Preferred Language
Articles
/
bijps-1604
A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
...Show More Authors

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.

 

Scopus Crossref
View Publication Preview PDF
Quick Preview PDF
Publication Date
Mon Jun 03 2024
Journal Name
Research Journal Of Chemistry And Environment
Molecular study of two medicinal leech species
...Show More Authors

he genus Hirudo is an invertebrate animal that got major concerns to human. However, genetics of Hirudo has been unwell considered in Iraq. In order to gain a deeper understanding in the outline of the genetic of Hirudo that were used in alternative medicine clinics, nineteen specimens of Hirudo were obtained. Fourteen of them (H.verbana, n=10; H. orientalis, n=4) were obtained from some different clinics and scientific centres in Baghdad, Iraq between January and March 2022, these specimens were considered as non-local leeches. The other (native isolates) leeches (H. orientalis, n=5) were collected in 2014 from two localities in Erbil, northern Iraq. ITS-2, COI and 12S-rRNA of Hirudo spp were amplified using conventional polymerase chain r

... Show More
Publication Date
Wed Jun 01 2022
Journal Name
Political Sciences Journal
US-Russian Interventions in the Caspian-Caucasus Basin Countries after 2001: (Strategies to Re-Impose Control and Influence as a Model)
...Show More Authors

Today, the five Caspian riparian states on the shores of the Caspian Sea (Kazakhstan, Turkmenistan, Azerbaijan, Russia, and Iran) have become a front for ambitions and international and regional competition, especially in light of the features and characteristics that natural geography has endowed them with and their enjoyment of a group of economic and mineral wealth that are not optimally exploited so far which made it a strategic attraction area for international trends and interventions, especially Western ones. It is a battleground for major international companies aiming to monopolize promising industrial investments in order to impose control and influence on the region’s resources and economic wealth and thus impose their forei

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Jun 30 2021
Journal Name
College Of Islamic Sciences
What Imam Ibn al-Subki disagreed with Imam al-Amadi in Tashnif al-Masma’, the chapter on analogy as a model
...Show More Authors

Takbiratul Ehram "The First Takbeer to Start Prayer" means: the words that the worshiper says to start his prayers, and refrain from anything invalidates it. the findings revealed that the four school jurists agreed that the prayer is not valid without Takbiratul Ehram "The First Takbeer to Start Prayer", and they disagreed on its description, so the majority of jurists said that it is a pillar, and some of them called it an obligatory, but Hanafi made it a condition. Likewise, the four jurists agreed that the one who articulates Takbiratul Ehram "The First Takbeer to Start Prayer" with the word: “Allahu Akbar,”; his Takbeer is correct, and they disagreed about the one who adds a word, or replaced it with another, where the m

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Aug 31 2022
Journal Name
Al-kindy College Medical Journal
A Spotlight on the Experience of E-learning as a Learning Method for the Undergraduate Pediatric Nursing Students in Iraq during the COVID-19 Pandemic
...Show More Authors

    The emergence of COVID-19 has resulted in an unprecedented escalation in different aspects of human activities, including medical education. Students and educators across academic institutions have confronted various challenges in following the guidelines of protection against the disease on one hand and accomplishing learning curricula on the other hand. In this short view, we presented our experience in implementing e-learning to the undergraduate nursing students during the present COVID-19 pandemic emphasizing the learning content, barriers, and feedback of students and educators. We hope that this view will trigger the preparedness of nursing faculties in Iraq to deal with this new modality of learning and improve it should t

... Show More
View Publication Preview PDF
Crossref (2)
Crossref
Publication Date
Mon May 27 2019
Journal Name
Al-academy
A Hypothesis of Architectural Environment Exercise for Actor Training (Continuous exercise space workshop – A model): هيثم عبد الرزاق علي
...Show More Authors

