Grant of 100% Clean Award to miRNA to siRNA Program

Thanks to the Softpedia Database and its Editorial Team for considering the miRNA to siRNA Program to be available as a freeware, added to the database and granted "100% Clean Award". Special thanks for also including Protein Stability Program.

Grant ward can be viewed here:

http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml

Download this program here:

http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml

Normal Mode Analysis of Breast Cancer Resistance Protein

The following preview shows you the trajectories observed in normal mode analysis using Amber94 force field with the homology model of Breast Cancer Resistance Protein (BCRP)

Video is copyright. Please ask a concern from me before using it.

Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies

This study will appear in International Journal of Pharmacy and Life Sciences in June Edition.


Exploring the Polymerase Activity of Chikungunya Viral non structural
Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking
Studies


S. Prasanth Kumar, Ravi G. Kapopara, Yogesh T. Jasrai and Himanshu A. Pandya
Department of Bioinformatics, ABC, Gujarat University, Ahmedabad- 380009.

Graphical Abstract

S. Prasanth Kumar, Ravi G. Kapopara, Mehul I. Patni, Himanshu A. Pandya, Yogesh T. Jasrai* and Saumya K. Patel. Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies. International Journal of Pharmacy and Life Sciences 3(6): pp. 1752-1765.

Chikungunya viral RNA-dependent RNA polymerase (RdRp) activity is conferred by non

structural protein 4 (nsp4), an important protein target towards the development of antiviral

compounds. The present study deals about the development of homology model of nsP4

followed by molecular docking with known RdRp inhibitors experimented in Hepatitis C virus

(HCV), HIV-1, Paramyxovirus, etc. The predicted catalytic site and two allosteric binding sites

were docked with nucleosidic and non-nucleosidic inhibitors. The best top five scoring ligands

were selected based upon the interaction profiles and a common pharmacophore was developed.

Copyrighted Material. Write a concern to the corresponding author for getting the
coordinates.Contact: prasanthbioinformatics@gmail.com

Grant of 100% Clean Award to Protein Stability Program

Thanks to the Softpedia Database and its Editorial Team for considering the Protein Stability Program to be available as a freeware, added to the database and granted "100% Clean Award"

Grant ward can be viewed here:
http://www.softpedia.com/progClean/Protein-Stability-Clean-210115.html 

Full text article is available here:
http://iioablett.pitt.edu/ojs/index.php/iioablett/article/view/12 

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Energy minimization of PfCRT (Plasmodium falsciparum chloroquine resistant transporter)

Google Scholar

CpGP Dynamics – The Dynamics of CpG Island and Promoter to Validate Nucleosomal Gene Expression

S. Prasanth Kumar
Department of Bioinformatics, Alagappa University, Karaikudi- 630003, India.
prasanthbioinformatics@gmail.com

Abstract

Computational prediction of nucleosome positioning relies upon in vitro and in vivo experimental outcome such as sequence positioning and exclusion signatures, structural thermodynamic details, histone-DNA interaction models, etc. On the other hand, CpG island and promoter prediction programs are available which depends upon the algorithm built by the predictive power of trained experimental datasets from sequencing projects. “CpGP dynamics –The dynamics of CpG island and promoter to validate nucleosomal gene expression” is a web based program which predicts the nucleosome- positioning (NP) and exclusion (NE) signatures in the user provided nucleotide sequence and presents a graphical output. It also utilizes the sequence positions of CpG island and promoter predicted by third-party programs as input to generate graphical sequence output. These two graphical outputs can be merged to discriminate the more accurate sequence positions of CpG island and promoter from a number of likelihood predictions. The program is freely accessible at http://www.cpgpdynamics.webs.com. 

Keywords: Nucleosome Positioning and Exclusion, CpG island, Promoter, Bioinformatics.

Full text will be available at:

http://www.sersc.org/journals/IJBSBT/vol4_no2/2.pdf

(Copyright has been retained by SERSC)