 in double adaptive elastic net technique we assume  different penalization parameters  for penalization different regression coefficients in both parameters λ1and  λ, also in adaptive ridge regression technique we assume different  penalization parameters for penalization different regression coefficients i

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Publication Date
Sun Jan 01 2017
Journal Name
Ieee/acm Transactions On Audio, Speech, And Language Processing
Underdetermined Convolutive Source Separation Using GEM-MU With Variational Approximated Optimum Model Order NMF2D
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