tag:blogger.com,1999:blog-69707751470704161142024-03-22T07:45:22.946+05:30PRASANTH VIRTUAL BIOINFO LABA Bioinformatics Portal for Innovative ResearchPRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.comBlogger49125tag:blogger.com,1999:blog-6970775147070416114.post-19548101049635728962013-05-19T16:24:00.000+05:302013-05-19T16:25:46.406+05:30Cationic fullerene quinazolinone conjugates as Tuberculosis HGPRT Inhibitors<br />
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<span style="color: blue;">Synthesis and biological evaluation of cationic fullerene quinazolinone conjugates and their binding mode with modeled Mycobacterium tuberculosis hypoxanthine-guanine phosphoribosyltransferase enzyme.</span></h1>
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<a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Patel%20MB%5BAuthor%5D&cauthor=true&cauthor_uid=23625031">Patel MB</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Kumar%20SP%5BAuthor%5D&cauthor=true&cauthor_uid=23625031">Kumar SP</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Valand%20NN%5BAuthor%5D&cauthor=true&cauthor_uid=23625031">Valand NN</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Jasrai%20YT%5BAuthor%5D&cauthor=true&cauthor_uid=23625031">Jasrai YT</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Menon%20SK%5BAuthor%5D&cauthor=true&cauthor_uid=23625031">Menon SK</a>.<br />
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Department of Chemistry, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India. Department of Bioinformatics, Applied Botany Centre, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.<br />
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The present work reports a series of novel cationic fullerene derivatives bearing a substituted-quinazolinone moiety as a side arm. Fullerene-quinazolinone conjugates synthesized using the 1,3-dipolar cycloaddition reaction of C60 with azomethine ylides generated from the corresponding Schiff bases of substituted quinazolinone were characterized by elemental analysis, FT-IR, 1H NMR, 13C NMR and ESI-MS and screened for their antibacterial activity against Mycobacterium tuberculosis (H 37 Rv strain). All the compounds exhibited significant activity with the most effective having MIC in the range of 1.562-3.125 μg/mL. Compound 9f exhibited good biological activity compared to standard drugs. We developed a computational strategy based on the modeled M. tuberculosis hypoxanthine-guanine phosphoribosyltransferase (HGPRT) using homology modeling techniques and studied its binding pattern with synthesized fullerene derivatives. We then explored the surface geometry of the protein to place the cage adjacent to the active site while optimizing its quinazolinone side arm to establish H bonding with active site residues.</div>
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<a href="http://link.springer.com/article/10.1007%2Fs00894-013-1820-1">http://link.springer.com/article/10.1007%2Fs00894-013-1820-1</a></div>
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PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-90586966059318453672013-05-19T16:19:00.001+05:302013-05-19T16:20:46.769+05:30Artemisinin Molecular Target<h3>
<span style="color: blue; font-family: inherit;"><b>Structural Insights into the Theoretical Model of Plasmodium falciparum NADH Dehydrogenase and its Interaction with Artemisinin and Derivatives: Towards Global Health Therapeutics.</b></span></h3>
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<b><span style="color: red; font-family: Times, 'Times New Roman', serif; line-height: 18px;">Kumar SP<span style="font-size: large; line-height: 1.125em;">,</span><span style="font-size: large; line-height: 1.125em;"> </span>Jasrai YT<span style="font-size: large; line-height: 1.125em;">,</span><span style="font-size: large; line-height: 1.125em;"> </span>Pandya HA<span style="font-size: large; line-height: 1.125em;">,</span><span style="font-size: large; line-height: 1.125em;"> </span>George LB<span style="font-size: large; line-height: 1.125em;">,</span><span style="font-size: large; line-height: 1.125em;"> </span>Patel SK</span><span style="color: red; font-family: Times, 'Times New Roman', serif; font-size: large; line-height: 1.125em;">.</span></b></h3>
<span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: small; line-height: 1.0915em;">Department of Bioinformatics, Applied Botany Centre, University School of Sciences , Gujarat University, Ahmedabad, India .</span><br />
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<span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: small; line-height: 17px;">Abstract</span><br />
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It is a continuing quest to uncover the principal molecular targets of malarial parasites to understand the antimalarial activity and mechanism of action of artemisinin, a potent antimalarial. A series of parasite proteins are experimentally validated as potential targets, such as translationally controlled tumor protein (TCTP) and sarco/endoplasmic reticulum membrane calcium ATP-ase (SERCA). The present study addressed the development of a theoretical model of Plasmodium falciparum NADH dehydrogenase with inference from artemisinin in vivo inhibitory activity. We report here the predicted binding modes of artemisinin and its derivatives. The modeled protein resembled the structural architecture of flavoproteins and oxidoreductases, consisting of two Rossmann folds and dedicated binding sites for its cofactors. Docked poses of the ligand dataset revealed its interactions at or near the si face, indicating being activated. This may aid in generation of reactive oxygen species, thereby disrupting the membrane potential of parasite mitochondria and leading to the clearance from the blood. These observations open up new strategies for development of novel therapeutics, or improvement of existing pharmacotherapies against malaria, a major burden for global health.</div>
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<a href="http://online.liebertpub.com/doi/abs/10.1089/omi.2012.0129">http://online.liebertpub.com/doi/abs/10.1089/omi.2012.0129</a></div>
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PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-62908715031174275562013-05-19T16:07:00.001+05:302013-05-19T16:10:48.396+05:30Novel cationic fullerene derivatized s-triazine scaffolds <br />
<a href="https://www.researchgate.net/publication/236621904_Novel_cationic_fullerene_derivatized_s-triazine_scaffolds_as_photoinduced_DNA_cleavage_agents_design_synthesis_biological_evaluation_and_computational_investigation?ev=prf_pub" style="cursor: pointer; text-decoration: none;"><b><span style="font-size: large;">Novel cationic fullerene derivatized s-triazine scaffolds as photoinduced DNA cleavage agents: design, synthesis, biological evaluation and computational investigation</span></b></a><br />
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<span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3AManishkumar%20B.%20Patel" style="color: black;">Manishkumar B. Patel</a>,<sup>a</sup> </span> <span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3AUma%20Harikrishnan" style="color: black;">Uma Harikrishnan</a>,<sup>a</sup> </span> <span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3ANikunj%20N.%20Valand" style="color: black;">Nikunj N. Valand</a>,<sup>a</sup> </span><span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3ADeval%20S.%20Mehta" style="color: black;">Deval S. Mehta</a>,<sup>c</sup> </span> <span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3AKuldeep%20V.%20Joshi" style="color: black;">Kuldeep V. Joshi</a>,<sup>a</sup> </span><span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3ASivakumar%20Prasanth%20Kumar" style="color: black;">Sivakumar Prasanth Kumar</a>,<sup>b</sup> </span> <span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3AKishor%20H.%20Chikhalia" style="color: black;">Kishor H. Chikhalia</a>,<sup>a</sup> </span><span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3ALinz%20Buoy%20George" style="color: black;">Linz Buoy George</a>,<sup>c</sup> </span> <span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3AYogesh%20T.%20Jasrai" style="color: black;">Yogesh T. Jasrai</a><sup>b</sup> and </span> <span class="author_link" style="display: inline-block; margin-right: -3px; padding: 0px; position: relative;"><a href="http://pubs.rsc.org/en/results?searchtext=Author%3AShobhana%20K.%20Menon" style="color: black;">Shobhana K. Menon</a><span style="font-size: 16px;">*</span><sup>a</sup> </span></div>
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<span style="font-size: xx-small;"><i>a. </i></span><span style="font-size: 11.818181991577148px;">Department of Chemistry, University School of Sciences, Gujarat University, Navrangpura, India </span><br />
<span style="font-size: 11.818181991577148px;">b. </span><span style="font-size: 11.818181991577148px; font-style: italic;">Department of Bioinformatics, Applied Botany Centre (ABC), University School of Sciences, Gujarat University, Navrangpura, India</span></div>
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<span style="font-size: 11.818181991577148px;">c. </span><span style="font-size: 11.818181991577148px; font-style: italic;">Department of Zoology and Biomedical Technology, University School of Sciences, Gujarat University, Navrangpura, India</span></div>
