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I would like to bring to your kind notice that programs hosted in this blog are  distributed under creative commons rights, which means no restriction in distribution, usage and exhibition with proper citation and acknowledgment. All the programs hosted here are developed by me. But, it is very disheartening that one of the readers/followers is removing all the cross-links which has been primarily used for uploading software and manuals. As a contributor in Science, no matter how little is it? please make room for others to reside and develop knowledge and don't be an obstacle for me and for others who are in real thrust for knowledge and developing something very important. I really apologize to those kind heart peoples who are always appreciating and praising my work for making such comments general which is very much important.

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“One has to go through all the experiences in Life because it makes you understand your own frailties and also helps you develop respect for God.”

N.R. Narayana Murthy

Virtual Epitope Excision: Strategies Developed from Mass Spectrometry Proteolytic Footprinting.

We will be bringing you shortly Virtual Epitope Excision: Strategies Developed from Mass Spectrometry Proteolytic Footprinting. An online server which will guide the choice of proteinases and the free fragments generation to scrutinize the entire mass spectrometry analysis. Another role of this server is to make you decide the prediction accuracy of other epitope prediction programs.

Combating Cancer through Epigenetic Modulation by Virtual Screening of Natural Bioactives

Ravi Kapopara*¹, S. Prasanth Kumar², Saumya K. Patel¹, Dhananjay K. Sadhu¹,  

Yogesh T. Jasrai¹, Himanshu A. Pandya¹ and Rakesh M. Rawal³

¹Bioinformatics Laboratory, Department of Botany, Gujarat University, Gujarat, India.

²Department of Bioinformatics, Alagappa University, Tamil Nadu, India

³Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology,

The Gujarat Cancer and Research Institute (GCRI), Gujarat, India.

Download the Author's Proof here:
http://www.slideshare.net/prasanthperceptron/ravi-kapopara-s-prasanth-kumar-sajeb-9804422

Abstract

Epigenetic events are due to altered gene expression without any changes in the genetic material and characteristic of heritability via cell division. The impact of epigenetic control over cancer is one among the thrust area of research in cancer biology. The present study deals about the virtual screening of plant derived natural bioactives directed against the key molecular regulators of the epigenetic events viz. DNA methyltransferases (DNMT1, DNMT2 and DNMT3B), Histone acetyltransferase (HAT), Histone deacetylase 8 (HDAC8), Histone H3 lysine 27 methyl transferase (H3K27MT) and Histone H3 specific lysine 4 demethylase (H3K4DM). This computational screening identified the most efficient binders with respect to individual targets in terms of ligand binding energy. We hope that structure optimization of the best scored docked conformations will reveal new insights and development of natural bioactives to combat cancer.  

Keywords: Epigenetics, Virtual screening, Natural bioactives, Ligand binding energy

Computational Analysis of Naturally Occurring Marine Compounds (NOMC) Targeting Gap Junctions and Cell Adhesive Molecules for the Identification of Anticancer Drug Targets

S.K. Patel*, S. Prasanth Kumar1, Y.T. Jasrai1,H.A. Pandya1, and R.M. Rawal2
1Department of Botany, University School of Sciences,
Gujarat University, Ahmedabad-382415, Gujarat, India
2Division of Medicinal Chemistry & Pharmacogenomics,
Department of Cancer Biology, The Gujarat Cancer & Research Institute,
Asarwa, Ahmedabad-380 016, India.

The Journal of Computational Intelligence in Bioinformatics 2011: 4(2), pp. 161-171

Abstract

Compounds and metabolites from marine organisms established a new arena

for marine pharmacy primarily due to their diverse biological activities. In the

long run of anticancer drug development pipeline, some of the naturally

occurring marine compounds (NOMCs) appear to be potential candidates and

few are commercialized. In the present study, investigation of NOMCs from

Marine Algae, Sponges, Corals, Bacteria, Cnardians, and Marine Fish was

carried out targeted against Gap junctions (Connexin 26, Connexin 43) and

Cell Adhesive molecules (Cadherins, Integrins) via molecular docking studies.

The in silico effectiveness of NOMCs was studied based upon the interaction

with the protein’s active site residues with less binding energy. The interacting

NOMCs were further filtered to predict the bioavailability and drug likeness

properties. Manoalide from Marine Sponges was shown to be a better

interacting ligand with low binding energy (-121.693 kcal/mol) and passed all

the physicochemical parameters for drug likeness. This work encourages the

development of NOMCs with some chemical modifications to augment more

efficacy and better activity.

Keywords: Naturally occurring marine compounds (NOMCs), Gap junctions,

Cell adhesive molecules, Molecular docking, Anticancer activity

MY RESEARCH PROFILE

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http://www.slideshare.net/prasanthperceptron/prasanth-kumar-cv-11397561