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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 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
Tue Jan 01 2019
Journal Name
Ieee Access
Implementation of Univariate Paradigm for Streamflow Simulation Using Hybrid Data-Driven Model: Case Study in Tropical Region
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Publication Date
Wed Nov 01 2017
Journal Name
Journal Of Engineering
Calculating Production Rate of each Branch of a Multilateral Well Using Multi-Segment Well Model: Field Example
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Multilateral wells require a sophisticated type of well model to be applied in reservoir simulators to represent them. The model must be able to determine the flow rate of each fluid and the pressure throughout the well. The production rate calculations are very important because they give an indication about some main issues associated with multi-lateral wells such as one branch may produce water or gas before others, no production rate from one branch, and selecting the best location of a new branch for development process easily.                                &nbsp

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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
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
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
Mon Jan 01 2018
Journal Name
Al–bahith Al–a'alami
The Communicative Integration in New Media: Building a Communicative Model
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The internet, unlike other traditional means of communication, has a flexibility to stimulate the user and allows him to develop it. Perhaps, the reason for the superiority of the internet over other traditional means of communication is the possibility of change and transmission from one stage to another in a short period. This means that the internet is able to move from the use to the development of the use and then the development of means and innovation as the innovation of the internet is a logical product of the interaction of the user with the network. The internet invests all the proposals and ideas and does not ignore any even if it is simple. This is represented in social networking sites which in fact reflects personal emotio

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Publication Date
Wed Sep 30 2015
Journal Name
College Of Islamic Sciences
Orbital factors in the hair Alberdony: (Denial is a model
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The theory of Pilgrims in the Magra is based on Dekru's view that the mgha is considered a pilgrim, and that the pilgrims are pilgrims
Tujia purely exposes the abstract temptation structure, and that the discharge of the Mfezouz Mfarouz is through factors
This theory tends to highlight the role of pilgrim function as a language
There is no preservation unless directed towards a particular outcome. Gemma can include morphine blindness
Or formulas that allow for the presentation of a pilgrimage to a writer in addition to the content of the news, and the guidance of the recipient
In one direction or another.
 The orbital masses are one of these morphines and functional components that achieve function
The Togolese

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Publication Date
Sat Jun 01 2024
Journal Name
University Of Thi-qar Journal Of Agricultural Research
A comparative histological, histometrical and hormonal study between the ovary and uterus of non-pregnant and pregnant local breed cat (Catus felius)
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Samples of the ovary and uterus of local breed cats used to investigate the histological, histometrical and hormonal features. The paraffin embedding technique was used for processing of tissue that stained by hematoxyline and eosin stain, and massons trichrom stain. Ovary of at proestrus or oestrus phases composed of outer cortex that covered by cuboidal germinal epithelium and inner medulla. Tunica albuginea composed of a thin layer of characterized by fusiform stromal cells. The cortex content groups of Oogonial cells, numerous primordial follicles, little primary, secondary and tertiary follicles in addition for 1-2 follicular cysts and mature corpus letium. In pregnant cat the thickness of ovarian cortex was significantly incre

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Publication Date
Wed Jan 30 2013
Journal Name
Al-kindy College Medical Journal
Using the Abbreviated Version of Modification of Diet in Renal Disease Formula as A Primary Estimate for the Prevalence of Undiagnosed Chronic Kidney Disease in Patients with Acute Stroke
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Introduction: The association between acute stroke and
renal function is well known. The aim of this study is to
know which group of patients with acute stroke is more
likely to have undiagnosed Chronic Kidney Disease and
which risk factors are more likely to be associated with.
Methods:We studied 77 patients who were diagnosed to
have an acute stroke.Patients were selected between
April2011andJune 2011 using the " 4-variable
Modification of
Diet in Renal Disease Formula " which estimates
Glomerular Filtration Rate using four variables :serum
creatinine ,age ,race and gender.
Results :The study included 38 male and 39 females
patients ,aged (35-95) years. Glomerular Filtration Rate in
patients wi

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