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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 Mar 30 2021
Journal Name
Scientific Review Engineering And Environmental Studies (srees)
Testing the performance of a solar energy cooling system in Baghdad city
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Renewable energy resources have become a promissory alternative to overcome the problems related to atmospheric pollution and limited sources of fossil fuel energy. The technologies in the field of renewable energy are used also to improve the ventilation and cooling in buildings by using the solar chimney and heat exchanger. This study addresses the design, construction and testing of a cooling system by using the above two techniques. The aim was to study the effects of weather conditions on the efficiency of this system which was installed in Baghdad for April and May 2020. The common weather in these months is hot in Baghdad. The test room of the design which has a size of 1 m3 was situated to face the geographical south. The te

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Publication Date
Sun Dec 02 2018
Journal Name
Indian Journal Of Public Health Research & Development
A revised checklist of the blister beetles genera (Coleoptera, Meloidae) from Iraq
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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Engineering
The Synergic Effects of Mineral Admixtures in Ternary Blended Cement: A Review
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In the last decades, using mineral admixture in concrete became very necessary to improve concrete properties and reduce CO2 emissions associated with the cement production process. Subsequently, more sustainable concrete can be obtained.  Ternary blended cement containing two different types of mineral admixture can achieve ambitious steps in this trend. In this research, the synergic effects of mineral admixtures in ternary blended cement and its effects on concrete fresh properties, strength, durability, and efficiency factors of mineral admixture in ternary blended cement, were reviewed. The main conclusion reached after reviewing many literature pieces is that the concrete with ternary blended cement

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Publication Date
Sat Jul 01 2017
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A REVISED CHECKLIST OF THE ROBBER FLY GENERA (DIPTERA, ASILIDAE) FROM IRAQ
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    A revised checklist of the robber fly genera (Diptera, Asilidae) was given during this study in Iraq. The investigation showed (21) genera belonging to seven subfamilies, two genera new recorded to entomofauna of Iraq (Promachus Loew, 1848 and Genus: Dysmacus Loew, 1860). Eight genera showed in this investigation and eleven genera were recorded previously to Iraq.

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Publication Date
Wed Jul 17 2019
Journal Name
Anbar University Journal
The Translation of Swearwords in Shakespeare’s Hamlet into Arabic: A Pragmatic Perspective
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Publication Date
Thu Oct 26 2023
Journal Name
Farmacia
THE DEVELOPMENT OF A BRAIN TARGETED MUCOADHESIVE AMISULPRIDE LOADED NANOSTRUCTURED LIPID CARRIER
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Publication Date
Mon Mar 18 2024
Journal Name
Inflammopharmacology
The effects of cholesterol and statins on Parkinson’s neuropathology: a narrative review
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Publication Date
Wed Aug 27 2025
Journal Name
Baghdad Science Journal
A Clustering Technique Based on the Hard K-Means (H.KM.) Method to Determine the Governorate That Have More Influence for Spreading COVID-19 in the Kingdom of Saudi Arabia
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Publication Date
Sun Oct 15 2023
Journal Name
Bionatura
Feline Calici Virus Isolation and Molecular Analysis in an Iraqi Cat in Baghdad
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The feline calicivirus (FCV) is a highly contagious and infectious virus that infects cats and causes moderate to stringent respiratory infections and oropharyngeal illness. It is prevalent in shelters and birthplace colonies and frequently infects kitten cats. 50 distinct cats were involved in the research, with samples acquired between October 2020 and January 2021. Swabs were taken from the oropharynx and conjunctiva, conditional on the signs of FCV disease septicity, to inspect viral nucleic acid from collecting samples, then extract the RNA from the swabs and turn it into a cDNA particle, and finally distinguishing the open reading frame nucleic acid gene 2 using a primer special for feline calicivirus, All specimens were taken

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Publication Date
Thu May 18 2023
Journal Name
Journal Of Engineering
Design and Implementation of a Generalized N-Digit Binary-To-Decimal Converter on an FPGA Seven-Segment Display Using Verilog Hdl
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It is often needed to have circuits that can display the decimal representation of a binary number and specifically in this paper on a 7-segment display. In this paper a circuit that can display the decimal equivalent of an n-bit binary number is designed and it’s behavior is described using Verilog Hardware Descriptive Language (HDL).
This HDL program is then used to configure an FPGA to implement the designed circuit.

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