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JOURNAL OF CLINICAL AND SCIENTIFIC RESEARCHThe JournalJournal of Clinical and Scientific Research [ISSN (print) 2277-5706 and ISSN (online) 2277-8357] is a peer-reviewedinternational multidisciplinary scientific journal published by Sri Venkateswara Institute of Medical Sciences (AUniversity established by act of A.P. State Legislature), Tirupati 517 507, India. The journal publishes original researchcommunications of clinical and biomedical research. It presents innovative and novel biomedical research that advancesor illuminates medical science as well as those that improve the clinical acumen. It is issued Quarterly, in four issuesper year: January, April, July and October.Abstracting and indexing informationJournal of Clinical and Scientific Research is indexed in Index Copernicus, Academic Index, Open J-gate, Directoryof Open Access Journals (DOAJ), Journal Seek, Indian Science Abstracts, Geneva Foundation for Medical Educationand Research, New Jour, Academic Journals Database, Research Bible and Directory of Research Journals Indexing(DRJI).Fast track review processThe journal promotes electronic submission and fast-track processing with submission to decision time of 3 months.No fees are charged for submission, processing and publication by the journal.Online accessFull-text of all the articles printed in this issue is available free at ion informationPrices include postage. For single issue 50 for print or CD version. Annual subscription rates are as follows:Institutional: 1000 for print version and 500 for CD version;Personal: 150 for print version; 100/- for CD version.Life subscription : 1500/- (non-refundable)Cheque/DD to be drawn in favour of ‘‘Executive Editor-in-Chief, JCSR, SVIMS, Tirupati’’.CopyrightThe entire contents of the Journal of Clinical and Scientific Research are protected under Indian and internationalcopyrights. The Journal, however, grants to all users a free, irrevocable, worldwide, perpetual right of access to, and alicense to use, distribute, perform and display the work publicly and make and distribute derivative works in anydigital medium for any reasonable non-commercial purpose, subject to proper attribution of authorship and ownershipof the rights.DisclaimerThe information and opinions presented in the Journal reflect the views of the authors and not of the Journal or itsEditorial Board or the Publisher. Publication does not constitute endorsement by the journal. Neither the Journal ofClinical and Scientific Research nor its publishers nor anyone else involved in creating, producing or delivering theJournal of Clinical and Scientific Research or the materials contained therein, assumes any liability or responsibilityfor the accuracy, completeness, or usefulness of any information provided in Journal of Clinical and Scientific Research,nor shall they be liable for any direct, indirect, incidental, special, consequential or punitive damages arising out of theuse of the Journal of Clinical and Scientific Research. The Journal of Clinical and Scientific Research, nor its publishers,nor any other party involved in the preparation of material contained in the Journal of Clinical and Scientific Researchrepresents or warrants that the information contained therein is in every respect accurate or complete, and they are notresponsible for any errors or omissions or for the results obtained from the use of such material. Readers are encouragedto confirm the information contained therein with other sources.CorrespondenceDr P.V.L.N. Srinivasa RaoExecutive Editor-in-ChiefJournal of Clinical and Scientific ResearchEditorial officeII Floor, New OPD BlockSri Venkateswara Institute of Medical SciencesTirupati 517 507Phone: 91-877-2287777; Ext. 2465e-mail: jcsr@svims.gov.in; editorjcsr@gmail.comi

JOURNAL OF CLINICAL AND SCIENTIFIC RESEARCHAn official quarterly peer reviewed publication ofSri Venkateswara Institute of Medical Sciences(A University established by an Act of Andhra Pradesh State Legislature)Tirupati 517 507, IndiaHonorary Editor-in-ChiefB. VengammaDirector-cum-Vice ChancellorExecutive Editor-in-ChiefP.V.L.N. Srinivasa RaoEditorsB.C.M. PrasadAlladi MohanAparna R.BitlaAssociate EditorsV. SureshK.V. Sreedhar BabuA. UmamaheswariN. HemanthJ. HarikrishnaR. JayapradaEditorial BoardRichard Quinton, Newcastle upon Tyne, UKKrishna Srihasam, Boston, USAV. Sree Krishna, Queensland, AustraliaP. Satish Chandra, Bengaluru, IndiaV. Siva Kumar, Tirupati, IndiaM. Hanumantha Rao, Tirupati, IndiaP.V.L.N. Murthy, Hyderabad, IndiaP. Rajagopal, Tirupati, IndiaY. Mutheeswaraiah, Tirupati, IndiaD. Rajasekhar, Tirupati, IndiaM.G. Sridhar, Puducherry, IndiaP.V. Ramasubba Reddy, Tirupati, IndiaM. S. Sridhar, Tirupati, IndiaT. Kannan, Hyderabad, IndiaM.A.K. Sukumar, Tirupati, IndiaRobert Fassett, Queensland, AustraliaS.K. Sharma, New Delhi, IndiaSrinivas Bollineni, Dallas, USASridhar Chitturi, Brisbane, AustraliaS. Ramakumar, Bengaluru, IndiaK. Radhakrishnan, Manipal, IndiaAlok Sachan, Tirupati, IndiaA.Y. Lakshmi, Tirupati, IndiaAbhijit Chaudhury, Tirupati, IndiaB.V. Phaneendra, Tirupati, IndiaD.V.R. Sai Gopal, Tirupati, IndiaP.V.G.K. Sarma, Tirupati, IndiaL. Jayaseelan, Vellore, IndiaR.V. Suresh, Tirupati, IndiaD. Jamuna, TirupatiPublished, produced and distributed by Sri Venkateswara Institute of Medical Sciences,Tirupati 517507, Andhra Pradesh, India. e-mail: jcsr@svims.gov.in, editorjcsr@gmail.comii

