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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
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Probabilistic Model building using the Transformation Entropy for the Burr type –xii Distribution
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Entropy define as uncertainty measure has been transfared by using the cumulative distribution function and reliability function for the Burr type – xii. In the case of data which suffer from volatility to build a model the probability distribution on every failure of a sample after achieving limitations function, probabilistic distribution. Has been derived formula probability distribution of the new transfer application entropy on the probability distribution of continuous Burr Type-XII and tested a new function and found that it achieved the conditions function probability, been derived mean and function probabilistic aggregate in order to be approved in the generation of data for the purpose of implementation of simulation

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Publication Date
Sun Mar 03 2013
Journal Name
Baghdad Science Journal
A Comparison of the Methods for Estimation of Reliability Function for Burr-XII Distribution by Using Simulation.
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This deals with estimation of Reliability function and one shape parameter (?) of two- parameters Burr – XII , when ?(shape parameter is known) (?=0.5,1,1.5) and also the initial values of (?=1), while different sample shze n= 10, 20, 30, 50) bare used. The results depend on empirical study through simulation experiments are applied to compare the four methods of estimation, as well as computing the reliability function . The results of Mean square error indicates that Jacknif estimator is better than other three estimators , for all sample size and parameter values

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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
A study to compare the internal fitness and marginal gap between single crowns and crowns within three-unite bridge of zirconia substructure fabricated by CAD-CAM system. (An In vitro study)
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ABSTRACT Purpose: the aim of this in vitro study was to compare the marginal gap and internal fitness between single crowns and the crowns within three-unit bridges of zirconium fabricated by CAD-CAM system. Materials and methods: A standard model from ivoclar company was used as a pattern to simulate three-units bridge (upper first molar and upper first premolar) as abutments used to fabricate stone models, eight single crowns for premolar and eight of three units bridges. Crowns and bridges fabricated by CAD-CAM system were cemented on their respective stone models then sectioned at the mid-point buccolingaully and misiodistaly and examined under stereomicroscope. Result: the marginal gap in premolar crowns and premolar within bridge we

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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Physics: Conference Series
The Fear Effect on a Food Chain Prey-Predator Model Incorporating a Prey Refuge and Harvesting
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Abstract<p>In this paper, we investigate the impact of fear on a food chain mathematical model with prey refuge and harvesting. The prey species reproduces by to the law of logistic growth. The model is adapted from version of the Holling type-II prey-first predator and Lotka-Volterra for first predator-second predator model. The conditions, have been examined that assurance the existence of equilibrium points. Uniqueness and boundedness of the solution of the system have been achieve. The local and global dynamical behaviors are discussed and analyzed. In the end, numerical simulations are confirmed the theoretical results that obtained and to display the effectiveness of varying each parameter</p> ... Show More
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Publication Date
Thu Feb 01 2024
Journal Name
International Communications In Heat And Mass Transfer
A comparative study of twisted and straight fins in enhancing the melting and solidifying rates of PCM in horizontal double-tube heat exchangers
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Publication Date
Wed Sep 20 2023
Journal Name
Journal Of Aeronautical Materials
Motor Response Speed And Its Relationship To The Performance Accuracy Of A Skills Of Passing From The Top And Smash Serve In Volleyball
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The game of volleyball requires the formation of new motor responses, which in turn requires special physical characteristics in the performance of that skill, and the correct and accurate performance during the performance of the skills of passing from the top and smash serve in volleyball cannot be developed or improved without a good level of accuracy and what is required to perform the movements in terms of responses to the defense and attack movements. Therefore, the researchers decided to identify the type of relationship between the motor response speed with the performance accuracy of the skills of passing from the top and the smash serve in volleyball. The research aims to: 1. Identifying the motor response speed of fourth-stage s

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Publication Date
Wed Dec 04 2013
Journal Name
Proceedings Of Nuclei Of Seyfert Galaxies And Qsos - Central Engine &amp; Conditions Of Star Formation — Pos(seyfert 2012)
Are Narrow Line Seyfert 1 galaxies a special class of Active Galactic Nuclei?
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No. Due to their apparently extreme optical to X-ray properties, Narrow Line Seyfert 1s (NLSy1s) have been considered a special class of active galactic nuclei (AGN). Here, we summarize observational results from different groups to conclude that none of the characteristics that are typically used to define the NLSy1s as a distinct group – from the, nowadays called, Broad Line Seyfert 1s (BLSy1s) – is unique, nor ubiquitous of these particular sources, but shared by the whole Type 1 AGN. Historically, the NLSy1s have been distinguished from the BLSy1s by the narrow width of the broad Hb emission line. The upper limit on the full width at half maximum of this line is 2000kms−1 for NLSy1s, while in BLSy1s it can be of several thousands

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Publication Date
Thu May 01 2025
Journal Name
Microbes And Infectious Diseases
Molecular detection and the frequency of a pore-forming toxin in Enterococcus faecalis isolated from urinary tract infections
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Publication Date
Mon May 01 2023
Journal Name
Journal Of Engineering
Measuring the Attribute Accuracy and Completeness for the OpenStreetMap Roads Networks for Two Regions in Iraq
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The OpenStreetMap (OSM) project aims to establish a free geospatial database for the entire world which is editable by international volunteers. The OSM database contains a wide range of different types of geographical data and characteristics, including highways, buildings, and land use regions. The varying scientific backgrounds of the volunteers can affect the quality of the spatial data that is produced and shared on the internet as an OSM dataset. This study aims to compare the completeness and attribute accuracy of the OSM road networks with the data supplied by a digitizing process for areas in the Baghdad and Thi-Qar governorates. The analyses are primarily based on calculating the portion of the commission (extr

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Publication Date
Mon May 01 2023
Journal Name
Journal Of Engineering
Measuring the Attribute Accuracy and Completeness for the OpenStreetMap Roads Networks for Two Regions in Iraq
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The OpenStreetMap (OSM) project aims to establish a free geospatial database for the entire world which is editable by international volunteers. The OSM database contains a wide range of different types of geographical data and characteristics, including highways, buildings, and land use regions. The varying scientific backgrounds of the volunteers can affect the quality of the spatial data that is produced and shared on the internet as an OSM dataset. This study aims to compare the completeness and attribute accuracy of the OSM road networks with the data supplied by a digitizing process for areas in the Baghdad and Thi-Qar governorates. The analyses are primarily based on calculating the portion of the commission (extra road) and

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