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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 Sep 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Semi parametric Estimators for Quantile Model via LASSO and SCAD with Missing Data
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In this study, we made a comparison between LASSO & SCAD methods, which are two special methods for dealing with models in partial quantile regression. (Nadaraya & Watson Kernel) was used to estimate the non-parametric part ;in addition, the rule of thumb method was used to estimate the smoothing bandwidth (h). Penalty methods proved to be efficient in estimating the regression coefficients, but the SCAD method according to the mean squared error criterion (MSE) was the best after estimating the missing data using the mean imputation method

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Publication Date
Wed Apr 02 2025
Journal Name
Current Studies On Probability And Statistics
SAR-HDP: Non-parametric Topic Model for Aspect categorisation based on online reviews
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Aspect categorisation and its utmost importance in the eld of Aspectbased Sentiment Analysis (ABSA) has encouraged researchers to improve topic model performance for modelling the aspects into categories. In general, a majority of its current methods implement parametric models requiring a pre-determined number of topics beforehand. However, this is not e ciently undertaken with unannotated text data as they lack any class label. Therefore, the current work presented a novel non-parametric model drawing a number of topics based on the semantic association present between opinion-targets (i.e., aspects) and their respective expressed sentiments. The model incorporated the Semantic Association Rules (SAR) into the Hierarchical Dirichlet Proce

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Publication Date
Tue Dec 01 2020
Journal Name
Minar International Journal Of Applied Sciences And Technology
INNOVATE GESTATIONAL AGE ESTIMATION MODEL FOR IRAQI FETUSES BASED ON ULTRASOUND IMAGES MEASUREMENTS
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Imaging by Ultrasound (US) is an accurate and useful modality for the assessment of gestational age (GA), estimation fetal weight, and monitoring the fetal growth during pregnancy, is a routine part of prenatal care, and that can greatly impact obstetric management. Estimation of GA is important in obstetric care, making appropriate management decisions requires accurate appraisal of GA. Accurate GA estimation may assist obstetricians in appropriately counseling women who are at risk of a preterm delivery about likely neonatal outcomes, and it is essential in the evaluation of the fetal growth and detection of intrauterine growth restriction. There are many formulas are used to estimate fetal GA in the world, but it's not specify fo

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Publication Date
Wed Mar 31 2021
Journal Name
Electronics
Adaptive Robust Controller Design-Based RBF Neural Network for Aerial Robot Arm Model
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Aerial Robot Arms (ARAs) enable aerial drones to interact and influence objects in various environments. Traditional ARA controllers need the availability of a high-precision model to avoid high control chattering. Furthermore, in practical applications of aerial object manipulation, the payloads that ARAs can handle vary, depending on the nature of the task. The high uncertainties due to modeling errors and an unknown payload are inversely proportional to the stability of ARAs. To address the issue of stability, a new adaptive robust controller, based on the Radial Basis Function (RBF) neural network, is proposed. A three-tier approach is also followed. Firstly, a detailed new model for the ARA is derived using the Lagrange–d’A

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Publication Date
Sun Dec 06 2009
Journal Name
Baghdad Science Journal
Mean-field Solution of the mixed spin-1 and spin-5/2Ising system with different single-ion anisotropies
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The mixed-spin ferrimagnetic Ising system consists of two-dimensional sublattices A and B with spin values and respectively .By used the mean-field approximation MFA of Ising model to find magnetism( ).In order to determined the best stabile magnetism , Gibbs free energy employ a variational method based on the Bogoliubov inequality .The ground-state (Phase diagram) structure of our system can easily be determined at , we find six phases with different spins values depend on the effect of a single-ion anisotropies .these lead to determined the second , first orders transition ,and the tricritical points as well as the compensation phenomenon .

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Publication Date
Fri Sep 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro The Effect of Canals Instrumented With Three Rotary Ni-Ti Systems on The Dislocation Resistance of Guttafusion® Versus Single Cone Obturation Technique
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Background: Complete seal of the root canal system following its chemo-mechanical debridement plays a pivotal role for achieving successful endodontic treatment. This can be established by reducing the gaps between the core filling material and root canal wall. Aim: To assess and compare the dislocation resistance of root canals obturated with GuttaFusion® and TotalFill BC sealer versus single cone obturation technique and TotalFill BC sealer after instrumentation of the canals with WaveOne, ProTaper Next and ProTaper Universal system. Material and Method: Sixty extracted human permanent mandibular premolars were conducted in the current study. The teeth were decorated and left the root with 15mm length; the roots were divided randoml

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Publication Date
Fri Mar 29 2024
Journal Name
Iraqi Journal Of Science
The Simulation Technique to Estimate the Parameters of Generalized Exponential Rayleigh Model
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     The paper shows how to estimate the three parameters of the generalized exponential Rayleigh distribution by utilizing the three estimation methods, namely, the moment employing estimation method (MEM), ordinary least squares estimation method (OLSEM),  and maximum entropy estimation method (MEEM). The simulation technique is used for all these estimation methods to find the parameters for the generalized exponential Rayleigh distribution. In order to find the best method, we use the mean squares error criterion. Finally, in order to extract the experimental results, one of object oriented programming languages visual basic. net was used

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Publication Date
Thu Jun 25 2020
Journal Name
International Journal Of Drug Delivery Technology
The Effects of Salvia officinalis Gel as an Adjunct to Scaling and Root Planning in Patients with Periodontitis (Clinical and Immunological Study)
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Background: Phytotherapy is the usage of herbal species with medicinal properties for the management of various diseases. Gingivitis and periodontitis are diseases that involve the role of both the bacteria and the host immune response. Over the years, various researches have shown the importance of herbal products in the management of periodontal diseases. Aims of the study: To evaluate the efficacy of locally applied Salvia officinalis gel as adjunctive in the treatment of chronic periodontitis. Subjects and methods: Fourteen patients (10 males and 4 females) with chronic periodontitis were enrolled in the present study with total number of twenty-eight periodontal pockets utilizing a split mouth design, the pockets were divided i

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The role of Job description and Perceived organizational support to achieving An Excellent Job performance - An Exploratory study of the views of a sample of department heads at Sulaimaniyah University.
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     This research Sought to identify the correlation relationships and the impact of each of the job description and perceived organizational support, Excellent Job performance of the heads of academic departments in the faculties of the University of Sulaymaniyah Iraqi Kurdistan Region, totaling (89) as President, and to achieve this was Default plan includes research variables as well as the formulation of a number of preparation fundamental assumptions, and researchers used a questionnaire for this purpose as a tool head of the collection of data and information, as it was distributed (80) copies, and the number of retrieved them (76) a copy of a valid statistical analysis, as well as conducting personal i

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Publication Date
Thu Jul 20 2023
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Study the Effect of Manganese Ion Doping on the Size- Strain of SnO2 nanoparticles Using X-Ray Diffraction Data
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In this study, SnO2 nanoparticles were prepared from cost-low tin chloride (SnCl2.2H2O) and ethanol by adding ammonia solution by the sol-gel method, which is one of the lowest-cost and simplest techniques. The SnO2 nanoparticles were dried in a drying oven at a temperature of 70°C for 7 hours. After that, it burned in an oven at a temperature of 200°C for 24 hours. The structure, material, morphological, and optical properties of the synthesized SnO2 in nanoparticle sizes are studied utilizing X-ray diffraction. The Scherrer expression was used to compute nanoparticle sizes according to X-ray diffraction, and the results needed to be scrutinized more closely. The micro-strain indicates the broadening of diffraction peaks for nano

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