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<img alt="Graphical abstract: Novel cationic fullerene derivatized s-triazine scaffolds as photoinduced DNA cleavage agents: design, synthesis, biological evaluation and computational investigation" src="http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=C3RA40950C" /></div>
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<span style="font-family: Trebuchet MS, sans-serif;"><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">A series of novel cationic fullerene (C</span><small style="color: #222222; line-height: 17.99715805053711px;"><sub>60</sub></small><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">) derivatives, bearing substituted s-triazine moiety as a side arm, synthesized by using the 1,3 dipolar cycloaddition reaction of C</span><small style="color: #222222; line-height: 17.99715805053711px;"><sub>60</sub></small><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;"> with azomethine ylides generated from the corresponding Schiff bases of substituted s-triazine is reported. All the synthesized compounds were characterized by elemental analysis, FT-IR, </span><small style="color: #222222; line-height: 17.99715805053711px;"><sup>1</sup></small><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">H NMR, </span><small style="color: #222222; line-height: 17.99715805053711px;"><sup>13</sup></small><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">C NMR and ESI-MS. The compounds </span><strong style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">7a</strong><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">, </span><strong style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">7d</strong><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">, </span><strong style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">7e</strong><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;"> and </span><strong style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;">7f</strong><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;"> cleaved the supercoiled pBR322 DNA into nicked form efficiently upon visible light irradiation in the presence of NADH. The photoinduced superoxide radical and hydroxyl radical generated may act as molecular species causing the DNA scission. Further, the interaction of synthesized molecules with pBR322 plasmid DNA was investigated using computational approaches.</span></span></div>
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<a href="http://pubs.rsc.org/en/content/articlelanding/2013/ra/c3ra40950c">http://pubs.rsc.org/en/content/articlelanding/2013/ra/c3ra40950c</a><span style="font-family: Trebuchet MS, sans-serif;"><span style="color: #222222; font-size: 11.818181991577148px; line-height: 17.99715805053711px;"> </span></span></div>
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PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-21468249611466841462012-12-06T10:05:00.002+05:302013-05-19T16:27:44.157+05:30Evolutionary and Molecular Aspects of Indian Tomato Leaf Curl Virus Coat ProteinSivakumar Prasanth Kumar, Saumya K. Patel, Ravi G. Kapopara,<br />
Yogesh T. Jasrai, and Himanshu A. Pandya<br />
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Department of Bioinformatics, Applied Botany Center, University School of Sciences, Gujarat University, Ahmedabad 380 009, India<br />
Department of Botany, University School of Sciences, Gujarat University, Ahmedabad 380 009, India<br />
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<span style="text-align: justify;">Tomato leaf curl disease (ToLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface, and stunted plant growth caused by tomato leaf curl virus (ToLCV). In the present study, we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, Gujarat (ToLCGV-[Vad]), India. We found that the amino acids in coat protein required for systemic infection, viral particle formation, and insect transmission to host cells were conserved amongst Indian strains. Phylogenetic studies on Indian ToLCV coat proteins showed evolutionary compatibility with other viral taxa. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the viral DNA required for encapsidation and nuclear shuttling was investigated through sequence- and structure-based approaches. We further emphasized the role of loops in coat protein structure as molecular recognition interface.</span><br />
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Download full text here:<br />
<a href="http://www.hindawi.com/journals/ijpg/2012/417935/">http://www.hindawi.com/journals/ijpg/2012/417935/</a><br />
<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529866/">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529866/</a></div>
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<a href="http://www.academia.edu/2243782/Evolutionary_and_Molecular_Aspects_of_Indian_Tomato_Leaf_Curl_Virus_Coat_Protein">http://www.academia.edu/2243782/Evolutionary_and_Molecular_Aspects_of_Indian_Tomato_Leaf_Curl_Virus_Coat_Protein</a></div>
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<br />PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-20527706971241132512012-08-16T10:57:00.002+05:302012-08-16T10:57:41.977+05:30Biocomputational Analysis of Filaggrin Sequence Repeats for Rheumatoid Arthritis<br />
Sivakumar Prasanth Kumar 1, Saumya K. Patel 1, Yogesh T. Jasrai *1, Himanshu A. Pandya 1 and Pappu Srinivasan 2<br />
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1. Department of Bioinformatics, Applied Botany Centre (ABC), University School of Sciences, Gujarat University, Ahmedabad - 380 009, India<br />
2. Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, India.<br />
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Electronic Journal of Biology, 2012, Vol. 8(2): 29-33
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You may access the complete text here: <a href="http://www.ejbio.com/pps/2012/29.pdf">http://www.ejbio.com/pps/2012/29.pdf</a><br />
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<b>Abstract</b><br />
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Anti-citrullinated antibodies are autoantibodies detected in the blood of rheumatoid arthritis (RA) patients in the early stage. These autoantibodies recognize an epitope of citrullinated peptides found on the surface of filaggrin protein and are crossreactive in immune response. Since the expression of filaggrin protein is associated with autoantibodies secretion, it may act as a potential serological marker for the detection of RA in early stage. In the present study, the contribution of filaggrin sequence repeats towards antigenicity was investigated using bioinformatic approaches. The electrostatic potential of citrullinated filaggrin repeats and its antigenicity was found to be the prominent factors for invoking such an immune response.<br />
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<b>Keywords:</b> Anti-citrullinated antibodies, epitope, filaggrin sequence repeats, rheumatoid arthritis, electrostatic potential, antigenicity.<br />
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PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-72096586047944788252012-07-27T17:27:00.000+05:302012-07-27T17:27:09.417+05:30Search Watch<div id="clustrmaps-widget">
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</script><noscript>&amp;amp;lt;a href="http://www4.clustrmaps.com/user/dd5fc079"&amp;amp;gt;&amp;amp;lt;img src="http://www4.clustrmaps.com/stats/maps-no_clusters/prasanthvirtualbioinfolab.blogspot.in--thumb.jpg" alt="Locations of visitors to this page" /&amp;amp;gt;&amp;amp;lt;/a&amp;amp;gt;</noscript>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-81259305213255087852012-06-29T17:56:00.001+05:302012-07-07T10:04:22.380+05:30Exploring the polymerase activity of chikungunya viral non structural protein 4 (nsP4) using molecular modeling, epharmacophore and docking studies<span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;">S. Prasanth Kumar, Ravi G. Kapopara, Mehul I. Patni, Himanshu A. Pandya, </span><b style="color: #222222; font-family: arial, sans-serif; font-size: 13px;">Yogesh T. Jasrai</b><span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;"> and Saumya K. Patel. Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies.</span><i style="color: #222222; font-family: arial, sans-serif; font-size: 13px;">International Journal of Pharmacy and Life Sciences</i><span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;"> 3(6): 1752-1765.</span>
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<span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;">Abstract</span><br />
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<span style="color: #222222; font-family: arial, sans-serif; font-size: x-small;">Chikungunya viral RNA-dependent RNA polymerase (RdRp) activity is conferred by non structural protein 4</span><br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: x-small;">(nsp4), an important protein target towards the development of antiviral compounds. The present study deals about <span style="background-color: white;">the development of homology model of nsP4 followed by molecular docking with known RdRp inhibitors</span></span><br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: x-small;">experimented in Hepatitis C virus (HCV), HIV-1, Paramyxovirus, etc. The predicted catalytic site and two allosteric <span style="background-color: white;">binding sites were docked with nucleosidic and non-nucleosidic inhibitors. The best top five scoring ligands were </span><span style="background-color: white;">selected based upon the interaction profiles and a common pharmacophore was developed. Further, RNA templateprimer </span><span style="background-color: white;">complex was docked within the template tunnel of modeled nsP4 to study the mode of polymerase activity.</span></span><br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: x-small;"><span style="background-color: white;"><br /></span></span><br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: x-small;">Key-Words: Chikungunya, nsP4, RdRp, Docking, Pharmacophore, Polymerase activity</span><br />
