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Prasanth Kumar Curriculum Vitae

Prasanth Kumar Curriculum Vitae

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  • 1. S/o A. Shivakumar, No. 15, Iyyanar Koil Street,S.PRASANTH KUMAR Veeman Nagar, Pondicherry- 605009, India. prasanthbioinformatics@gmail.com www.prasanthvirtualbioinfolab.blogspot.com Ph.:+91-9909893929OBJECTIVE: To be associated with a progressive organization that gives me the scope to apply myknowledge and skills and also involve myself as a part of the team that work towards the growth of theorganization.EDUCATIONAL QUALIFICATIONS: COURSE INSTITUTION SECUREDM.Sc (BIOINFORMATICS) Alagappa University, 88.80 % (NAAC Accredited “A” Grade State University) (I Rank Holder) Karaikudi-630 003, PROVISIONALLY Tamil Nadu. SELECTED FOR DST INSPIRE FELLOWSHIP Achariya Arts and Science College, 77.97 %B.Sc (BIOINFORMATICS) (Affiliated to Pondicherry University), (I Rank Holder) Pondicherry-605 110.RESEARCH PUBLICATIONS: 1. P. Srinivasan, A. Sudha, A. Shahul Hameed, S. Prasanth Kumar and M. Karthikeyan, 2011. Screening of medicinal plant compounds against NS5B polymerase of hepatitis C virus (HCV) using molecular docking studies. Journal of Pharmacy Research 4(1): pp.136- 140. 2. S. Prasanth Kumar, P. Srinivasan, Saumya K. Patel, Ravi Kapopara and Yogesh T. Jasrai, 2011. In silico development of inhibitors against pantothenate synthetase of Mycobacterium tuberculosis. Journal of Advanced Bioinformatics and Research 2(2): pp. 142-148. 3. Saumya K. Patel, S. Prasanth Kumar, Himanshu A. Pandya, Yogesh T. Jasrai and Mehul I. Patni, 2011. 2D-QSAR analysis of dihydrofolate reductase (DHFR) inhibitors with activity in Toxoplasma gondii and Lactobacillus casei. Journal of Advanced Bioinformatics and Research 2(2): pp.161-166. 4. S. K. Patel, S. Prasanth Kumar, Y. T. Jasrai, H. A. Pandya and R. M. Rawal, 2011. Computational analysis of naturally occurring marine compounds (NOMC) targeting gap 1
  • 2. junctions and cell adhesive molecules for the identification of anticancer drug targets. The Journal of Computational Intelligence in Bioinformatics 4(2): pp. 161-171.5. S. Prasanth Kumar, 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.57-62.6. S. Prasanth Kumar and Muthusamy Meenatchi, 2011. Virtual quantification of protein stability using applied kinetic and thermodynamic parameters. IIOAB Letters 1: pp.x-xx.7. Ravi Kapopara, S. Prasanth Kumar, Saumya K. Patel, Dhananjay K. 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-Special Issue 1(S1): pp.12-16.8. Pappu Srinivasan, Sivakumar Prasanth Kumar, Muthusamy Karthikeyan, Jeyaram Jeyakanthan, Yogesh T. Jasrai, Himanshu A. Pandya, Rakesh M. Rawal and Saumya K. Patel, 2011. Epitope-based immunoinformatics and molecular docking studies of nucleocapsid protein and ovarian tumor domain of Crimean-Congo hemorrhagic fever virus. Frontiers in Bioinformatics and Computational Biology 2(72): 1-9. doi: 10.3389/fgene.2011.00072.9. S. Prasanth Kumar, Ravi G. Kapopara, Saumya K. 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). Asian Journal of Biomedical and Pharmaceutical Sciences 1(3): pp.01-12.10. S. Prasanth Kumar, Ravi G. Kapopara, Yogesh. T. Jasrai and Rakesh M. Rawal, 2012. Computational studies on the interaction of core histone tail domains with CpG island. International Journal of Pharma and Biosciences 3(1): pp. B581-590.11. S. Prasanth Kumar. Docking and in silico bioavailability analysis of CDK6 flavonol inhibitors and its analogues for acute lymphoblastic leukemia. The Journal of Computational Intelligence in