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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
Tue Jun 15 2021
Journal Name
Al-academy
Abstract Expressionist features in drawings by Eric Bartot and Serwan Baran " A Comparative Study": علي ابراهيم مردان
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  Amidst the changes resulting from the subject matter of expression in art. The necessity of searching for the expressive features of thought that leaves different imprints with aesthetic features and values which called for re-modifying the expressive vision of contemporary drawings. Therefore, this research has been concerned with the study of (abstract expressive features in the drawings of (Serwan Baran) and (Eric Barto) - a comparative study), and the research includes four chapters. The first chapter is devoted to explaining the research problem, its importance, need, purpose, and limits, then determining the most important terms mentioned in it. Where the research problem dealt with the subject of abstract expressive feature

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Publication Date
Sat Jan 01 2022
Journal Name
Ssrn Electronic Journal
Developing a Predictive Model and Multi-Objective Optimization of a Photovoltaic/Thermal System Based on Energy and Exergy Analysis Using Response Surface Methodology
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Publication Date
Fri Jan 01 2016
Journal Name
Arpn Journal Of Engineering And Applied Sciences
Implementation And Evaluation Of Apm 2.6 - Controlled Quadcopter With Aerial Imagery As A Case Study
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Publication Date
Sat Apr 01 2023
Journal Name
Journal Of Engineering
Estimation of Water and Energy Saving by Rainwater Harvesting: Sulaimani City as a Case Study
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Rainwater harvesting could be a possible solution to decrease the consequences of water scarcity and energy deficiency in Iraq and the Kurdistan Region of Iraq (KRI). This study aims to calculate the water and energy (electricity) saved by rainwater harvesting for rooftops and green areas in Sulaimani city, KR, Iraq. Various data were acquired from different formal entities in Sulaimani city. Moreover, Google Earth and ArcMap 10.4 software were used for digitizing and calculating the total rooftop and green areas. The results showed that for the used runoff coefficients (0.8 and 0.95), the harvested rainwater volumes were 2901563 and 12197131 m³ during the study period (2005 – 2006) and (2019-2020). Moreover, by compa

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Publication Date
Mon Feb 08 2021
Journal Name
Public Works Management & Policy
Causes of Problems in Post-Disaster Emergency Re-Construction Projects—Iraq as a Case Study
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This study examines the causes of time delays and cost overruns in a selection of thirty post-disaster reconstruction projects in Iraq. Although delay factors have been studied in many countries and contexts, little data exists from countries under the conditions characterizing Iraq during the last 10-15 years. A case study approach was used, with thirty construction projects of different types and sizes selected from the Baghdad region. Project data was gathered from a survey which was used to build statistical relationships between time and cost delay ratios and delay factors in post disaster projects. The most important delay factors identified were contractor failure, redesigning of designs/plans and change orders, security is

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Publication Date
Sat May 30 2020
Journal Name
Neuroquantology
Comparative Study for Optoelectronic Properties of Zn (Te, Se) Solar Cells
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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Comparative Study of Gamma- Ray Shielding Parameters for Different Epoxy Composites
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In the current work various types of epoxy composites were added to concrete to enhance its effectiveness as a gamma- ray shield. Four epoxy samples of (E/clay/B4C) S1, (E/Mag/B4C) S2, (EPIL) S3 and (Ep) S4 were used in a comparative study of gamma radiation attenuation properties of these shields that calculating using Mont Carlo code (MCNP-5). Adopting Win X-com software and Artificial Neural Network (ANN), µ/ρ revealed great compliance with MCNP-5. By applying (µ/ρ) output for gamma at different energies, HVL, TVL and MFP have been also estimated. ANN technique was simulated to estimate (µ/ρ) and dose rates. According to the results, µ/ρ of all epoxy samples scored higher than standard concrete. Both S2 and S3 samples having h

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Publication Date
Sat Jan 01 2022
Journal Name
Mustansiriya Medical Journal
Molecular Detection of Agglutinin-Like Sequence 1 Gene in Candida albicans that is Isolated from Diabetic Foot Patients
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Objectives:

Candida albicans is a microbe living within the natural human flora and is found in the upper respiratory tract, mouth, intestines, and vagina. C. albicans is able to cause infections that range from superficial infections of the skin to life-threatening systemic infections.

Aim of Study:

Detection of virulence gene agglutinin-like sequence (ALS) 1 by using molecular technology from clinical samples (C. albicans

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Publication Date
Sat Feb 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation The Performance efficiency of the general company for lather Industries (a practical study)
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The performa of evaluation process is a process that should be carried out by all industrial management in order to stand on aspects of development or underdevelopment of the various departments and activities in its industrial project for the purpose of identifying obstacles and find out the causes and then avoid them quickly. And intended to rectify the performance evaluation of the  activities of  industrial project  or economic union by measuring the results achieved within a specific operational process and compare it to what is already targeted, and often the time for comparison of one year.

The process of performance evaluation depends upon several criteria and indicators within the

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Assessment of in Vitro Effect of Three Fluoride Releasing Agents on Enamel Demineralization around Orthodontic Brackets
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