<br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;"><br /></span><br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;">Download the article</span><br />
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;"><br /></span><br />
<a href="http://www.ijplsjournal.com/issues%20PDF%20files/june_2012/5.pdf">http://www.ijplsjournal.com/issues%20PDF%20files/june_2012/5.pdf</a>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-664448405308932362012-06-21T11:15:00.000+05:302012-06-21T11:15:43.121+05:30My published results now in APBS homepage in Graphical format<div>
<br /></div>
<div>
Dears,</div>
<div>
<br /></div>
<div>
I am very pleased to disclose that my published results in graphical format has been uploaded by Dr. Nathan Baker in his APBS homepage. Thank You Very Much, Sir. </div>
<div>
<br /></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIj4FdUcxsoCZfXhXlSO9_nWWzEBd5lPHuVTHpqJ6jZ5jD8v4d-USCArXTiZvSGud8dngToC8T6FTeC1qPczKRdTJdaDPleioJcNgv9GSML04vXcy5AgdvPvx7aQSKWTNGMWUIW-OrLrQk/s1600/Prasanth+APBS.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="230" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIj4FdUcxsoCZfXhXlSO9_nWWzEBd5lPHuVTHpqJ6jZ5jD8v4d-USCArXTiZvSGud8dngToC8T6FTeC1qPczKRdTJdaDPleioJcNgv9GSML04vXcy5AgdvPvx7aQSKWTNGMWUIW-OrLrQk/s400/Prasanth+APBS.png" width="400" /></a></div>
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<br /></div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-67713635118107710832012-05-12T13:14:00.002+05:302012-05-12T13:17:04.051+05:30Grant of 100% Clean Award to miRNA to siRNA Program<span style="font-size: 13.5pt;">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.</span><br />
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<br /></div>
<div style="margin-bottom: 0.0001pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">
<span style="font-size: 13.5pt;">Grant ward can be viewed here:<o:p></o:p></span></div>
<div style="margin-bottom: 0.0001pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">
<a href="http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml">http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml</a>
</div>
<div style="margin-bottom: 0.0001pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">
<br /></div>
<div style="margin-bottom: 0.0001pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">
<span style="font-size: 18px;">Download this program here:</span></div>
<div style="margin-bottom: 0.0001pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">
<a href="http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml">http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml</a>
</div>
<div style="margin-bottom: 0.0001pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">
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<span style="font-size: medium;"><br /></span></div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-13971049385563198582012-05-11T14:56:00.000+05:302012-05-11T14:56:11.782+05:30Normal Mode Analysis of Breast Cancer Resistance Protein<div dir="ltr" style="text-align: left;" trbidi="on">
<br />
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)<br />
<br />
Video is copyright. Please ask a concern from me before using it.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dx-VRzjUniE_Vo4A_a8guXnmqNzMgvwH8e_RgUxaEcjzgGp80blwEJHfdKDIat5H6t5HR00yGHoJcJV8rIQuQ' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
<br /></div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-82432248527569798752012-04-23T10:43:00.001+05:302012-07-07T10:06:21.851+05:30Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies<div dir="ltr" style="text-align: left;" trbidi="on">
<br />
This study will appear in International Journal of Pharmacy and Life Sciences in June Edition.<br />
<br />
<br />
<b>Exploring the Polymerase Activity of Chikungunya Viral non structural</b><br />
<b>Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking</b><br />
<b>Studies</b><br />
<b><br /></b><br />
S. Prasanth Kumar, Ravi G. Kapopara, Yogesh T. Jasrai and Himanshu A. Pandya<br />
Department of Bioinformatics, ABC, Gujarat University, Ahmedabad- 380009.<br />
<br />
<b>Graphical Abstract</b><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvq0bYCJa1wEqm3hdoEgP6nGHHhL6wMzHbdcgqT5FxlTAk10rjB0IjWPQn1N9ynjZsClqlBTYEuCyZtgg52cmPVMhV00BaaueGzaSjhVazcFQj6rG_Zk5_7rba_5yJoNO-QnIw7Du7PSW-/s1600/Capture.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="283" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvq0bYCJa1wEqm3hdoEgP6nGHHhL6wMzHbdcgqT5FxlTAk10rjB0IjWPQn1N9ynjZsClqlBTYEuCyZtgg52cmPVMhV00BaaueGzaSjhVazcFQj6rG_Zk5_7rba_5yJoNO-QnIw7Du7PSW-/s320/Capture.JPG" width="320" /></a></div>
<b>S. Prasanth Kumar</b>, 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.<br />
<b><br /></b><br />
<div style="text-align: justify;">
<div style="text-align: left;">
Chikungunya viral RNA-dependent RNA polymerase (RdRp) activity is conferred by non</div>
</div>
<div style="text-align: justify;">
<div style="text-align: left;">
structural protein 4 (nsp4), an important protein target towards the development of antiviral</div>
</div>
<div style="text-align: justify;">
<div style="text-align: left;">
compounds. The present study deals about the development of homology model of nsP4</div>
</div>
<div style="text-align: justify;">
<div style="text-align: left;">
followed by molecular docking with known RdRp inhibitors experimented in Hepatitis C virus</div>
</div>
<div style="text-align: justify;">
<div style="text-align: left;">
(HCV), HIV-1, Paramyxovirus, etc. The predicted catalytic site and two allosteric binding sites</div>
</div>
<div style="text-align: justify;">
<div style="text-align: left;">
were docked with nucleosidic and non-nucleosidic inhibitors. The best top five scoring ligands</div>
</div>
<div style="text-align: justify;">
<div style="text-align: left;">
were selected based upon the interaction profiles and a common pharmacophore was developed.</div>
</div>
<b><br /></b><br />
<b>Copyrighted Material.</b> Write a concern to the corresponding author for getting the<br />
coordinates.Contact: prasanthbioinformatics@gmail.com<br />
<br /></div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-82047785845207699262012-03-19T10:33:00.001+05:302012-03-19T17:05:06.294+05:30Grant of 100% Clean Award to Protein Stability Program<div dir="ltr" style="text-align: left;" trbidi="on">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"<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVa79L0dWpyZNsDI9pJA4HkYXUafaIlpe2aIdXoly0GgapRvnxK3UYqa8-I7dxEG-o7CmVAA0fTzZWM-WUEM8V9_gQz-8lbG9pjSHLC9CfZLWwtzO_RRwnbSuihA9-SaLmZidboDl215_E/s1600/award.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="193" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVa79L0dWpyZNsDI9pJA4HkYXUafaIlpe2aIdXoly0GgapRvnxK3UYqa8-I7dxEG-o7CmVAA0fTzZWM-WUEM8V9_gQz-8lbG9pjSHLC9CfZLWwtzO_RRwnbSuihA9-SaLmZidboDl215_E/s320/award.JPG" width="320" /></a></div><br />
<br />
Grant ward can be viewed here:<br />
<a href="http://www.softpedia.com/progClean/Protein-Stability-Clean-210115.html" target="_blank">http://www.softpedia.com/progClean/Protein-Stability-Clean-210115.html </a><br />
<br />
Full text article is available here:<br />
<a href="http://iioablett.pitt.edu/ojs/index.php/iioablett/article/view/12" target="_blank">http://iioablett.pitt.edu/ojs/index.php/iioablett/article/view/12 </a><br />
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<br />
<b>S. Prasanth Kumar</b><br />
Department of Bioinformatics, Alagappa University, Karaikudi- 630003, India.<br />
prasanthbioinformatics@gmail.com<br />
<br />
<b>Abstract</b><br />
<div style="text-align: justify;">
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 <a href="http://cpgpdynamics.webs.com/">http://www.cpgpdynamics.webs.com.</a> </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="text-align: left;"><b>Keywords: </b>Nucleosome Positioning and Exclusion, CpG island, Promoter, Bioinformatics.</span></div>
<div style="text-align: justify;">
<span style="text-align: left;"><br />
</span></div>
<div style="text-align: justify;">
<span style="text-align: left;">Full text will be </span><span style="text-align: left;">available at:</span></div>
<div style="text-align: justify;">
<a href="http://www.sersc.org/journals/IJBSBT/vol4_no2/2.pdf">http://www.sersc.org/journals/IJBSBT/vol4_no2/2.pdf</a>
</div>
<div style="text-align: justify;">
(Copyright has been retained by SERSC)</div>
<div style="text-align: justify;">
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</div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-26888267407784142612012-02-10T15:16:00.001+05:302012-02-10T15:16:57.466+05:30Emergence of TYLCV: Bioinformatic Analysis<div dir="ltr" style="text-align: left;" trbidi="on">Soon, we will publish Bioinformatic Analysis of coat protein from TYLCV.</div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-11656990889428016972011-11-08T20:21:00.000+05:302011-11-08T20:21:21.110+05:30My Research Article Views on Google World<div dir="ltr" style="text-align: left;" trbidi="on">Dear Readers,<br />