Bioinformatics, Accepted.12. S. Prasanth Kumar, Saumya K. Patel, Ravi Kapopara, Yogesh T. Jasrai, Himanshu A. Pandya and P. Srinivasan, 2011. Biocomputational analysis of citrullinated fillagrin sequence repeats for rheumatoid arthritis. PRAJNA, Accepted.13. S. Prasanth Kumar. CpGP dynamics- The dynamics of CpG island and promoter to validate nucleosomal gene expression. International Journal of Bio-Science and Bio- Technology, Review Awaiting. Program is accessible at http://cpgpdynamics.webs.com.14. Sapna Mishra, Yogesh T. Jasrai, Himanshu. A. Pandya, S. Prasanth Kumar, D.B. Choksi, and Hetalkumar Panchal. Prediction of MHC binding peptides and epitopes from coat protein of apple infecting virus ACLSV. PRAJNA, Communicated. 2
  • 3. 15. S. Prasanth Kumar, Yogesh T. Jasrai and Himanshu A. Pandya. Pharmacophore assisted- molecular field similarity and QSAR studies on HIV protease inhibitors. (Manuscript is in preparation). 16. S. Prasanth Kumar, Yogesh T. Jasrai and Himanshu A. Pandya. Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein. (Manuscript is in preparation).RESEARCH PROJECTS CARRIED OUT: 1. “Pharmacophore mapping and 3D QSAR studies of Cannabinoid System specific to Pain Neuromodulation and Neuroinflammation” Guidance: Dr. P. Srinivasan, Institute: Alagappa University, Karaikudi-630 003, Tamil Nadu. Status: Completed (M.Sc Dissertation).RESEARCH AREA OF INTEREST: 1. Molecular Modeling 2. Sequence AnalysisPROFESSIONAL EXPERIENCE: 1. Worked as Visiting Faculty in Department of Bioinformatics, Gujarat University, Ahmedabad, From Nov-2010 to Nov-2011. 2. Worked as Visiting Faculty in Department of Zoology (Course: Human Genetics), Gujarat University, Ahmedabad, From Feb-2011 to Apr-2011.ACADEMIC EXCELLANCE AND ACCOLADES: 1. Provisionally selected for DST INSPIRE Fellowship 2011-12. 2. Recipient of ABAP Young Scientist Award (Research Article Presentation) for outstanding research work (Screening of Medicinal Plants for Inhibitors of NS5B polymerase of Hepatitis C Virus (HCV) using Molecular Docking Studies) given by the Association of Biotechnology and Pharmacy on an International Symposium on Emerging Trends in Biomedical and Nanotechnology: Relevance to Human Heath, held at Acharya Nagarjuna University, Guntur, Andhra Pradesh between Dec19-21, 2009. 3. 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” in 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. 4. Secured Alagappa University I Rank Award for outstanding performance in examinations -M.Sc (BIOINFORMATICS): 2008-10. 3
  • 4. 5. Secured Pondicherry University Gold Medal for outstanding performance in examinations -B.Sc (BIOINFORMATICS): 2005-08 and received the Achievement award, 2008-09 for the same from the college. 6. Awarded with Pasumpon Muthuramalinga Thevar Scholarship for outstanding performance in M.Sc (BIOINFORMATICS) examinations for securing I Rank.BIOINFORMATICS SOFTWARES/SERVERS DEVELOPED: 1. Organic Virtual Library (ORVIL) – A Combinatorial Library Construction based on Organic Constituents and without Scaffold Hopping (Perl Script). URL: http://prasanthvirtualbioinfolab.blogspot.com/p/organic-virtual-library-orvil- program.html 2. Virtual Quantification of Protein Stability using Applied Kinetic and Thermodynamic Parameters (Executable). URL: http://virtualprotstab.webs.com URL: http://prasanthvirtualbioinfolab.blogspot.com/p/protein-stability-program- developed-by.html 3. CpGP dynamics- The Dynamics of CpG Island and Promoter to Validate Nucleosomal Gene Expression (Server) URL: http://cpgpdynamics.webs.com 4. CONFRENE- Conformational Energy Prediction from Docked Conformations (Server) URL: Soon to be available onlineABSTRACTS PUBLICATION AND SEMINAR/POSTERS PRESENTATION: 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. 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. 3. S. Prasanth Kumar, 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). 4. Ravi G. Kapopara, S. Prasanth Kumar, 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 4
