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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 Jul 30 2024
Journal Name
Academia Open
Positioning Preterm Newborns for Cardiorespiratory Stability A Global Insight
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Publication Date
Fri Nov 01 2013
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Podophyllin (10%) Ointment: A New Therapeutic Modality for Psoriasis
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KE Sharquie, AA Noaimi, WK Al-Janabi, Journal of Cosmetics, Dermatological Sciences and Applications, 2013

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Publication Date
Wed Jun 10 2009
Journal Name
Iraqi Journal Of Laser
A new achromatic glass for near infrared laser instruments
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This research investigates new glasses which are best suitable for design of optical systems
working in the infrared region between 1.01 to 2.3μm. This work is extended to Oliva & Gennari
(1995,1998) research in which they found that the best known achromatic pairs are (BAF2-IRG2; SRF2-
IRG3; BAF2-IRG7; CAF2-IRGN6; BAF2-SF56A and BAF2-SF6). Schott will most probably stop the
production of these very little used and commercially uninteresting IRG glasses. In this work equally
good performances can be obtained by coupling BAF2, SRF2&CAF2 with standard glasses from Schott
or Ohara Company. The best new achromatic pairs found are (SRF2-S-TIH10; CAF2-S-LAL9; CAF2-SLAL13
and CAF2-S-BAH27). These new achromatic pai

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Publication Date
Thu Sep 01 2022
Journal Name
Journal Of Engineering
Methods for Removing Dyes from Polluted Water; A Review
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Most of the water pollutants with dyes are leftovers from industries, including textiles, wool and others. There are many ways to remove dyes such as sorption, oxidation, coagulation, filtration, and biodegradation, Chlorination, ozonation, chemical precipitation, adsorption, electrochemical processes, membrane approaches, and biological treatment are among the most widely used technologies for removing colors from wastewater. Dyes are divided into two types: natural dyes and synthetic dyes.

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Publication Date
Thu May 18 2023
Journal Name
College Of Islamic Sciences
Borrowing in a diwan Moon Tree for Nazik Angels
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The moon tree, the lover of the night, cholera, the sea changes its colors are poetic products left by the pioneer of free poetry, as many have called her. She used to write poetry and publish it in magazines and newspapers until she published it with collections that came into existence from an early age. Several factors helped her in that that contributed to the formation of her personality and the maturity of her talent, including factors Family, including environmental, and psychological, until she later became the focus of attention of many, so she became taught in the universities of London, and students stood by her method of writing free poetry, this poetic color that Badr Shaker Al-Sayyab participated in pioneering. Whoever exam

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Publication Date
Sat Oct 01 2016
Journal Name
International Journal Of Pure And Apllied Mathematics
A SEMI ANALYTICAL ITERATIVE TECHNIQUE FOR SOLVING DUFFING EQUATIONS
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Publication Date
Fri Mar 31 2023
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
A Cryptosystem for Database Security Based on RC4 Algorithm
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Because of vulnerable threats and attacks against database during transmission from sender to receiver, which is one of the most global security concerns of network users, a lightweight cryptosystem using Rivest Cipher 4 (RC4) algorithm is proposed. This cryptosystem maintains data privacy by performing encryption of data in cipher form and transfers it over the network and again performing decryption to original data. Hens, ciphers represent encapsulating system for database tables

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Publication Date
Thu Mar 09 2017
Journal Name
Sensors
A Multimodality Hybrid Gamma-Optical Camera for Intraoperative Imaging
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The development of low profile gamma-ray detectors has encouraged the production of small field of view (SFOV) hand-held imaging devices for use at the patient bedside and in operating theatres. Early development of these SFOV cameras was focussed on a single modality—gamma ray imaging. Recently, a hybrid system—gamma plus optical imaging—has been developed. This combination of optical and gamma cameras enables high spatial resolution multi-modal imaging, giving a superimposed scintigraphic and optical image. Hybrid imaging offers new possibilities for assisting clinicians and surgeons in localising the site of uptake in procedures such as sentinel node detection. The hybrid camera concept can be extended to a multimodal detec

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Publication Date
Wed Feb 29 2012
Journal Name
Al-khwarizmi Engineering Journal
Design a Fault Tolerance for Real Time Distributed System
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This paper designed a fault tolerance for soft real time distributed system (FTRTDS). This system is designed to be independently on specific mechanisms and facilities of the underlying real time distributed system. It is designed to be distributed on all the computers in the distributed system and controlled by a central unit.

Besides gathering information about a target program spontaneously, it provides information about the target operating system and the target hardware in order to diagnose the fault before occurring, so it can handle the situation before it comes on. And it provides a distributed system with the reactive capability of reconfiguring and reinitializing after the occurrence of a failure.

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Publication Date
Wed Jul 06 2022
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Pixel Based Techniques for Gray Image Compression: A review
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Currently, with the huge increase in modern communication and network applications, the speed of transformation and storing data in compact forms are pressing issues. Daily an enormous amount of images are stored and shared among people every moment, especially in the social media realm, but unfortunately, even with these marvelous applications, the limited size of sent data is still the main restriction's, where essentially all these applications utilized the well-known Joint Photographic Experts Group (JPEG) standard techniques, in the same way, the need for construction of universally accepted standard compression systems urgently required to play a key role in the immense revolution. This review is concerned with Different

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