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Thank you for your kind encouragement. I would like to thank all the faculties and research scientists for their excellent communication. I would also like to extend my warm welcome to my readers, followers and students. </div><br />
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<span style="font-size: 11.0pt;">1.<span style="font-size: 7pt;"> </span></span><st2:personname w:st="on"><st1:givenname w:st="on"><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">P.</span></st1:givenname><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;"> <st1:sn w:st="on">Srinivasan</st1:sn></span></st2:personname><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">, <st2:personname w:st="on"><st1:givenname w:st="on">A.</st1:givenname> <st1:sn w:st="on">Sudha</st1:sn></st2:personname>, <st2:personname w:st="on"><st1:givenname w:st="on">A.</st1:givenname> <st1:middlename w:st="on">Shahul</st1:middlename>
<st1:sn w:st="on">Hameed</st1:sn></st2:personname>, <st2:personname w:st="on"><st1:givenname w:st="on"><b>S.</b></st1:givenname><b> <st1:middlename w:st="on">Prasanth</st1:middlename>
<st1:sn w:st="on">Kumar</st1:sn></b></st2:personname> and <st2:personname w:st="on"><st1:givenname w:st="on">M.</st1:givenname> <st1:sn w:st="on">Karthikeyan</st1:sn></st2:personname>,
2011. </span><span style="font-size: 11.0pt;">Screening of medicinal plant
compounds against NS5B polymerase of hepatitis C virus (HCV) using molecular
docking studies. </span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">Journal of Pharmacy Research 4(1): pp.136-140</span><span style="font-size: 11.0pt;">. <b><o:p></o:p></b></span></div>
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<span style="font-size: 11.0pt;">2.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname>, </span></b><st2:personname w:st="on"><st1:givenname w:st="on"><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">P.</span></st1:givenname><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;"> <st1:sn w:st="on">Srinivasan</st1:sn></span></st2:personname><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">, <st2:personname w:st="on"><st1:givenname w:st="on">Saumya</st1:givenname>
<st1:middlename w:st="on">K.</st1:middlename> <st1:sn w:st="on">Patel</st1:sn></st2:personname>,
<st2:place w:st="on">Ravi</st2:place> Kapopara</span><span style="font-size: 7.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;"> </span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">and <st2:personname w:st="on"><st1:givenname w:st="on">Yogesh</st1:givenname>
<st1:middlename w:st="on">T.</st1:middlename> <st1:sn w:st="on">Jasrai</st1:sn></st2:personname></span>,
2011. <span class="citationjournal"><i><span style="font-size: 11.0pt;">In silico</span></i></span><span class="citationjournal"><span style="font-size: 11.0pt;"> development of inhibitors
against pantothenate synthetase of <i>Mycobacterium
tuberculosis</i></span></span>. <span style="font-size: 11.0pt;">Journal of
Advanced Bioinformatics and Research 2(2): pp. 142-148. <i><o:p></o:p></i></span></div>
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<span style="font-size: 11.0pt;">3.<span style="font-size: 7pt;"> </span></span><st2:personname w:st="on"><st1:givenname w:st="on"><span style="font-size: 11.0pt;">Saumya</span></st1:givenname><span style="font-size: 11.0pt;"> <st1:middlename w:st="on">K.</st1:middlename> <st1:sn w:st="on">Patel</st1:sn></span></st2:personname><span style="font-size: 11.0pt;">,
<st2:personname w:st="on"><st1:givenname w:st="on"><b>S.</b></st1:givenname><b>
<st1:middlename w:st="on">Prasanth</st1:middlename> <st1:sn w:st="on">Kumar</st1:sn></b></st2:personname>,
<st2:personname w:st="on"><st1:givenname w:st="on">Himanshu</st1:givenname> <st1:middlename w:st="on">A.</st1:middlename> <st1:sn w:st="on">Pandya</st1:sn></st2:personname>,
<st2:personname w:st="on"><st1:givenname w:st="on">Yogesh</st1:givenname> <st1:middlename w:st="on">T.</st1:middlename> <st1:sn w:st="on">Jasrai</st1:sn></st2:personname><sup>
</sup>and <st2:place w:st="on"><st1:sn w:st="on">Mehul</st1:sn> <st1:sn w:st="on">I.</st1:sn></st2:place>
Patni, 2011. 2D-QSAR analysis of dihydrofolate reductase (DHFR) inhibitors with
activity in <i>Toxoplasma gondii</i> and <i>Lactobacillus casei. </i>Journal of
Advanced Bioinformatics and Research 2(2): pp.161-166.<i><o:p></o:p></i></span></div>
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<span style="font-size: 11.0pt; mso-fareast-language: ZH-CN;">4.<span style="font-size: 7pt;"> </span></span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">S. <st2:personname w:st="on"><st1:givenname w:st="on">K.</st1:givenname>
<st1:sn w:st="on">Patel</st1:sn></st2:personname>, <st2:personname w:st="on"><st1:givenname w:st="on"><b>S.</b></st1:givenname><b> <st1:middlename w:st="on">Prasanth</st1:middlename>
<st1:sn w:st="on">Kumar</st1:sn></b></st2:personname>, <st2:personname w:st="on"><st1:givenname w:st="on">Y.</st1:givenname> <st1:middlename w:st="on">T.</st1:middlename> <st1:sn w:st="on">Jasrai</st1:sn></st2:personname>,<sub> </sub><st2:personname w:st="on"><st1:givenname w:st="on">H.</st1:givenname> <st1:middlename w:st="on">A.</st1:middlename> <st1:sn w:st="on">Pandya</st1:sn></st2:personname><sup> </sup>and <st2:personname w:st="on"><st1:givenname w:st="on">R.</st1:givenname> <st1:middlename w:st="on">M.</st1:middlename>
<st1:sn w:st="on">Rawal</st1:sn></st2:personname>, 2011. Computational
analysis of naturally occurring marine compounds (NOMC) targeting gap junctions
and cell adhesive molecules for the identification of anticancer drug targets.</span><span style="font-size: 11.0pt;"> The Journal of Computational Intelligence in
Bioinformatics 4(2): pp. 161-171.</span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;"><o:p></o:p></span></div>
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<span style="font-size: 11.0pt;">5.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname></span></b><span style="font-size: 11.0pt;">, 2011. Organic Virtual Library (ORVIL) – A
combinatorial library construction based on organic constituents and without
scaffold hopping. International Journal of Applied Research on Information
Technology and Computing 2(2): pp.57-62.<o:p></o:p></span></div>
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6.<span style="font-size: 7pt;"> </span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname></span></b><span style="font-size: 11.0pt;"> and <st2:personname w:st="on"><st1:givenname w:st="on">Muthusamy</st1:givenname>
<st1:sn w:st="on">Meenatchi</st1:sn></st2:personname>, 2011. Virtual quantification
of protein stability using applied kinetic and thermodynamic parameters. <span class="citationjournal">IIOAB Letters 1: pp.21-28</span>. </span><o:p></o:p></div>
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<span style="font-size: 11.0pt;">7.<span style="font-size: 7pt;"> </span></span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">Ravi Kapopara, <b>S. Prasanth Kumar</b>, <st2:personname w:st="on"><st1:givenname w:st="on">Saumya</st1:givenname> <st1:middlename w:st="on">K.</st1:middlename>
<st1:sn w:st="on">Patel</st1:sn></st2:personname>, <st1:givenname w:st="on">Dhananjay</st1:givenname>
<st1:middlename w:st="on">K.</st1:middlename> Sadhu, Yogesh T. Jasrai, Himanshu
A. Pandya and Rakesh M. Rawal, 2011. Virtual screening of natural bioactives in
combating cancer through epigenetic modulation. South Asian Journal of
Experimental Biology 1(5-S1): pp.12-16. </span><span style="font-size: 11.0pt; mso-bidi-font-weight: bold;"><o:p></o:p></span></div>
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<span class="citationjournal"><span style="font-size: 11.0pt;">8.<span style="font-size: 7pt;">
</span></span></span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">Pappu Srinivasan, <b>Sivakumar Prasanth
Kumar</b>, Muthusamy Karthikeyan, Jeyaram Jeyakanthan, Yogesh T. Jasrai,
Himanshu A. Pandya, Rakesh M. Rawal and Saumya K. Patel</span><span style="font-size: 11.0pt;">, 2011. </span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">Epitope-based
immunoinformatics and molecular docking studies of nucleocapsid protein and ovarian
tumor domain of Crimean-Congo hemorrhagic fever virus.</span><span style="font-size: 11.0pt;"> Frontiers in Bioinformatics and Computational Biology
2(72): 1-9. </span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">doi: 10.3389/fgene.2011.00072</span><span class="citationjournal"><span style="font-size: 11.0pt;">. <b>PMID: 22303367; </b></span></span><b><span style="font-size: 11.0pt; mso-fareast-font-family: Batang; mso-fareast-language: KO;">PMC3268625.</span></b><span class="citationjournal"><span style="font-size: 11.0pt;"><o:p></o:p></span></span></div>
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<span class="citationjournal"><span style="font-size: 11.0pt;"> <o:p></o:p></span></span></div>
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<span class="citationjournal"><span style="font-size: 11.0pt;">9.<span style="font-size: 7pt;"> </span></span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname> <st1:sn w:st="on">Kumar</st1:sn></st2:personname>,
</span></b><st2:place w:st="on"><span style="font-size: 11.0pt;">Ravi</span></st2:place><span style="font-size: 11.0pt;"> <st2:personname w:st="on"><st1:givenname w:st="on">G.</st1:givenname>
<st1:sn w:st="on">Kapopara</st1:sn></st2:personname>, <st1:givenname w:st="on">Saumya</st1:givenname>
<st1:middlename w:st="on">K.</st1:middlename> Patel, Mehul I. Patni, Yogesh T.