  • 5. Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 162). 5. Saumya K. Patel, S. Prasanth Kumar, 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). 6. Mehul I. Patni, S. Prasanth Kumar, 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). 7. Vishal H. Desai, Chirag N. Patel, Vijay P. Mehta, S. Prasanth Kumar, 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).BIOINFORMATICS SKILLS:Programming Languages : C, Java (Basics)Scripting Languages : Perl, Bioperl, HTML, CSS, Java ScriptDatabase Development : MySQL, OracleServer Side : Windows, Ubuntu, Linux, FedoraDatabases : NCBI, EMBOSS, ExPASy Toolkits, Genome Browsers, Swiss-Prot, PIR, PDB and all prominent bioinformatics databasesMolecular Docking : Schrodinger- Glide Module, ArgusLab, Hex, Molegro, AutoDock, AutoDock Vienna, ICMPro, DockProtein-Protein Docking : PatchDock, Hex, Zdock, GRAMMX, ClusProProtein-DNA Docking : HADDOCK, HexProtein Modeling : Homology Modeling: Swiss Model, Geno 3D, EsyPred3D, PrimeX, What if, Modeller 9v7, FUGUE, SCFBIO Sanjeevani Fold Recognition: 3DFold PHYRE server, Ab initio: Rosetta, Robetta, SCFBIO Bhageerath.DNA Modeling : 3D-DARTSequence Alignment : BLAST, FASTA, Clustal W, Clustal X, T-CoffeeStructure Alignment : Superimpose, DALIActive Site Identification : CASTp, QFinder, SCFBIO Active Site Prediction Server, 5
  • 6. PrimeFunctional Site Identification : ConSurfEnergy Minimization : Yasara, NOMAD-Ref, GromacsStructure Manipulation : UCSF Chimera, Yasara, Rasmol, PyMol, QMol, spdbv and other online and offline toolsStructure Verification : SAVS, RAMPAGE, PROCHECK, ERRATMolecular Descriptors : DART package, Molinspiration,OSIRIS,MODELHaplotype Analysis : Haploview, PHASEGene Identification : GenScan, GRAILXPGenome Analysis : VISTA, Lagan, MAVID, EMBOSSToxicity : Marvin Plugins, Qik-Prop, Toxmatch, FAF-DrugsPharmacophore Analysis : Schrodinger - Phase Module, Ligand Scout, PharmaGistMolecular Dynamics : NAMAD, ProtomolMolecular Dynamics : VMD, HyperChem, TinkerSimulationsQSAR : Phase-Schrodinger SuiteConformation-ActivityRelationship : ZMM Molecular Modeling Package, ICM ProPhylogenetic Analysis : PHYLIP package, MEGA packageImmunoinformatics : Epitope Prediction, Reverse Vaccinology, etcCommercial Software : Schrödinger Suite, BioSuite, Accelrys Discovery StudioACADEMIC TRAININGS: 1. Participated as “Invited Faculty” for training Bioinformatics basic softwares in “Hands on Molecular Techniques” organized by Bhishma Agri-Research Biotech Co., Ahmedabad on Aug 31, 2011. 2. Participated in the Workshop on “Clinical research and Clinical Data Management” conducted by The Institute of Computational Biology (IOCB), Bangalore between Feb 07-10, 2008.PARTICIPATIONS: 1. Trained in a “Workshop in Advancements in Bio-Computational Statistics” held at Dept. of Botany, USSC, Gujarat University. Organized by Bioinformatics Laboratory, Dept. of Botany, Gujarat University on Jun 20-24, 2011. 2. Trained in a “Workshop on Intellectual Property Rights Awareness-2011 (WIPRA-2011)” held at Dept. of Botany, USSC, Gujarat University. Organized by IPR Cell and Dept. of Botany, Gujarat University on Jun 16, 2011. 3. Participated in “Fourth Seminar on Modern Laboratory Techniques in Molecular Biology” conducted by Indian Association for Cancer Research-Gujarat Chapter, The Gujarat Cancer & 6