The peculiarity of the theater does not lie in its dramatic content because many literary genres and other artistic styles share with it in this content. The peculiarity of the theater lies in contemplating the drama through what is architectural, and this architectural axis is what distinguishes its character. It is a spatial poetry which is composed by the laws of physics and chemistry, (Weight, height, distance, rhythm, gravity, impulses and chemical excretions). i.e., what cannot be expressed in words. This is a game of space to exchange and organize energy and communicate in space by the living body, which contains the possibilities of the living drawing in space: in the time and place. This research deals with the importance of the

... Show More
View Publication Preview PDF
Crossref
Publication Date
Tue Feb 01 2022
Journal Name
Desalination And Water Treatment
A novel forward osmosis for treatment of high-salinity East Baghdad oilfield produced water as a part of a zero liquid discharge system
...Show More Authors

This study investigated a novel application of forward osmosis (FO) for oilfield produced water treatment from the East Baghdad oilfield affiliated to the Midland Oil Company (Iraq). FO is a part of a zero liquid discharge system that consists of oil skimming, coagulation/flocculation, forward osmosis, and crystallization. Treatment of oilfield produced water requires systems that use a sustainable driving force to treat high-ionic-strength wastewater and have the ability to separate a wide range of contaminants. The laboratory-scale system was used to evaluate the performance of a cellulose triacetate hollow fiber CTA-HF membrane for the FO process. In this work, sodium chloride solution was used as a feed solution (FS) with a concentratio

... Show More
View Publication Preview PDF
Publication Date
Mon Aug 14 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Study of Cross Sections for 10 Li 10 Reaction From Cross Sections of Li a,n) Reaction Using the Reciprocity Theory for the Ground State
...Show More Authors

In this study, light elements Li ,10B for (a,n) and (n,a) reactions
as well as o-particle energy from threshold energy to 10 MeV are
used according to the available data of reaction cross sections. The
more recent cross sections data of (a,n) and (n,a) reactions are
reproduced in fine steps 42 Kev for 10B(n,o) Li in the specified
energy range, as well as cross section (o,n) Values were derived from
the published data of (n,a) as a function of a-energy in the same fine
energy steps by using the principle inverse reactions. This calculation
involves only the ground state of Li OB in the reactions 'Li(a,n) B
B (n,a) Li
Introduction
When two charged nuclei overcome their Coulomb repulsion, a
rearrangement

... Show More
View Publication Preview PDF
Publication Date
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research & Development
A Study of the Vertical Position of the Mental Foramen using Cone-Beam Computed Tomography
...Show More Authors

View Publication
Scopus Crossref
Publication Date
Tue Apr 02 2019
Journal Name
Artificial Intelligence Research
A three-stage learning algorithm for deep multilayer perceptron with effective weight initialisation based on sparse auto-encoder
...Show More Authors

A three-stage learning algorithm for deep multilayer perceptron (DMLP) with effective weight initialisation based on sparse auto-encoder is proposed in this paper, which aims to overcome difficulties in training deep neural networks with limited training data in high-dimensional feature space. At the first stage, unsupervised learning is adopted using sparse auto-encoder to obtain the initial weights of the feature extraction layers of the DMLP. At the second stage, error back-propagation is used to train the DMLP by fixing the weights obtained at the first stage for its feature extraction layers. At the third stage, all the weights of the DMLP obtained at the second stage are refined by error back-propagation. Network structures an

... Show More
View Publication
Crossref (1)
Crossref
Publication Date
Sat Jan 01 2022
Journal Name
Journal Of The Mechanical Behavior Of Materials
A spherical fuzzy AHP model for contractor assessment during project life cycle
...Show More Authors
Abstract<p>Measurement of construction performance is essential to a clear image of the present situation. This monitoring by the management team is necessary to identify locations where performance is exceptionally excellent or poor and to identify the primary reasons so that the lessons gained may be exported to the firm and its progress strengthened. This research attempts to construct an integrated mathematical model utilizing one of the recent methodologies for dealing with the fuzzy representation of experts’ knowledge and judgment considering hesitancy called spherical fuzzy analytic hierarchy process (SFAHP) method to assess the contractor’s performance per the project performance pa</p> ... Show More
View Publication
Scopus (7)
Crossref (7)
Scopus Clarivate Crossref