Jasrai, Himanshu A. Pandya and Rakesh M. Rawal, 2011. Molecular descriptor enhancement
of a common structure towards the development of α-glucosidase and α-amylase inhibitors
for post-prandial hyperglycemia (PPHG). <span class="citationjournal">Asian
Journal of Biomedical and Pharmaceutical Sciences 1(3): pp.01-12. <o:p></o:p></span></span></div>
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<span class="citationjournal"><span style="font-size: 11.0pt; mso-fareast-language: ZH-CN;">10.<span style="font-size: 7pt;"> </span></span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname>, </span></b><st2:place w:st="on"><span style="font-size: 11.0pt;">Ravi</span></st2:place><span style="font-size: 11.0pt;"> <st2:personname w:st="on"><st1:givenname w:st="on">G.</st1:givenname>
<st1:sn w:st="on">Kapopara</st1:sn></st2:personname>, Yogesh. <st2:personname w:st="on"><st1:givenname w:st="on">T.</st1:givenname> <st1:sn w:st="on">Jasrai</st1:sn></st2:personname>
and <st2:personname w:st="on"><st1:givenname w:st="on">Rakesh</st1:givenname> <st1:middlename w:st="on">M.</st1:middlename> <st1:sn w:st="on">Rawal</st1:sn></st2:personname>,
2012. Computational studies on the interaction of core histone tail domains
with CpG island. <span class="citationjournal"> International Journal of Pharma and
Biosciences 3(1): pp. B581-590<b>.</b></span></span><span class="citationjournal"><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;"><o:p></o:p></span></span></div>
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<span style="font-size: 11.0pt;">11.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname> <st1:sn w:st="on">Kumar</st1:sn></st2:personname></span></b><span style="font-size: 11.0pt; mso-bidi-font-weight: bold;">, <st2:place w:st="on">Ravi</st2:place>
<st1:givenname w:st="on">G.</st1:givenname> Kapopara, Saumya K. Patel, Himanshu
A. Pandya and Yogesh T. <st1:sn w:st="on">Jasrai</st1:sn>, 2012. Conformational
Ensemble of Digoxin and Digitoxin and its Interamolecular Energy in Torsional
Space. International Journal of Pharmacy and Biological Sciences 2(2): pp.
57-66.</span><b><span style="font-size: 11.0pt;"> </span></b><span style="font-size: 11.0pt; mso-bidi-font-weight: bold;"> <b><o:p></o:p></b></span></div>
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<span style="font-size: 11.0pt;">12.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname></span></b><span style="font-size: 11.0pt;">, <st2:place w:st="on">Ravi</st2:place> <st2:personname w:st="on"><st1:givenname w:st="on">G.</st1:givenname> <st1:sn w:st="on">Kapopara</st1:sn></st2:personname>,
<st2:place w:st="on"><st1:sn w:st="on">Mehul</st1:sn> <st1:sn w:st="on">I.</st1:sn></st2:place>
Patni, Himanshu A. Pandya, Yogesh T. <st1:sn w:st="on">Jasrai</st1:sn> and <st2:personname w:st="on"><st1:givenname w:st="on">Saumya</st1:givenname> <st1:middlename w:st="on">K.</st1:middlename> <st1:sn w:st="on">Patel</st1:sn></st2:personname>.
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.<o:p></o:p></span></div>
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<span style="font-size: 11.0pt;">13.<span style="font-size: 7pt;"> </span></span><span style="font-size: 11.0pt;">Saumya Patel, <b>S.</b>
<b>Prasanth Kumar</b> and Mehul Patni, 2012. Statistical and Biocomputational
Studies on Spondyloarthritis. <st2:personname w:st="on"><st1:givenname w:st="on">Tatiana</st1:givenname>
<st1:sn w:st="on">Melnic</st1:sn></st2:personname> (<st1:givenname w:st="on">Ed</st1:givenname>),
LAP LAMBERT Academic Publishing GmbH & Co. KG, Saarbrűcken, Germany, <b>ISBN:
978-3-659-14306-9</b>.<o:p></o:p></span></div>
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<span style="font-size: 11.0pt;">14.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname></span></b><span style="font-size: 11.0pt;">, <st1:givenname w:st="on">Saumya</st1:givenname> <st1:middlename w:st="on">K.</st1:middlename> Patel and Himanshu A. Pandya, 2012. Normal and
binding mode analysis of breast cancer resistance protein. <st2:personname w:st="on"><st1:givenname w:st="on">Alina</st1:givenname> <st1:sn w:st="on">Covali</st1:sn></st2:personname>
(<st1:givenname w:st="on">Ed</st1:givenname>), LAP LAMBERT Academic Publishing
GmbH & Co. KG, Saarbrűcken, Germany, <b>ISBN: 978-3-659-15312-9</b>.<o:p></o:p></span></div>
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<span style="font-size: 11.0pt;">15.<span style="font-size: 7pt;"> </span></span><span style="font-size: 11.0pt;">Saumya Patel, <b>Prasanth Kumar</b> and Yogesh T.
Jasrai, 2012. <span style="color: #222222;">Molecular Optimization of Calcineurin
Inhibitors for Prion Disease</span>: A Pharmacophore Study. Tatiana Melnic (Ed),
LAP LAMBERT Academic Publishing GmbH & Co. KG, Saarbrűcken, Germany, <b>ISBN:
</b><b><span style="color: #222222;">978-3-659-15895-7</span></b>.
<o:p></o:p></span></div>
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<span style="font-size: 11.0pt;">16.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname></span></b><span style="font-size: 11.0pt;">. </span><span style="font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">CpGP dynamics- The dynamics of CpG island
and promoter to validate nucleosomal gene expression</span><span class="citationjournal"><span style="font-size: 11.0pt;">. International Journal of
Bio-Science and Bio-Technology 4(2): pp. 11-26. Program is accessible at </span></span><b><span style="color: navy; font-size: 11.0pt; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;"><a href="http://cpgpdynamics.webs.com/">http://cpgpdynamics.webs.com</a>.</span></b><span style="font-size: 11.0pt; mso-bidi-font-weight: bold;"><o:p></o:p></span></div>
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<span style="font-size: 11.0pt;">17.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname>
<st1:sn w:st="on">Kumar</st1:sn></st2:personname></span></b><span style="font-size: 11.0pt;">. Docking and <i>in silico</i> bioavailability analysis
of CDK6 flavonol inhibitors and its analogues for acute lymphoblastic leukemia.
