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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
Thu Mar 31 2022
Journal Name
Iraqi Geological Journal
Geological Model of the Khabour Reservoir for Studying the Gas Condensate Blockage Effect on Gas Production, Akkas Gas Field, Western Iraq
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The Khabour reservoir, Ordovician, Lower Paleozoic, Akkas gas field which is considered one of the main sandstone reservoirs in the west of Iraq. Researchers face difficulties in recognizing sandstone reservoirs since they are virtually always tight and heterogeneous. This paper is associated with the geological modeling of a gas-bearing reservoir that containing condensate appears while production when bottom hole pressure declines below the dew point. By defining the lithology and evaluating the petrophysical parameters of this complicated reservoir, a geological model for the reservoir is being built by using CMG BUILDER software (GEM tool) to create a static model. The petrophysical properties of a reservoir were computed using

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Publication Date
Thu Jun 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Examining the Asymmetric Impacts of Interest and Exchange Rate on Investment in Egypt for the Period 1976-2020: Applying NARDL Model
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Most of the studies conducted in the past decades focused on the effect of interest rates and exchange rates on domestic investment under the assumption that the independent variables have the same effect on the dependent variable, but there were limited studies that investigated the unequal effects of changes in interest rates and exchange rates, both positive and negative, on domestic investment.  This study used a nonlinear autoregressive distributed lag (NARDL) model to assess the unequal effects of the real interest rate and real exchange rate variables on domestic investment in Egypt for the period 1976 - 2020.  The results revealed that positive and negative shocks for both exchange rates have unequal effects on

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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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Publication Date
Fri Oct 31 2025
Journal Name
Mathematical Modelling Of Engineering Problems
Heterogeneous Traffic Management in SDN-Enabled Data Center Network Using Machine Learning-SPIKE Model
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Software-Defined Networking (SDN) has evolved network management by detaching the control plane from the data forwarding plane, resulting in unparalleled flexibility and efficiency in network administration. However, the heterogeneity of traffic in SDN presents issues in achieving Quality of Service (QoS) demands and efficiently managing network resources. SDN traffic flows are often divided into elephant flows (EFs) and mice flows (MFs). EFs, which are distinguished by their huge packet sizes and long durations, account for a small amount of total traffic but require disproportionate network resources, thus causing congestion and delays for smaller MFs. MFs, on the other hand, have a short lifetime and are latency-sensitive, but they accou

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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
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Synthesis of Bimetallic Au–Pt / TiO2 Catalysts as an Efficient Catalyst for the Photodegradation of Crystal Violet Dye
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     Bimetallic Au –Pt catalysts supporting TiO2 were synthesised using two methods; sol immobilization and impregnation methods. The prepared catalyst underwent a thermal treatment process at 400◦ C, while the reduction reaction under the same condition was done and the obtained catalysts were identified with transmission electron microscopy (TEM) and energy-dispersive spectroscopy (EDS). It has been found that the prepared catalysts have a dimension around 2.5 nm and the particles have uniform orders leading to high dispersion of platinum molecules .The prepared catalysts have been examined as efficient photocatalysts to degrade the Crystal violet dye under UV-light. The optimum values of Bimetallic Au –Pt catalysts supp

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Synthesis of Bimetallic Au–Pt / TiO2 Catalysts as an Efficient Catalyst for the Photodegradation of Crystal Violet Dye
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     Bimetallic Au –Pt catalysts supporting TiO2 were synthesised using two methods; sol immobilization and impregnation methods. The prepared catalyst underwent a thermal treatment process at 400 C, while the reduction reaction under the same condition was done and the obtained catalysts were identified with transmission electron microscopy (TEM) and energy-dispersive spectroscopy (EDS). It has been found that the prepared catalysts have a dimension around 2.5 nm and the particles have uniform orders leading to high dispersion of platinum molecules .The prepared catalysts have been examined as efficient photocatalysts to degrade the Crystal violet dye under UV-light. The optimum values of Bimetallic Au –

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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'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
Mon Apr 03 2023
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a Training Program for Children with Autism and their Mothers Based on the Picture Exchange Commination System to Confront Some of Basic Disorders for these Children
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Abstract

The current research aims to examine the effectiveness of a training program for children with autism and their mothers based on the Picture Exchange Communication System to confront some basic disorders in a sample of children with autism. The study sample was (16) children with autism and their mothers in the different centers in Taif city and Tabuk city. The researcher used the quasi-experimental approach, in which two groups were employed: an experimental group and a control group. Children aged ranged from (6-9) years old. In addition, it was used the following tools: a list of estimation of basic disorders for a child with autism between (6-9) years, and a training program for children with autism

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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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