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Amr Alhossary, Yaw Awuni, Chee Keong Kwoh, Yuguang Mu
Dengue fever is a febrile illness caused by Dengue Virus, which belongs to the Flaviviridae family. Among its proteome, the nonstructural protein 5 (NS5) is the biggest and most conserved. It has a primer-independent RNA-dependent RNA polymerase (RdRp) domain at its C-Terminus. Zou et al. studied the biological relevance of the two conserved cavities (named A and B) within the NS5 proteins of dengue virus (DENV) and West Nile Virus (WNV) using mutagenesis and revertant analysis and found four mutations located at cavity B having effects on viral replication...
June 2018: Journal of Bioinformatics and Computational Biology
Ya-Qi Cai, Ya-Ting Bao, Hong-Jin Wang, Xiao-Dong Ren, Lin-Fang Huang, Jie He, Tian-Tian Liu, Rui Zeng
This paper aimed to investigate the anti-influenza virus activity of the genus Paeonia, screen potential anti-influenza virus compounds and predict targets of anti-influenza virus to explore the mechanism of anti-influenza virus activity. First of all, a total of 301 compounds of the genus Paeonia were summarized from the literatures in recent ten years. The candidate active ingredients from the genus Paeonia were identified by database such as PubChem and Chemical Book. The ligands were constructed by ChemDraw, Avogadro and Discovery Studio Visualizer...
April 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Ya-Ting Bao, Yue Wang, Xiao-Dong Ren, Lin-Fang Huang, Rui Zeng
This paper aimed to investigate the antibacterial activity of flowers and leaves from Paeonia rockii, screen antibacterial compounds and predict targets of antibacterial to explore its multi-component, multi-target antibacterial mechanism. In this study, minimal inhibitory concentration(MIC) of seven strains of Staphylococcus aureus, S. epidermidis´╝î Bacillus subtilis, B. cereus, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa were determined by microdilution method. Uniprot databases was used to find the antibacterial targets, and RCSB was used to identify targets associated with antimicrobial activity as docked receptor proteins...
February 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Nafisa M Hassan, Amr A Alhossary, Yuguang Mu, Chee-Keong Kwoh
"Virtual Screening" is a common step of in silico drug design, where researchers screen a large library of small molecules (ligands) for interesting hits, in a process known as "Docking". However, docking is a computationally intensive and time-consuming process, usually restricted to small size binding sites (pockets) and small number of interacting residues. When the target site is not known (blind docking), researchers split the docking box into multiple boxes, or repeat the search several times using different seeds, and then merge the results manually...
November 13, 2017: Scientific Reports
Amr Alhossary, Stephanus Daniel Handoko, Yuguang Mu, Chee-Keong Kwoh
MOTIVATION: The need for efficient molecular docking tools for high-throughput screening is growing alongside the rapid growth of drug-fragment databases. AutoDock Vina ('Vina') is a widely used docking tool with parallelization for speed. QuickVina ('QVina 1') then further enhanced the speed via a heuristics, requiring high exhaustiveness. With low exhaustiveness, its accuracy was compromised. We present in this article the latest version of QuickVina ('QVina 2') that inherits both the speed of QVina 1 and the reliability of the original Vina...
July 1, 2015: Bioinformatics
Stephanus Daniel Handoko, Xuchang Ouyang, Chinh Tran To Su, Chee Keong Kwoh, Yew Soon Ong
Predicting binding between macromolecule and small molecule is a crucial phase in the field of rational drug design. AutoDock Vina, one of the most widely used docking software released in 2009, uses an empirical scoring function to evaluate the binding affinity between the molecules and employs the iterated local search global optimizer for global optimization, achieving a significantly improved speed and better accuracy of the binding mode prediction compared its predecessor, AutoDock 4. In this paper, we propose further improvement in the local search algorithm of Vina by heuristically preventing some intermediate points from undergoing local search...
September 2012: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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