The Journal of Computational Intelligence in Bioinformatics, <b>Accepted</b>.<b><o:p></o:p></b></span></div>
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<span style="font-size: 11.0pt;">18.<span style="font-size: 7pt;"> </span></span><b><span style="font-size: 11.0pt;">S. Prasanth Kumar</span></b><span style="font-size: 11.0pt;">, <st1:givenname w:st="on">Saumya</st1:givenname> <st1:middlename w:st="on">K.</st1:middlename> Patel, Yogesh T. <st1:sn w:st="on">Jasrai</st1:sn>,
<sup> </sup><st2:personname w:st="on"><st1:givenname w:st="on">Himanshu</st1:givenname> <st1:middlename w:st="on">A.</st1:middlename>
<st1:sn w:st="on">Pandya</st1:sn></st2:personname> and <st1:givenname w:st="on">P.</st1:givenname>
Srinivasan, 2012. Biocomputational analysis of citrullinated fillagrin sequence
repeats for rheumatoid arthritis. Electronic Journal of Biology, 8(2):29-33. <b><o:p></o:p></b></span></div>
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<b>ABSTRACTS PUBLICATION AND POSTERS PRESENTATION:</b><br />
<br />
1. Poster Presented and Recognized as Best Research Work in the 4th Seminar on Modern Laboratory Techniques in Molecular Biology on the topic “in silico Epitope-based Immunoinformatics and Molecular Docking Studies of Nucleocapsid Protein (NP) and Ovarian Tumor (OTU) Domain of Crimean-Congo Haemorrhagic Fever Virus (CCHFV)” held at Gujarat Cancer and Research Institute (GCRI), Ahmedabad on Feb 28, 2011.<br />
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2. Presented a work on “Initiation of Eukaryotic Genome Replication: Interaction of RFC and Brd4 proteins” in Tamil National Scientific Conference, held at Alagappa University between Sept 11-13, 2009 and published ISBN-93-80043-33-3<br />
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3. <b>S. Prasanth Kumar</b>, Ravi G. Kapopara, Saumya K. Patel, Yogesh T. Jasrai, Himanshu A. Pandya and Rakesh M. Rawal. Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein. (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 158).<br />
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4. Ravi G. Kapopara, <b>S. Prasanth Kumar</b>, Yogesh T. Jasrai, Himanshu A. Pandya and Rakesh M. Rawal. Management of Diabetes by Developing New Alpha Glucosidase Inhibitors (AGIs). (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 162).<br />
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5. Saumya K. Patel, <b>S. Prasanth Kumar</b>, Ravi G. Kapopara, Yogesh T. Jasrai and Himanshu A. Pandya. Plant Bioactive Driven Fragment-based Drug Designing and Epitope-baesd Immunoinformatics Study of EspC protein of Mycobacterium tuberculosis. (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 166).<br />
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6. Mehul I. Patni, <b>S. Prasanth Kumar</b>, Saumya K. Patel, Yogesh T. Jasrai and Himanshu A. Pandya. 2D-QSAR Analysis of ACE Inhibitors with Activity in Oryctolagus cuniculus and Rattus norvegicus. (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 167).<br />
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7. Vishal H. Desai, Chirag N. Patel, Vijay P. Mehta, <b>S. Prasanth Kumar</b>, Yogesh T. Jasrai and Himanshu A. Pandya. Bioinformatic analysis on Maize sugary1 gene (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Budding Researchers, pp. 173).<br />
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PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-46430413157748260092011-10-17T13:15:00.000+05:302011-10-17T14:09:19.816+05:30ABSTRACTS PUBLISHED IN THE NATIONAL SYMPOSIUM<div dir="ltr" style="text-align: left;" trbidi="on"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: 11pt;">ABSTRACTS PUBLISHED IN THE Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, </span><span class="Apple-style-span" style="font-size: 15px;">held at Department of Botany, Gujarat University, Ahmedabad- 380 009 between Oct 13-15, 2011.</span></span><br />
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<span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif;">Download these abstracts in PDF format here: <a href="http://www.slideshare.net/prasanthperceptron/soft-copy-of-abstracts">http://www.slideshare.net/prasanthperceptron/soft-copy-of-abstracts</a></span><br />
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<div class="MsoNormal"><b><span style="font-family: 'Times New Roman'; font-size: 14pt;"><span class="Apple-style-span" style="color: #20124d;">Code: IO- 2 Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein </span><o:p></o:p></span></b></div><div class="MsoNormal"><b><span style="color: magenta; font-family: 'Times New Roman'; font-size: 14pt;">(Young Scientist Awarded Presentation)</span></b><br />
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<span class="Apple-style-span" style="background-color: white; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 15px; line-height: 20px;"><span class="Apple-style-span" style="color: #20124d; font-family: 'Trebuchet MS', sans-serif;"><span class="Apple-style-span" style="font-size: 15px; line-height: 24px;"><b>DOWNLOAD THE PRESENTATION HERE:</b></span></span><br />
<span class="Apple-style-span" style="color: #20124d; font-family: 'Trebuchet MS', sans-serif;"><span class="Apple-style-span" style="font-size: 15px; line-height: 24px;"><b><a href="http://www.slideshare.net/prasanthperceptron/s-prasanth-kumar-young-scientist-awarded-presentation" style="color: black; text-decoration: none;">http://www.slideshare.net/prasanthperceptron/s-prasanth-kumar-young-scientist-awarded-presentation</a></b></span></span></span></div><div class="MsoNormal"><br />
</div><div class="MsoNormal"><b><u><span style="font-family: 'Times New Roman'; font-size: 12pt;">S. Prasanth Kumar</span></u></b><u><sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">1</span></sup></u><span style="font-family: 'Times New Roman'; font-size: 12pt;">, <st1:place w:st="on">Ravi</st1:place> G. Kapopara<sup>1,</sup> Saumya K. Patel<sup>1</sup>, Yogesh T. Jasrai*, Himanshu A. Pandya<sup>1</sup> and Rakesh M. Rawal<sup>2</sup><o:p></o:p></span></div><div class="MsoNormal"><sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">1</span></sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">Bioinformatics Laboratory, Department of Botany, University School of Sciences,Gujarat University, Ahmedabad- 380 009. </span><sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">2</span></sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, The Gujarat Cancer & Research Institute (GCRI), </span><span style="font-family: 'Times New Roman'; font-size: 12pt;">Ahmedabad- 380 016.<o:p></o:p></span></div><div class="MsoNormal"><b><br />
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</b></div><div class="MsoNormal"><b><span style="font-family: 'Times New Roman'; font-size: 12pt;">ABSTRACT<o:p></o:p></span></b></div><div class="MsoNormal"><div style="text-align: justify;"><span style="font-family: 'Times New Roman'; font-size: 12pt;">Tomato leaf curl disease (TLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface and stunted plant growth caused by tomato yellow leaf curl virus (TYLCV). In the present study, we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, <st1:place w:st="on">Gujarat</st1:place> (ToLCGV-[Vad]). We found that the amino acids in coat protein required for systemic infection, viral particle formation and insect transmission to host cells were sufficiently diverged. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the plant DNA required for host cell arrest and propagation of viral particle was studied. We further emphasized the role of loops in coat protein structure as molecular recognition interface.<o:p></o:p></span><br />
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</span></div></div><div class="MsoNormal"><div style="text-align: justify;"><b><span style="font-family: 'Times New Roman'; font-size: 12pt;">Keywords:</span></b><span style="font-family: 'Times New Roman'; font-size: 12pt;"> Tomato leaf curl disease, Tomato yellow leaf curl virus, Geminate viral particle, Evolution, Modeling.<o:p></o:p></span></div></div><div class="MsoNormal"><br />
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<b><span style="color: #20124d; font-family: 'Times New Roman'; font-size: 14pt;">Code: IO-6 Management of Diabetes by Developing New Alpha Glucosidase Inhibitors (AGIs)</span></b></div><div class="MsoNormal"><b><span style="font-family: 'Times New Roman'; font-size: 14pt;"><br />
</span></b></div><div class="MsoNormal"><st1:place w:st="on"><span style="font-family: 'Times New Roman'; font-size: 12pt;">Ravi</span></st1:place><span style="font-family: 'Times New Roman'; font-size: 12pt;"> G. Kapopara</span><span style="font-family: 'Times New Roman'; font-size: 12pt;">*<sup>1</sup> <b>S. Prasanth Kumar</b><sup>1</sup>, Yogesh T. Jasrai<sup>1</sup>, Himanshu A. Pandya<sup>1</sup> and Rakesh M. Rawal<sup>2</sup><o:p></o:p></span></div><div class="MsoNormal"><sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">1</span></sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009. </span><sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">2</span></sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, The Gujarat Cancer & Research Institute (GCRI), </span><span style="font-family: 'Times New Roman'; font-size: 12pt;">Ahmedabad- 380 016.<o:p></o:p></span></div><div class="MsoNormal"><b><br />
