Tuesday, October 25, 2016

Most Accessed Article: Characterizing the Zika Virus Genome – A Bioinformatics Study




Characterizing the Zika Virus Genome – A Bioinformatics Study



Author(s):


Ashesh Nandy, Sumanta Dey, Subhash C. Basak, Dorota Bielinska-Waz and Piotr WazPages 87-97 (11)


Abstract:


Background: The recent epidemic of Zika virus infections in South and Latin America have raised serious concern on its ramifications for the population in the Americas and spread of the virus worldwide. The Zika virus disease is a relatively new phenomenon for which sufficient and comprehensive data and investigative reports have not been available to date.
Objective: To carry out a bioinformatics study of the available Zika virus genomic sequences to characterize the virus.
Method: 2D graphical representation method is used for visual rendering and compute sequence parameters and descriptors of the African and Asian-American groups of the Zika viruses to characterize the sequences. We also used MEGA5.2 and other software to compute various biological properties of interest like phylogenetic relationships, transition-transversion ratios, amino acid usage, codon usage bias and hydropathy index of the Zika genomes and virions.
Results: The phylogenetic relationships show that the African and Asian-American Zika virus genomes are grouped in two clades. The 2D plots of typical genomes of these types also show dramatic differences indicating that the gene sequences at the 5’-end coding regions for the structural proteins are rather strongly conserved. Among other characteristics, the transition/transversion ratio matrices for the sequences in each of the two clades show that analogous to the dengue virus, the transition rates are about 10 to 15 times the transversion rates.
Conclusion: These findings are important for computer-assisted approaches towards surveillance of emerging Zika virus strains as well as in the design of drugs and vaccines to combat the growth and spread of the Zika virus.
Keywords:

Zika virus, Zika virus phylogeny, Zika virus characterization, African and Asian-American clades, 2D graphical representation, amino acid changes, cladewise transition-transversion ratios, Zika sequence descriptors.
Affiliation:

Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India.


Graphical Abstract:






For More Information Please Visit Our Website Current Computer Aided-Drug Design


Wednesday, October 19, 2016

Podcast on Lemont B. Kier: A Bibliometric Exploration of his Scientific Production and its Use


Podcast on Lemont B. Kier: A Bibliometric Exploration of his Scientific Production and its Use



Wednesday, October 5, 2016

Podcast on Introduction to Molecular Topology Basic Concepts and Application to Drug Design'


Podcast on Introduction to Molecular Topology Basic Concepts and Application to Drug Design'


Current Computer Aided-Drug Design


Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design.


Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.



Articles from the journal Current Computer Aided-Drug Design, 
12 Issue 1:


  • Editorial: Computer-Assisted Approaches as Decision Support Systems in the Overall Strategy of Combating Emerging Diseases: Some Comments Regarding Drug Design, Vaccinomics, and Genomic Surveillance of the Zika Virus
  • Using Deep Learning for Compound Selectivity Prediction
  • Applications of Receptor- and Ligand-based Models in Inverse Docking Experiments: Recognition of Dihydrofolate Reductase Using 7,8-Dialkyl- 1,3-Diaminopyrrolo[3,2-f]Quinazolines
  • 1-R-2-([1,2,4]Triazolo[1,5-c]quinazoline-2-ylthio)etanon(ol)s: Synthesis, Bioluminescence Inhibition, Molecular Docking Studies, Antibacterial and Antifungal Activities
  • 3D-QSAR Studies on the Biological Activity of Imidazolidinylpiperidinylbenzoic Acids as Chemokine Receptor Antagonists
  • Artificial Neural Network Analysis of Pharmacokinetic and Toxicity Properties of Lead Molecules for Dengue Fever, Tuberculosis and Malaria
  • Metabolic Electron Attachment as a Primary Mechanism For Toxicity Potentials of Halocarbons
  • Identification of Novel BACE1 Inhibitors by Combination of Pharmacophore Modeling, Structure-Based Design and In Vitro Assay
Courtesy by : Bentham Insight

Podcast on Drug DNA Interaction by Dr. Ashesh Nandy

Podcast on Drug DNA Interaction by Dr. Ashesh Nandy


Current Computer Aided-Drug Design


Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design.


Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.


