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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
Sun May 01 2022
Journal Name
Journal Of Engineering
Comparative Study between the Behavior of the Concrete Thrust Block and the Restraint Joint in a Water Distribution System; Review
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Thrust blocks and restraint joints are the two most popular methods of counteracting the thrust force that generated at pipe fittings (bends, Tee, wye, reducers, dead ends, etc…). Both systems perform the same function, which is to prevent the joints from separating from the pipes. The aim of the study is to review previous studies and scientific theories related to the study and design of thrust blocks and restraint joints to study the behavior of both systems under thrust force and to study the factors and variables that affect the behavior of these systems. The behavior of both systems must be studied because they cannot be abandoned, as each system has conditions whose use is more feasible, scientific, and economic

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Publication Date
Sun Oct 01 2023
Journal Name
Applied Sciences
Multiobjective Optimization of Stereolithography for Dental Bridge Based on a Simple Shape Model Using Taguchi and Response Surface Methods
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Stereolithography (SLA) has become an essential photocuring 3D printing process for producing parts of complex shapes from photosensitive resin exposed to UV light. The selection of the best printing parameters for good accuracy and surface quality can be further complicated by the geometric complexity of the models. This work introduces multiobjective optimization of SLA printing of 3D dental bridges based on simple CAD objects. The effect of the best combination of a low-cost resin 3D printer’s machine parameter settings, namely normal exposure time, bottom exposure time and bottom layers for less dimensional deviation and surface roughness, was studied. A multiobjective optimization method was utilized, combining the Taguchi me

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Publication Date
Tue Apr 01 2025
Journal Name
Journal Of Engineering
Comparative Analysis of The Combined Model (Spatial and Temporal) and Regression Models for Predicting Murder Crime
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This research dealt with the analysis of murder crime data in Iraq in its temporal and spatial dimensions, then it focused on building a new model with an algorithm that combines the characteristics associated with time and spatial series so that this model can predict more accurately than other models by comparing them with this model, which we called the Combined Regression model (CR), which consists of merging two models, the time series regression model with the spatial regression model, and making them one model that can analyze data in its temporal and spatial dimensions. Several models were used for comparison with the integrated model, namely Multiple Linear Regression (MLR), Decision Tree Regression (DTR), Random Forest Reg

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Publication Date
Fri Oct 14 2022
Journal Name
Diagnostics
Determination of the Accuracy of Salivary Biomarkers for Periodontal Diagnosis
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Background: We aimed to investigate the accuracy of salivary matrix metalloproteinases (MMP)-8 and -9, and tissue inhibitor of metalloproteinase (TIMP)-1 in diagnosing periodontitis and in distinguishing periodontitis stages (S)1 to S3. Methods: This study was a case–control study that included patients with periodontitis S1 to S3 and subjects with healthy periodontia (controls). Saliva was collected, and then, clinical parameters were recorded, including plaque index, bleeding on probing, probing pocket depth, and clinical attachment level. Diagnosis was confirmed by assessing the alveolar bone level using radiography. Salivary biomarkers were assayed using an enzyme-linked immunosorbent assay. Results: A total of 45 patients (15

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Publication Date
Sun Feb 10 2019
Journal Name
Journal Of The College Of Education For Women
Development and Implementation a Programmable Model for Evaluation Pumping Technique
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This work represents development and implementation a programmable model for evaluating pumping technique and spectroscopic properties of solid state laser, as well as designing and constructing a suitable software program to simulate this techniques . A study of a new approach for Diode Pumped Solid State Laser systems (DPSSL), to build the optimum path technology and to manufacture a new solid state laser gain medium. From this model the threshold input power, output power optimum transmission, slop efficiency and available power were predicted. different systems configuration of diode pumped solid state laser for side pumping, end pump method using different shape type (rod,slab,disk) three main parameters are (energy transfer efficie

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Publication Date
Sun Jan 01 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
A reliable numerical simulation technique for solving COVID-19 model
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Publication Date
Wed Jun 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Design a supply chain model for Baghdad Soft Drinks Company
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In this paper, a mathematical model was built for the supply chain to reduce production, inventory, and transportation in Baghdad Company for Soft Drink. The linear programming method was used to solve this mathematical model. We reduced the cost of production by reduced the daily work hours, the company do not need the overtime hours to work at the same levels of production, and the costs of storage in the company's warehouses and agents' stores have been reduced by making use of the stock correctly, which guarantees reducing costs and preserving products from damage. The units transferred from the company were equal to the units demanded by the agents. The company's mathematical model also achieved profits by (84,663,769) by re

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Publication Date
Sun Jun 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Phase Behavior Compositional Model for Jambour Cretaceous Oil Reservoir
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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Evaluating the reality of applying the curriculum axis according to the Iraqi academic accreditation standards / a comparative study of a sample of governmental and private universities and colleges
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The research aims to get acquainted with the evaluation of the reality of the application of the curriculum axis from among the eight Iraqi academic accreditation standards in a sample of governmental and private universities and colleges in Iraq and to identify the main and secondary reasons for it as well as to provide proposed mechanisms and procedures to help reduce gaps, If the research problem is represented in the weak availability of the requirements of the curriculum axis in universities and colleges (the study sample) due to the weak documentation and successful implementation of them and interest in them is still below the level of ambition, In order to arrive at scientific facts, the researchers adopted the comparativ

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Publication Date
Thu Dec 15 2022
Journal Name
Bionatura
Comparative morphoanatomical study for the same rodents species in Iraq
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Samples (4th) reviewed are deposited and stored in the Iraqi Natural History Museum (INHM), and there are 4th of them. Sciurus anomalous (Güldenstädt, 1785) species are preserved and mummified. It is a Caucasian squirrel (S. anomalus) that was medium in size, with a grayish-to-chestnut color, a golden gray back, and a golden tail. It is found in the forests of East and Southeast Asia. The variety possessed for the study was previously registered in the vertebrate literature by several authors and was stored by scientific methods in the museum. As a result of the multiplication and growth of these species, and to know the environmental changes that occurred in them, they were compared with models and samples found throughout Iraq

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