</b></div><div class="Normal14"><span style="font-size: 12pt;"><b>ABSTRACT</b><o:p></o:p></span></div><div class="MsoNormal"><div style="text-align: justify;"><span style="font-family: 'Times New Roman'; font-size: 12pt;">The most challenging goal in the management of diabetic patient is to achieve normal blood glucose levels caused by post-prandial hyperglycemia (PPHG) or hyperinsulinemia, the individual risk factor contributes to the development of macrovascular complications. Synthetic hypoglycemic agents are available which has its own limitations and serious side-effects. The present study deals about the development of a common small molecular structure by enhancing the molecular descriptors required for binding with α-glucosidase and α-amylase enzymes, the two major targets of PPHG and to develop a monosaccharide-type inhibitor with many insights derived from pharmacophore studies, molecular alignment and molecular docking studies of known inhibitors. A hypothesis was designed which suggest the essential and/or minimal requirement of molecular descriptors to be an efficient binder of these two hydrolytic enzymes and subsequently, molecules with naturally occurring flavonoid structural architecture obeying the hypothesis was developed and evaluated in silico.<o:p></o:p></span></div><div style="text-align: justify;"><span style="font-family: 'Times New Roman'; font-size: 12pt;"><br />
</span></div></div><div class="MsoNormal"><div style="text-align: justify;"><b><span style="font-family: 'Times New Roman'; font-size: 12pt;">Keywords</span></b><span style="font-family: 'Times New Roman'; font-size: 12pt;">: Post-prandial hyperglycemia, Molecular descriptors, α-glucosidase, α-amylase, Pharmacophore features, Molecular docking, Hypothesis design.<o:p></o:p></span><br />
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</div><div class="MsoNormal"><o:p></o:p></div><div class="MsoNormal"><b><span style="color: #20124d; font-family: 'Times New Roman'; font-size: 14pt;">Code: IP-3 Plant Bioactive Driven Fragment-based Drug Designing and Epitope-based Immunoinformatics Study of EspC protein of <i>Mycobacterium tuberculosis</i></span></b><span style="font-family: 'Times New Roman'; font-size: 14pt;"><o:p></o:p></span><br />
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<span style="font-family: 'Times New Roman'; font-size: 12pt;">Saumya K. Patel<sup>1</sup></span><span style="font-family: 'Times New Roman'; font-size: 12pt;">, <b>S. Prasanth Kumar</b><sup>1</sup>, <st1:place w:st="on">Ravi</st1:place> G. Kapopara<sup>1</sup>, </span><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif; font-size: 16px;">Yogesh T. Jasrai<sup>1</sup> and Himanshu A. Pandya<sup>1</sup></span></div><div class="MsoNormal"><sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">1</span></sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009<o:p></o:p></span></div><div class="MsoNormal"><b><br />
</b></div><div class="MsoNormal"><b><span style="color: black; font-family: 'Times New Roman'; font-size: 12pt;">ABSTRACT<o:p></o:p></span></b></div><div class="MsoNormal"><div style="text-align: justify;"><span style="color: black; font-family: 'Times New Roman'; font-size: 12pt;">Multi-drug resistant <i>Mycobacterium tuberculosis</i> is one of the major obstacles for the treatment of tuberculosis. ESX-1 secretion system establishes infection in host cells by secreting virulence factors. Genes belonging to this system are attenuated in currently used BCG vaccine strain and are no longer proven efficacy in treating tuberculosis. In the present study, vasicine, a plant bioactive from Vasaka herb having known antitubercular properties is used to develop inhibitors against a chief component of the ESX-1 secretory pathway, called EspC through fragment-based drug designing approach. Epitope-based immunoinformatics study of EspC protein is also carried out which showed regions of interest for developing vaccines with due consideration across all the genetically heterogeneous inheritance. It is found that designing T-cell epitopes against the C-terminal region of EspC protein will have greater benefits as compared to other regions as it acts as a recognition element for its cognate AAA ATPases and protein interaction. Hence, designing inhibitors based on plant bioactive with known activity will direct to the generation of potential antitubercular lead molecules. In the other hand, the <i>in vitro</i> expression studies of EspC in individuals with heterogeneous genetic inheritance will helpful in choosing a better region for developing vaccine without any harm to the human. <o:p></o:p></span></div><div style="text-align: justify;"><span style="color: black; font-family: 'Times New Roman'; font-size: 12pt;"><br />
</span></div></div><div class="MsoNormal"><div style="text-align: justify;"><b><span style="color: black; font-family: 'Times New Roman'; font-size: 12pt;">Key-words: </span></b><span style="color: black; font-family: 'Times New Roman'; font-size: 12pt;">ESX-1 secretion system, Vasaka herb, fragment-based drug designing, immunoinformatics<o:p></o:p></span><br />
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</div><span class="Apple-style-span" style="color: #20124d; font-size: 16px;"><b><span style="font-family: 'Times New Roman'; font-size: 14pt;">Code: IP-4 </span></b><b><span style="font-family: 'Times New Roman'; font-size: 14pt;">2D-QSAR Analysis of ACE Inhibitors with Activity in </span></b></span><o:p><span class="Apple-style-span" style="color: #20124d;"> <span class="Apple-style-span" style="font-size: 16px;"> </span></span><span class="Apple-style-span" style="font-size: 16px;"><b><i><span style="color: #20124d; font-family: 'Times New Roman'; font-size: 14pt;">Oryctolagus cuniculus </span></i></b><b><span style="font-family: 'Times New Roman'; font-size: 14pt;"><span class="Apple-style-span" style="color: #20124d;">and </span><i><span class="Apple-style-span" style="color: #20124d;">Rattus norvegicus </span></i></span></b></span></o:p><br />
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<span class="Apple-style-span" style="font-size: 16px;"><st2:sn w:st="on"><span style="font-family: 'Times New Roman'; font-size: 12pt;">Mehul</span></st2:sn><span style="font-family: 'Times New Roman'; font-size: 12pt;"> <st2:sn w:st="on">I.</st2:sn> Patni<sup>1</sup></span><span style="font-family: 'Times New Roman'; font-size: 12pt;"><b>,</b> <b><st1:place w:st="on">S. Prasanth</st1:place> Kumar<sup>1</sup></b>, Saumya K. Patel<sup>1</sup>, </span></span> <span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif; font-size: 16px;">Yogesh T. Jasrai*<sup>1</sup> and Himanshu A. Pandya<sup>1</sup></span><br />
<div class="MsoNormal" style="font-size: 12pt; text-align: left;"><sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">1</span></sup><span style="font-family: 'Times New Roman'; font-size: 12pt;">Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009<o:p></o:p></span></div><div class="MsoNormal" style="font-size: 12pt;"><b><br />
</b></div><div class="MsoNormal" style="font-size: 12pt;"><b><span style="font-family: 'Times New Roman'; font-size: 12pt;">ABSTRACT <o:p></o:p></span></b></div><div class="MsoNormal" style="font-size: 12pt; text-align: justify;"><span style="font-family: 'Times New Roman'; font-size: 12pt;">Quinapril, an inhibitor of angiotensin-converting enzyme </span><span style="font-family: 'Times New Roman'; font-size: 12pt;">(ACE), is a known drug prescribed in the treatment of hypertension and congestive heart failure. Due to its side effect such as angioedema, the patient has to discontinue the chemotherapy. In the present study, ACE inhibitors which are structurally similar to Quinapril and had reported biological activity in model organisms such as <i>Oryctolagus Cuniculus</i> and <span class="m1fontsize"><i>Rattus norvegicus</i></span> was considered. A 2D-QSAR was modeled based on certain topological and constitutional descriptors along with its biological activity and found best inhibitory molecules<i>. in vitro</i> validation of these inhibitors will be an alternative for effective drug development against hypertension.<o:p></o:p></span><br />
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</div><o:p><b><span style="color: #20124d; font-family: 'Times New Roman'; font-size: 14pt; line-height: 115%;">Code: JP-5 Bioinformatics analysis on Maize <i>sugary 1 </i>gene</span></b></o:p><br />
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<div><span style="font-family: 'Times New Roman'; font-size: 12pt; line-height: 115%;">Vishal H. Desai, Chirag N. Patel, Vijay P. Mehta, <b>S. Prasanth Kumar</b>, </span><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif; font-size: 16px; line-height: 18px;">Yogesh T. Jasrai and Himanshu A. Pandya</span><br />
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</span></div><div class="MsoNormal" style="text-align: justify; text-justify: inter-ideograph;"><span style="font-family: 'Times New Roman'; font-size: 12pt; line-height: 115%;">Bioinformatics Laboratory, Department of Botany, <st1:place w:st="on"><st1:placename w:st="on">Gujarat</st1:placename> <st1:placetype w:st="on">University</st1:placetype></st1:place>, Ahmedabad-380 009.<o:p></o:p></span></div><div class="MsoNormal" style="text-align: justify; text-justify: inter-ideograph;"><br />
</div><div class="MsoNormal" style="text-align: justify; text-justify: inter-ideograph;"><b><span style="font-family: 'Times New Roman'; font-size: 12pt; line-height: 115%;">ABSTRACT<o:p></o:p></span></b></div><div class="MsoNormal" style="text-align: justify; text-justify: inter-ideograph;"><span style="font-family: 'Times New Roman'; font-size: 12pt; line-height: 115%;">Maize (<i>Zea mays</i> Linn.) holds a unique position in the global agricultural ground due to its high carbohydrate content. Maize <i>sugary 1</i> (su1) gene encodes an essential starch debranching enzyme (SBEIIb) which hydrolysis α-(1→6) glycosidic bonds involved in starch biosynthesis. Genetic mutations in this gene contributes for the shrunken and immature kernel phenotypically and accumulation of simple sugars genotypically. In the present study, su1 gene was analyzed using Bioinformatics approaches. We made attempts to search for homologs in other sugar-rich plants. The maize su1 gene was predicted to be the characteristic feature promoting starch content and no evolutionary trace was identified. Further, maize cultivars distributed throughout the world showed a conserved pattern. We also noticed that the contents of GC bases are found to be relatively higher showing signs of highly de-regularized gene structure (CpG island). Conceptual translation of gene sequence provided an insight of ordered structure with a single stretch of disorderness at its N-terminal. Thus, we emphasize that the de-regularized gene structure of su1 makes its own way to diverge from other plant genera and the protein (enzyme) secondary structure level information showed that it is dense with high helix- rich content and a member of isoamylase enzyme family.<o:p></o:p></span><br />
