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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
Fri Feb 05 2010
Journal Name
Etri Journal
MC-MIPOG: A Parallel t-Way Test Generation Strategy for Multicore Systems
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Publication Date
Sun Aug 01 2021
Journal Name
International Journal Of Mechanical Engineering And Robotics Research
Adaptive Approximation-Based Feedback Linearization Control for a Nonlinear Smart Thin Plate
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This paper proposes feedback linearization control (FBLC) based on function approximation technique (FAT) to regulate the vibrational motion of a smart thin plate considering the effect of axial stretching. The FBLC includes designing a nonlinear control law for the stabilization of the target dynamic system while the closedloop dynamics are linear with ensured stability. The objective of the FAT is to estimate the cubic nonlinear restoring force vector using the linear parameterization of weighting and orthogonal basis function matrices. Orthogonal Chebyshev polynomials are used as strong approximators for adaptive schemes. The proposed control architecture is applied to a thin plate with a large deflection that stimulates the axial loadin

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Publication Date
Sun Mar 28 2021
Journal Name
Iraqi Journal For Electrical And Electronic Engineering
A Light Weight Multi-Objective Task Offloading Optimization for Vehicular Fog Computing
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Most Internet of Vehicles (IoV) applications are delay-sensitive and require resources for data storage and tasks processing, which is very difficult to afford by vehicles. Such tasks are often offloaded to more powerful entities, like cloud and fog servers. Fog computing is decentralized infrastructure located between data source and cloud, supplies several benefits that make it a non-frivolous extension of the cloud. The high volume data which is generated by vehicles’ sensors and also the limited computation capabilities of vehicles have imposed several challenges on VANETs systems. Therefore, VANETs is integrated with fog computing to form a paradigm namely Vehicular Fog Computing (VFC) which provide low-latency services to mo

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Publication Date
Sun Jul 01 2012
Journal Name
Applied Soft Computing
A new evolutionary based routing protocol for clustered heterogeneous wireless sensor networks
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Publication Date
Tue Aug 06 2024
Journal Name
Fullerenes, Nanotubes And Carbon Nanostructures
Preparation and characterization of PVA/MWCNT nanocomposites: a composition dependence study of structural, optical and mechanical properties
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Publication Date
Thu Nov 08 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Impact of Life Events upon Onset of Depression Disorder In AL-Diwanyia Governorate : A Case-Control Study
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Objective: The aim of this study is to find out the impact of life events upon onset of depression, to describe the
prevalence of life events among depressed patients.
Methodology: Retrospective a case-control study conducted in AL-Diwanyia Teaching Hospital, Psychiatric
Department on A non-probability (purposive sample) of (60) depressed patients and (60) of healthy person were matched
with them from general population. The data were collected through the use of semi-structured interview by
questionnaire, which consists of two parts (1) divide, section A. cover letter and B. Sociodemographic data which consists
of 9-items, (2) Life events questionnaire consists of 51-items distributed to six dimensions include, family

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Publication Date
Wed Jun 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Effects of various analgesics on pain perception and rate of tooth movement: a randomized controlled clinical study
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Background: Pain is one of the most reported side effects of orthodontic treatment despite the advanced technology in orthodontics. Many analgesics have been introduced to control orthodontic pain including acetaminophen and selective and nonselective nonsteroidal anti-inflammatory drugs. The great concern about these drugs is their adverse effect on rate of teeth movement. Aims: The purpose of this study was to evaluate and compare the effect of acetaminophen, ibuprofen and etoricoxib on pain perception and their influence on the rate of teeth movement during leveling and alignment stage. Methods: Forty patients were evenly and randomly distributed in a blinded way to one of four groups: placebo (starch capsules), acetaminophen 500mg th

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Publication Date
Tue Apr 03 2007
Journal Name
Um-salama Science Journal
A study of adsorption in aqueous solution of p,o,m-Chlorophenol on Iraqi siliceouns rocks powder
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Adsorption of Chlorophenol compounds in aqueous solution on Iraqi siliceouns rocks powder have been investigated. UV technique has been used to determine the adsorption isotherms. The results showed that the adsorption isotherms obeyed Freundlich adsorption equation. The adsorption was endothermic process, increasing temperature leads to increasing adsorption.  H,  S,  G were calculated. The results showed that the adsorption increases with increasing acidity of solutions

Publication Date
Mon Apr 01 2019
Journal Name
Journal Of Engineering
Removal of Methyl Orange from Aqueous Solutions by Adsorption Using Corn Leaves as Adsorbent Material
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A comparative study was done on the adsorption of methyl orange dye (MO) using non-activated and activated corn leaves with hydrochloric acid as an adsorbent material. Scanning electron microscopy (SEM) and Fourier Transform Infrared spectroscopy (FTIR) were utilized to specify the properties of adsorbent material. The effect of several variables (pH, initial dye concentration, temperature, amount of adsorbent and contact time) on the removal efficiency was studied and the results indicated that the adsorption efficiency increases with the increase in the concentration of dye, adsorbent dosage and contact time, while inversely proportional to the increase in pH and temperature for both the treated and untreated corn leav

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Publication Date
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Uptake of Fluoride from Water Using Recycled Raw Beef Bone as an Environmently Freindly Waste
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Excessive intake of fluoride, mainly through drinking water is a serious health hazard affecting humans worldwide. In this study, the defluoridation capacities of locally available raw waste beef bones have been estimated. Several experimental parameters including contact time, pH, bone dose, fluoride initial concentration, bone grains size, agitation rate, and the effect of co-existence of anions in actual samples of wastewater were studied for fluoride removal from aqueous solutions. Results indicated excellent fluoride removal effeciency up to 99.7% at fluoride initial concentration of 10 mg F/L and 120 min contact time. Maximum fluoride uptake was obtained at neutral pH range 6-7. Fluoride removal kinetic was well described by the ps

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