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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
Sun Sep 24 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Using The Ultrasonic Waves For Studying Thermal And Elastic Properties as a Function of Porosity in Sintered ceramic
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Ultrasonic pulse echo measurements on porous alumina as ceramic

material with porosities ranging from (20-40)% showed effect of volume

fraction of porosity on both thermal and elastic properties. A quadratic relationships, by using a least squares method, is deduced for the dependence of the shear velocity, longitudinal velocity, shear modulus, Young's modulus,  bulk  modulus, Poisson 's ratio, Debye temperature, specific heat, and thermal conductivity on the total  porosity. By these relationships,  the  thermal  and  elastic  properties  results  of  pore-free alumina  were  calculated.  The  elastic  properties  results  of  

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Publication Date
Tue Jun 15 2021
Journal Name
Al-academy
The Physical Performance Of The Actor Within The Shows Of Anas Abdul Samad ( the play silence as the cry as a model): حليم هاتف جاسم
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The body has the ability to effect the audience in the the theatrical show , since he or she is transmitter , sender , seen and viewer of the humanitarian discourse as well the the images and connotations of the theatrical show, it is a tool of communication that substitutes for millions of spoken words, the modern schools of direction focused on the body language of the actor and gave it prominence in depicting facts by different connotations. The researcher studies the physical performance of the actor throughout focusing on the connotational dimensions of the body within the theatrical show , as well as the positioning of performative body within the modern schools of direction depending on the theatrical show (Rebuke ) of the Iraqi d

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Publication Date
Tue Mar 15 2022
Journal Name
Al-academy
The semiotics of the visual image of women in the discourse of empowerment, Saudi Arabia Kingdom as a model
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We studied, in this paper, the semiotics of the visual image of women in the discourse of empowerment, through three models of advertising images expressing the particularities of the Saudi Arabian environment.

We aim to know how the mark operates and how it is interpreted, as a semantic process in which the meaning ranges from description to interpretation, and we studied two hypotheses:

-The advertising image is a structure in which the mark corresponds to the reality and the discourse to the context.

-The significance is not found in the visual sign or in the textual sign of the advertising image, but in the creative event that opens up to the social, cultural, and psychological context, and creates a field of dia

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Publication Date
Sun May 01 2022
Journal Name
Civil Engineering Journal
Phases of Urban Development Impact on the Assessment of Thermal Comfort: A Comparative Environmental Study
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Millions of pilgrims and visitors from numerous parts of the world flock to Karbala (one of the most prominent ideological and religious places in central Iraq) each year to visit the holy shrines in Karbala due to their sanctity. Many improvements have been made to the Two Holy Shrines (THS), the Shrines of Imam Husayn and Imam Abbas, and the area between them (ATHS), due to the high temperatures in this region and to improve pedestrian thermal comfort. Studies on improving outdoor thermal comfort in Karbala are scarce. Hence, this research aims to look into historical and current architectural changes and how they affect thermal comfort. On the hottest summer day, the ENVI-met software program was used to simulate the building des

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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
A Comparative Study of the Photostabilization of Polyvinyl Chloride with Nano and Micro Nickel Oxide
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NiO nanoparticle synthesis by chemical method and characterized by XRD with crystal size 11.72
nm and grain size 13 nm from FESEM image also NiO micro used ,two NiO as an additive to evaluate the
possibility of producing photodegradable polymers, the practical application of solid-phase photocatalytic
degradation of polyvinyl chloride (PVC- NiO composite films) was investigated. PVC has a negative impact
on the environment since its polymer degrades slowly, yet it has a wide range of industrial applications and
the amount used shows no evidence of diminishing use. Thus, a synthesis of modified PVC- NiO micro and
nano has been studied with 0, 50, 100, 150, 200, 250, and 300 (hours) as irradiation time a

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Publication Date
Sun May 01 2022
Journal Name
Civil Engineering Journal
Phases of Urban Development Impact on the Assessment of Thermal Comfort: A Comparative Environmental Study
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Millions of pilgrims and visitors from numerous parts of the world flock to Karbala (one of the most prominent ideological and religious places in central Iraq) each year to visit the holy shrines in Karbala due to their sanctity. Many improvements have been made to the Two Holy Shrines (THS), the Shrines of Imam Husayn and Imam Abbas, and the area between them (ATHS), due to the high temperatures in this region and to improve pedestrian thermal comfort. Studies on improving outdoor thermal comfort in Karbala are scarce. Hence, this research aims to look into historical and current architectural changes and how they affect thermal comfort. On the hottest summer day, the ENVI-met software program was used to simulate the building des

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Publication Date
Mon Apr 03 2023
Journal Name
Chemistryselect
Development and Validation of Spectrophotometric Methods for the Quantitative Determination of Doxycycline Hyclate in Pure Form and Pharmaceutical Formulations Using Flow‐Injection and Batch procedures: A Comparative Study
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Abstract<p>Doxycycline hyclate is an antibiotic drug with a broad‐spectrum activity against a variety of gram‐positive and gram‐negative bacteria and is frequently used as a pharmacological agent and as an effector molecule in an inducible gene expression system. A sensitive, reliable and fast spectrophotometric method for the determination of doxycycline hyclate in pure and pharmaceutical formulations has been developed using flow injection analysis (FIA) and batch procedures. The proposed method is based on the reaction between the chromogenic reagent (V<sup>4+</sup>) and doxycycline hyclate in a neutral medium, resulting in the formation of a yellow compound that shows maximum absorbance at 3</p> ... Show More
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Publication Date
Wed Mar 01 2023
Journal Name
Human Gene
The deubiquitylase-ubiquitin-specific protease 4 absence in HeLa cells leads to a reduction in Semliki Forest virus replication
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Publication Date
Wed Nov 15 2023
Journal Name
Oncology And Radiotherapy
Synthesis, spectroscopic characterization, molecular docking, antioxidant and anticancer studies of some metal complexes from tetraazamacrocyclic Schiff base ligand
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Five novel nickel, iron, cobalt, copper, and mercury complexes were synthesized from tetraazamacrocyclic Schiff base ligand (L), which were derived from 3-(4-(dimethyl amino) benzylidene) pentane-2,4-dione and 1,2- diaminocyclohexane in a 2:2 molar ratio. Many physico-chemical and spectroscopic techniques, including melting point, 1HNMR, 13CNMR, elemental analysis, molar conductance, magnetic susceptibility, UV-Vis, FT-IR, and thermogravimetric analysis (TGA), were used to characterize the Schiff base ligand and all metal complexes. The octahedral geometry of all the complexes [MLCl2] is confirmed by spectroscopic analyses. All substances' biological properties, such as their in vitro antioxidant activity or level of free radical scavenging

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Publication Date
Sun Apr 23 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Comparative study for Effect of the Using of Aged Garlic Extract and Row Garlic extract added to drinking water as Immune Modulators of Broiler Infected with Gomboro
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   This study included the effect of Aged garlic extract (AgE) and Row garlic extract (RgE)as immune modulators for treating or redusing the infection of boiler by Gomboro.       This is made of measuring the stress index and serum antibodies levels against Gomboro virous( GV) estimated by HI,the study also detected the effect of each extract as antioxidents in broiler by estimation of peroxynitrite in serum . 300 chicks infected with Gumboro diseas brought at day ( 21 ) old and divided into three groups , the first group A was given the ( RgE ) at level of 5% with drinking water , the group B was given 5% of  ( AgE ) and group C is left as control group and wasn't given anything.  &

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