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</b></span></div></div></div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-55702355661620237832011-09-27T11:40:00.000+05:302011-10-17T13:47:41.511+05:30Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein<div dir="ltr" style="text-align: left;" trbidi="on"><div class="MsoNormal" style="text-align: center;"></div><div style="text-align: left;"><div class="separator" style="clear: both; text-align: center;"><span class="Apple-style-span" style="line-height: 24px;">S. <st2:personname w:st="on"><st1:givenname w:st="on">Prasanth</st1:givenname> <st1:sn w:st="on">Kumar<sup>1</sup></st1:sn></st2:personname>, <st2:personname w:st="on"><st1:givenname w:st="on">Yogesh</st1:givenname> <st1:middlename w:st="on">T.</st1:middlename> <st1:sn w:st="on">Jasrai</st1:sn></st2:personname>*<sup>1</sup>, <st2:personname w:st="on"><st1:givenname w:st="on">Himanshu</st1:givenname> <st1:middlename w:st="on">A.</st1:middlename> <st1:sn w:st="on">Pandya<sup>1</sup></st1:sn></st2:personname> and <st2:personname w:st="on"><st1:givenname w:st="on">Rakesh</st1:givenname> <st1:middlename w:st="on">M.</st1:middlename> <st1:sn w:st="on">Rawal<sup>2</sup></st1:sn></st2:personname></span></div></div><br />
<div align="center" class="MsoNormal" style="text-align: center;"><span class="Apple-style-span" style="line-height: 24px;"><sup><span style="font-size: 10pt; line-height: 150%;">1</span></sup><span style="font-size: 10pt; line-height: 150%;">Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009.</span></span></div><div class="MsoNormal"><div style="text-align: center;"><div style="line-height: 150%;"><sup><span style="font-size: 10pt; line-height: 150%;">2</span></sup><span style="font-size: 10pt; line-height: 150%;">Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, The Gujarat Cancer & Research Institute (GCRI), </span><span style="font-size: 10pt; line-height: 150%;">Ahmedabad- 380 016 </span></div><div style="line-height: 150%;"><b></b></div><div class="MsoNormal" style="display: inline !important; margin-left: 0.75in; text-align: justify; text-indent: -0.25in;"><b></b></div><div style="font-size: 11pt; line-height: 150%; text-align: center;"><div class="MsoNormal" style="display: inline !important; line-height: 150%; margin-left: 0.75in; text-align: justify; text-indent: -0.25in;"><b><b><span style="font-size: 11pt;"><br />
</span></b></b></div></div><div style="text-align: left;"><b><span class="Apple-style-span" style="color: #20124d; font-family: 'Trebuchet MS', sans-serif; font-size: 15px; line-height: 24px;">Recipient of Young Scientist Award for Research Article Presentation on “Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein” on an National Symposium on “Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources” held at Department of Botany, Gujarat University, Ahmedabad- 380 009 between Oct 13-15, 2011.</span></b><br />
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<span class="Apple-style-span" style="color: #20124d; font-family: 'Trebuchet MS', sans-serif;"><span class="Apple-style-span" style="font-size: 15px; line-height: 24px;"><b>DOWNLOAD THE PRESENTATION HERE:</b></span></span><br />
<span class="Apple-style-span" style="color: #20124d; font-family: 'Trebuchet MS', sans-serif;"><span class="Apple-style-span" style="font-size: 15px; line-height: 24px;"><b><a href="http://www.slideshare.net/prasanthperceptron/s-prasanth-kumar-young-scientist-awarded-presentation">http://www.slideshare.net/prasanthperceptron/s-prasanth-kumar-young-scientist-awarded-presentation</a></b></span></span></div><br />
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</div></div><div class="MsoNormal" style="line-height: 150%; text-align: justify; text-justify: inter-ideograph;"><b><span style="line-height: 150%;">ABSTRACT<span class="Apple-style-span" style="font-size: medium;"><o:p></o:p></span></span></b><br />
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<div class="MsoNormal" style="line-height: 150%; mso-layout-grid-align: none; text-align: justify; text-autospace: none; text-justify: inter-ideograph;">Tomato leaf curl disease (TLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface and stunted plant growth caused by tomato yellow leaf curl virus (TYLCV). In the present study, we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, <st1:place w:st="on">Gujarat</st1:place> (ToLCGV-[Vad]). We found that the amino acids in coat protein required for systemic infection, viral particle formation and insect transmission to host cells were sufficiently diverged. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the plant DNA required for host cell arrest and propagation of viral particle was studied. We further emphasized the role of loops in coat protein structure as molecular recognition interface.</div><div class="MsoNormal" style="line-height: 150%; mso-layout-grid-align: none; text-align: justify; text-autospace: none; text-justify: inter-ideograph;"><br />
</div><div class="MsoNormal" style="line-height: 150%; mso-layout-grid-align: none; text-align: justify; text-autospace: none; text-justify: inter-ideograph;"><b>Keywords:</b> Tomato leaf curl disease, Tomato yellow leaf curl virus, Geminate viral particle, Evolution, Modeling.</div><div class="MsoNormal"><br />
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<div class="MsoNormal" style="text-align: center;"><div style="text-align: left;"><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif;"><b>S. <st1:personname w:st="on"><st2:givenname w:st="on">Prasanth</st2:givenname> <st2:sn w:st="on">Kumar</st2:sn></st1:personname>*<sup>1</sup>, <st1:place w:st="on">Ravi</st1:place> <st1:personname w:st="on"><st2:givenname w:st="on">G.</st2:givenname> <st2:sn w:st="on">Kapopara</st2:sn></st1:personname>*<sup>1</sup>, <st1:personname w:st="on"><st2:givenname w:st="on">Saumya</st2:givenname> <st2:middlename w:st="on">K.</st2:middlename> <st2:sn w:st="on">Patel<sup>1</sup></st2:sn></st1:personname>,</b></span><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif;"><b><st1:personname w:st="on"><st2:givenname w:st="on">Yogesh</st2:givenname> <st2:middlename w:st="on">T.</st2:middlename> <st2:sn w:st="on">Jasrai<sup>1</sup></st2:sn></st1:personname>, <st1:personname w:st="on"><st2:givenname w:st="on">Himanshu</st2:givenname> <st2:middlename w:st="on">A.</st2:middlename> <st2:sn w:st="on">Pandya<sup>1</sup></st2:sn></st1:personname> and <st1:personname w:st="on"><st2:givenname w:st="on">Rakesh</st2:givenname> <st2:middlename w:st="on">M.</st2:middlename> <st2:sn w:st="on">Rawal<sup>2</sup></st2:sn></st1:personname></b></span></div></div><div align="center" class="MsoNormal" style="text-align: center;"><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif;"><b><br />
</b></span></div><div class="MsoNormal"><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif;"><b><sup>1</sup>Bioinformatics Laboratory, Department of Botany, <st1:placetype w:st="on">University</st1:placetype> <st1:placetype w:st="on">School</st1:placetype> of Sciences, <st1:place w:st="on"><st1:placename w:st="on">Gujarat</st1:placename> <st1:placetype w:st="on">University</st1:placetype></st1:place>, Ahmedabad-380 009.</b></span></div><div class="MsoNormal"><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif;"><b><sup>2</sup>Division of Cancer Biology, Department of Medicinal Chemistry and Pharmacogenomics, <st1:place w:st="on">Gujarat</st1:place> Cancer and Research Institute (GCRI), Ahmedabad- 380016.</b></span></div><br />
Please navigate to this page for full text article: <a href="http://jbiopharm.com/index.php/ajpsbr/article/view/39">http://jbiopharm.com/index.php/ajpsbr/article/view/39</a><br />
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<b>ABSTRACT:</b><br />
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<div class="MsoNormal" style="line-height: 150%; text-align: justify;">The most challenging goal in the management of diabetic patient is to achieve normal blood glucose levels caused by post-prandial hyperglycemia (PPHG) or hyperinsulinemia, the individual risk factor contributes to the development of macrovascular complications. Synthetic hypoglycemic agents are available which has its own limitations and serious side-effects. The present study deals about the development of a common small molecular structure by enhancing the molecular descriptors required for binding with α-glucosidase and α-amylase enzymes, the two major targets of PPHG and to develop a monosaccharide-type inhibitor with many insights derived from pharmacophore studies, molecular alignment and molecular docking studies of known inhibitors. An hypothesis was designed which suggest the essential and/or minimal requirement of molecular descriptors in order to be an efficient binder of these two hydrolytic enzymes and subsequently, molecules with naturally occurring flavonoid structural architecture obeying the hypothesis was developed and evaluated <i>in silico</i>.</div></div>PRASANTH VIRTUAL BIOINFO LABhttp://www.blogger.com/profile/12837831641180620102noreply@blogger.com0tag:blogger.com,1999:blog-6970775147070416114.post-90312512407514842022011-08-09T12:11:00.000+05:302011-08-09T12:11:29.539+05:30Prasanth Virtual Bioinfo Lab<div dir="ltr" style="text-align: left;" trbidi="on"><div class="separator" style="clear: both; text-align: center;"><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.youtube.com/embed/Wa2VtIefQMw?feature=player_embedded' frameborder='0'></iframe></div><br />
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