Articles from the journal Current Computer Aided-Drug Design, 12 Issue 1:


  • Editorial: Computer-Assisted Approaches as Decision Support Systems in the Overall Strategy of Combating Emerging Diseases: Some Comments Regarding Drug Design, Vaccinomics, and Genomic Surveillance of the Zika Virus
  • Using Deep Learning for Compound Selectivity Prediction
  • Applications of Receptor- and Ligand-based Models in Inverse Docking Experiments: Recognition of Dihydrofolate Reductase Using 7,8-Dialkyl- 1,3-Diaminopyrrolo[3,2-f]Quinazolines
  • 1-R-2-([1,2,4]Triazolo[1,5-c]quinazoline-2-ylthio)etanon(ol)s: Synthesis, Bioluminescence Inhibition, Molecular Docking Studies, Antibacterial and Antifungal Activities
  • 3D-QSAR Studies on the Biological Activity of Imidazolidinylpiperidinylbenzoic Acids as Chemokine Receptor Antagonists
  • Artificial Neural Network Analysis of Pharmacokinetic and Toxicity Properties of Lead Molecules for Dengue Fever, Tuberculosis and Malaria
  • Metabolic Electron Attachment as a Primary Mechanism For Toxicity Potentials of Halocarbons
  • Identification of Novel BACE1 Inhibitors by Combination of Pharmacophore Modeling, Structure-Based Design and In Vitro Assay
Courtesy by : Bentham Insight

Highlighted Article Flyer for the journal “Current Computer-Aided Drug Design” Volume 11, Number 4



courtesy by : https://benthamsciencepublishers.wordpress.com/2016/07/15/highlighted-article-flyer-for-the-journal-current-computer-aided-drug-design/ 

Recently Published Issue of the Journal Current Computer-Aided Drug Design



Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design. It is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.

Following are the articles from the Journal of Current Computer Aided-Drug Design, 10 Issue 4


Article: Characteristics of Influenza HA-NA Interdependence Determined Through a Graphical Technique


Author(s): Ashesh Nandy, Tapati Sarkar, Subhash C. Basak, Papiya Nandy and Sukhen Das


Article: Theoretical Modeling of HPV: QSAR and Novodesign with Fragment Approach


Author(s):
Girinath G. Pillai, Lauri Sikk, Tarmo Tamm, Mati Karelson, Peeter Burk and Kaido Tamm

Article: Docking Modes of BB-3497 into the PDF Active Site – A Comparison of the Pure MM and QM/MM Based Docking Strategies



Author(s):
Tripti Kumari, Upasana Issar and Rita Kakkar

Article: 3D-QSAR Analysis on ATR Protein Kinase Inhibitors Using CoMFA and CoMSIA


Author(s):
Xiurong Li, Mao Shu, Yuanqiang Wang, Rui Yu, Shuang Yao and Zhihua Lin

Article: Pharmacophore Based 3DQSAR of Phenothiazines as Specific Human Butyrylcholinesterase Inhibitors for Treatment of Alzheimer’s Disease;


Author(s): Harish S. Kundaikar, Neha P. Agre and Mariam S. Degani


Article: A Combined Cheminformatics and Computational Approach for the Prediction of Anti-HIV Small Molecules


Author(s): Naghmeh Poorinmohammad and Hassan Mohabatkar


Article: A Structural Feature of the Non-Peptide Ligand Interactions with Mice Mu-Opioid Receptors


Author(s): Hamid R. Noori, Christian Mucksch and Herbert M. Urbassek



Article: 3D Modeling of Dengue Virus NS4B and Chikungunya Virus nsP4: Identification of a Common Drug Target and Designing a Single Antiviral Inhibitor


Author(s): Garisekurthi Satheesh, Nagu P. Prabhu and Musturi Venkataramana


Article: Development of a Two-Step Indirect Method for Modeling Ecom50


Author(s):
Lowell H. Hall, L. Mark Hall, Dennis W. Hill, Douglas M. Hawkins, Ming-Hui Chen and David F. Grant

Article: Virtual Screening and Synthesis of Novel Antitubercular Agents Through Interaction-Based Pharmacophore and Molecular Docking Studies


Author(s):
Deepak Bhattarai, Muhammad Muddassar, Jae Wan Jang, Seung Kon Hong, Eunice Eunkyeong Kim, Taegwon Oh, Sang-Nae Cho, Ae Nim Pae and Gyochang Keum

Courtesy by Bentham Insight

Current Computer Aided-Drug Design, 12 Issue 2



Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design.
Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.

Articles from the journal Current Computer Aided-Drug Design, 12 Issue 2

For details on the articles, please visit this link :: http://bit.ly/2aNd20q
courtesy by  : https://benthamsciencepublishers.wordpress.com/2016/08/26/new-issue-current-computer-aided-drug-design-12-issue-2/