  • 7. Research Institute (GCRI) and The Gujarat Cancer Society held at Gujarat Cancer and Research Institute (GCRI), Ahmedabad on Feb 28, 2011. 4. Participated in National workshop on “Application of Molecular Modeling and Structural Bioinformatics” held at Dept. of Bioinformatics, Alagappa University between Jan 27-29, 2010 5. Participated in International Colloquium on “Emerging Biotechnology in Agriculture, Animal Health and Productivity (ICEB 09)” conducted by Alagappa University between Feb 22-27, 2009. 6. Participated in National Seminar on “Current Trends in Bioinformatics Teaching and Research” conducted by Pondicherry University between Feb 16-18, 2009. 7. Participated in “National Seminar on Molecular Modeling and Drug Designing (NasMoID’09)” conducted by the Dept.of Bioinformatics, Alagappa University between March 18-19, 2009. 8. Participated in “National Seminar on Advancements in Bioelectronics and Biosensors (NSABB’09)” conducted by the Dept. of Bioelectronics and Biosensor, Alagappa University between Mar 19-20, 2009. 9. Participated in National Seminar on “Application of Genomics and Bioinformatics on Animal Health and Management (NSGB’09)” conducted by the Dept. of Animal Health and Management, Alagappa University between Mar 25-26, 2009. 10. Participated in “International Symposium on Stem Cells and Regenerative Medicine” conducted by NCRM Niche on Stem Cells and Regenerative Medicine held on Oct 24, 2009. 11. Participated in “Genesis ’06 “conducted by the Pondicherry University on 28th Feb 2006. 12. Participated in “1 (P) Indep Coy Combined annual Training Camp of National Cadet Corps” conducted by the NCC Indep Coy, Pondicherry between June 20-29, 2000.PERSONAL DETAILS: Name : S. Prasanth Kumar Gender : Male Date of Birth : 27.08.1987 Religion & Caste : Hindu; Vanniar [ OBC (Non Creamy Layer) ] Email ID : prasanthbioinformatics@gmail.com Website : www.prasanthvirtualbioinfolab.blogspot.com Telephone No. : +91-9909893929 Father’s Name : A. Shivakumar 7
  • 8. To read, write and : English, Hindi, Tamil. speak Address for : No. 15, Iyyanar Koil Street, Communication Veeman Nagar, Pondicherry- 605009, India.REFERENCES:Dr. P. Srinivasan, Dr. Yogesh T. JasraiProfessor, Professor and Head,Department of Bioinformatics, Bioinformatics Coordinator,Alagappa University, Department of Botany,Karaikudi-630 003, Tamil Nadu, INDIA University School of Sciences,email: sri.bioinformatics@gmail.com Gujarat University,website: http://www.psrinivasan.webs.com Ahmedabad-380 009, Gujarat, INDIA email: yjasrai@yahoo.comDr. Rakeshkumar M. Rawal Mrs. M. Meenachi,Senior Scientific Officer Associate Professor and Head,Department of Cancer Biology, Department of Bioinformatics,Division of Medicinal Chemistry and Achariya Arts and Science College,Pharmacogenomics, (Affiliated to Pondicherry University)The Gujarat Cancer & Research Institute (GCRI), Pondicherry-605 110, INDIAAsarwa, Ahmedabad - 380 016, email: meenubiotec@gmail.comGujarat, INDIA.email: rakeshmrawal@gmail.com DECLARATIONI hereby declare that the above furnished information is correct and true to the best of my knowledge.*Date: 03/02/2012.Place: Pondicherry. S. Prasanth Kumar*Last Updated 8
  • 9. SNAPSHOTS OF THE PROGRAMS & SERVER DEVELOPED Snapshot of Protein Stability Program (Windows Executable) 9
  • 10. Command line interface of ORVIL (Organic Virtual Library) program (Perl Script) 10
  • 11. Webshot of CpGP dynamics program (Javascript) 11