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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 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
Thu Jun 01 2023
Journal Name
Journal Of Engineering
Proposing a General Formula for Evaluating the Parametric Cost Using MLR Method
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This research takes up address the practical side by taking case studies for construction projects that include the various Iraqi governorates, as it includes conducting a field survey to identify the impact of parametric costs on construction projects and compare them with what was reached during the analysis and the extent of their validity and accuracy, as well as adopting the approach of personal interviews to know the reality of the state of construction projects. The results showed, after comparing field data and its measurement in construction projects for the sectors (public and private), the correlation between the expected and actual cost change was (97.8%), and this means that the data can be adopted in the re

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A study of fermi hole for some atomic systems
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the electron correlation effect for inter-shell can be described by evaluating the fermi hole and partial fermi hole for Li atom comparing with Be+ and B+2 ions

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Publication Date
Wed Jul 01 2015
Journal Name
Al–bahith Al–a'alami
Iraqi Press and its Role in Shaping Electoral Awareness (Iraqi Parliamentary Elections on 30 April, 2014 as a Model)
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The parliamentary election is one of the features of democratic systems that give individuals the right to participate in government and political election-making. Typically, the process of parliamentary elections received wide attention from media, as well as attention from large segments of the public because they understand the vast importance to assume political positions and associated fates of people and their destinies. Its importance comes from the fact that it allows citizens the right to participate in managing the public affairs by granting their confidence and voices to the elected president or his representatives in the parliamentary.
Media task is to emerge democratic societies, in particular, in the mission of urging p

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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
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 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
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
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Study of the properties of Ru-isotopes using the proton-neutron interacting boson model (IBM-2)
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The proton-neutron interacting boson model (IBM-2) has been used to make a schematic study of the Ruthenium ( ) isotopes of mass region around with and . For each isotope of the values of the IBM-2 Hamiltonian parameters, which yield an acceptable results for excitation energies in comparison with those of experimental data, have been determined. Fixed values of the effective charges ( ) and of the proton and neutron g factors ( and ) have been chosen for all isotopes under study. The calculated electric quadrupole moments of state, transitions, the magnetic dipole moments transitions and mixing ratios are in reasonable agreement with the experimental data.

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Publication Date
Mon Mar 01 2021
Journal Name
Iraqi Journal Of Physics
Study of the proton halo structure of nuclei 23Al and 27P using the binary cluster model
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The neutron, proton, and matter densities of the ground state of the proton-rich 23Al and 27P exotic nuclei were analyzed using the binary cluster model (BCM). Two density parameterizations were used in BCM calculations namely; Gaussian (GS) and harmonic oscillator (HO) parameterizations. According to the calculated results, it found that the BCM gives a good description of the nuclear structure for above proton-rich exotic nuclei. The elastic form factors of the unstable 23Al and 27P exotic nuclei and those of their stable isotopes 27Al and 31P are studied by the plane-wave Born approximation. The main difference between the elastic form factors of unstable nuclei and the

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