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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 Feb 20 2022
Journal Name
Papers In Physics
Electronic and optical properties of nickel-doped ceria: A computational modelling study
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Cerium oxide (CeO2), or ceria, has gained increasing interest owing to its excellent catalytic applications. Under the framework of density functional theory (DFT), this contribution demonstrates the eect that introducing the element nickel (Ni) into the ceria lattice has on its electronic, structural, and optical characteristics. Electronic density of states (DOSs) analysis shows that Ni integration leads to a shrinkage of Ce 4f states and improvement of Ni 3d states in the bottom of the conduction band. Furthermore, the calculated optical absorption spectra of an Ni-doped CeO2 system shifts towards longer visible light and infrared regions. Results indicate that Ni-doping a CeO2 system would result in a decrease of the band gap. Finally,

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Publication Date
Thu Mar 10 2022
Journal Name
Oral Surgery
Evaluation of buffered local anaesthesia in dental extraction: A randomized controlled study
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Buffering of Local anaesthesia (LA) has been suggested as a mechanism to improve injection comfort and hasten the onset of anaesthesia. Aim This study aimed to evaluate the effectiveness of buffered LA in the extraction of maxillary premolars and molars. Materials and Methods This randomized controlled study included 100 patients who were indicated for extraction of maxillary posterior teeth, they were randomly divided into two groups; a study group that received infiltration of buffered 2% lidocaine hydrochloride with 1:80,000 epinephrine LA, and a control group that received non-buffered 2% lidocaine hydrochloride with 1:80,000 epinephrine LA. The buffering was performed using the Onset® LA buffering system (Onpharma®). The outcome va

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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Engineering
Using a novel approach to determine the pore pressure of West Qurna 15 oil well in South of Iraq
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Pore pressure means the pressure of the fluid filling the pore space of formations. When pore pressure is higher than hydrostatic pressure, it is named abnormal pore pressure or overpressure. When abnormal pressure occurred leads to many severe problems such as well kick, blowout during the drilling, then, prediction of this pressure is crucially essential to reduce cost and to avoid drilling problems that happened during drilling when this pressure occurred. The purpose of this paper is the determination of pore pressure in all layers, including the three formations (Yamama, Suliay, and Gotnia) in a deep exploration oil well in West Qurna field specifically well no. WQ-15 in the south of Iraq. In this study, a new appro

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Publication Date
Mon Feb 13 2023
Journal Name
Bmc Oral Health
The reliability of using light therapy compared with LASER in pain reduction of temporomandibular disorders: a randomized controlled trial
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Abstract<sec> <title>Background

Temporomandibular Disorders (TMD) refer to a group of symptoms where pain is the most leading cause to demand a treatment by the patient. Light therapies are of great importance at current times due to its biosafety and non-invasive quality when used for the management of TMD symptoms. This study aimed to evaluate the efficacy of red LED light with low-level LASER in treating TMD patients.

Materials and methods

A double-blind randomized clinical study was conducted and included 60 patients along 3 groups (20 for e

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Publication Date
Thu Sep 01 2022
Journal Name
Human Gene
Tissue inhibitor of metalloproteinase-1 (TIMP-1) serum level and genetic polymorphisms associated with cutaneous leishmania infections
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Introduction: Cutaneous leishmaniasis is considered a parasitic contagion resulting from the flagellated parasite belonging to the genus of Leishmania. Also, cutaneous leishmaniasis is a zoonotic ailment transmitted through the bloodsucking sand-flies bite (belonging to the Phlebotomus genus). The disease's reservoirs included wild or semi-domesticated animals, in general rodents and dogs. Tissue inhibitor metalloproteinase-1 (TIMP-1) is one of the extracellular matrix proteins that have a role in vessel wall degeneration and aneurysm development. In addition, it belongs to the zinc-dependent endopeptidases family that are involved in the degradation of connective tissues proteins which are included in vascular integrity maintenance. The Ge

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Publication Date
Sun Dec 01 2013
Journal Name
Journal Of International Academic Research For Multidisciplinary
SYNTHESIS AND LIQUID CRYSTALLINE BEHAVIOUR OF NEW SERIES CONTAINING 1, 3-OXAZEPINE AND 1, 3-THIAZOLE RINGS
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The synthesis and properties of two new series of compounds having 1,3-Oxazepineand 1,3-thiazole rings connected through azo linkage are reported. These compounds weresynthesized by the reaction of phthalic anhydride with Schiff bases. The molecular structuresof these compounds were verified by elemental analysis, FTIR and 1HNMR spectroscopy.The mesomorphic behaviors of these compounds were studied by optical polarizedmicroscopy (OPM) and differential scanning calorimetry (DSC). All compounds of the twoseries show liquid crystalline properties. The influence of the central oxazepine and thiazolerings and the terminal substituents on the type and temperature range of the mesomorphousproperties of these compounds has been elucidated

Publication Date
Tue Jul 31 2012
Journal Name
Journal Of The College Of Education - University Of Tikrit
Synthesis, Spectroscopic and Biological Studies of some Metal Complexes with 1-phenyl-2(1-phenyl ethylidene) hydrozine.
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Publication Date
Sun Nov 23 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Validity of 3D Reconstructed Computed Tomographic Image in Using Craniometrical Measurements of the Skull for Sex Differentiation (An Iraqi Study)
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Background: The skull offers a high resistance of adverse environmental conditions over time, resulting in the greater stability of the dimorphic features as compared to other skeletal bony pieces. Sex determination of human skeletal considered an initial step in its identification. The present study is undertaken to evaluate the validity of 3D reconstructed computed tomographic images in sex differentiation by using craniometrical measurements at various parts of the skull. Materials and Method: 3D reconstructed computed tomographic scanning of 100 Iraqi subject, (50 males and 50 females) were analyzed with their age range from20-70 years old. Craniometrical linear measurements were located and marked on both side of the 3D skull images.

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Publication Date
Tue May 11 2021
Journal Name
Photonics And Nanostructures - Fundamentals And Applications
The spontaneous emission performance of a quantum emitter coupled to a hybrid plasmonic waveguide with specified output polarization for on-chip plasmonic single-photon source
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Nowadays, most of the on-chip plasmonic single-photon sources emit an unpolarized stream of single photons that demand a subsequent polarizer stage in a practical quantum cryptography system. In this paper, we numerically demonstrated the coupling of the light emitted from a quantum emitter (QE) at 700 nm wavelength to the propagation mode supported by an on-chip hybrid plasmonic waveguide (HPW) polarization rotator. Our results proved that the light emitted is linearly polarized at 0º, 45º/−45º, and 90º with propagation lengths of 5 μm, 3.3 μm, and 3.9 μm, respectively. Moreover, high power-conversion efficiency was obtained from an applied transverse magnetic (TM) mode (0º-polarization) to a transverse electric (TE) (90º-polari

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Publication Date
Thu Jul 01 2021
The spontaneous emission performance of a quantum emitter coupled to a hybrid plasmonic waveguide with specified output polarization for on-chip plasmonic single-photon source
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