Journal of Clinical and Scientific ResearchVol.3 Suppl 1April-June 2014ISSN(print) 2277-5706ISSN(online) 2277-83575th National Seminar on Bioinformatics (NSBI 2014)Editor’s MessageviiiScientific ProgrammeixInvited LecturesA disorder induced domino-like destabilization mechanism governs theαfolding and functional dynamics of the repeat protein IΚBαSrinivasan Sivanandan, Athi N. NaganathanS1Structural bioinformatics and protein foldingGautham NS2Accelerating drug discovery using computational drug designRaghu RS3Viral proteomics: a novel approach for human therapeuticsSai Gopal DVRS4Proteomic approaches in combination with systems biology to reveal cancerrelevant biomarkers and proteins from intracellular signaling pathwaysRamesh US5A computational and experimental approach for design of inhibitors for celldivision proteinMukesh DobleS6Antibiotic resistance-challenges and recent approachesLakshmi VVS7Identifying drug targets for common inhibitor design against strains of bacterialleaf blight and bacterial leaf streak pathogens of riceMarisetti Hemanth KumarS8Down regulation of NF-KB by α -mangostin: Autodock analysisUma Maheswari Devi PalempalliS9Oral PresentationsTemperature dependent extracellular synthesis and characterization ofnanoscale calcium pyrophosphate crystals using marine thermophilic bacteriaSupraja NiiiS10

Molecular modelling strategies of drug designTulasi GS11In silico modelling and drug designing of epidermal growth factor receptor(EGFR) involved in CancerJayasimha Rayalu Daddam, Bhargavi CH, Venkata Swamy Tangeti, Ramesh KonkaS12Role of glycolysis enzymes in cancer developmentRavi babu B, Jagadish Naik MS13Structure based pharmacophore modelling and virtual screening of potentinhibitors for ADAMTS1Anushree Majumdar, Puja, Rathi SuganyaS14Validation of Bhageerath and Bhageerath-H software toolsRanganadha Reddy A, Bhanu Prakash KS15New anti-inflammatory p-acetamido phenol derivatives: molecular dockingand synthesisKiruthiga B, Valentina PS16Docking studies on the anti-diabetic potency and efficacy of the glycosidesjamboline and chrysantheminAnita Priyadharshini K, Valentina PS17Prediction and analysis of novel inhibitors against estrogen-related receptor alphaSuneetha Y, Kumaraswamy Naidu CS18Prediction and analysis of inhibitors for phosphoprotein phosphatase-2AUma Devi B, Kumaraswamy Naidu C, Suneetha YS19Analysis of structural impact of CHEK2 variations in breast cancerKumaraswamy Naidu C, Suneetha Y, Megana KSNMS20Drug designing of hypothetical protein (HSP) 90Madhuri T, Lakshmi Kalyani B, Suvarnalatha Devi PS21Preliminary analysis of data on prevailing breast cancer in the district of GunturPriyadarshini P, Rajeswari JS22Identification and docking studies of phyto constituents as competitive antagonistsagainst metabotropic glutamate receptor 5, towards a better drug lead for epilepsyVijayasri S, Soumendu Sanyal, Waheeta HopperS23Energy based pharmacophore modelling and virtual screening for identificationβof potential inhibitors for GSK3βSheeman JB, Sivaranjani, Anshika Srivastava, Waheeta HopperS24iv

Phylogeny of estuarial prawn on Alikuppam coast, TamilnaduMuthukumaran, Nagalakshmama M, Vijaya Baskara Rao AS25Development of a new rating scale as a need to make improvements to an existingmeasure in the qualification process for drug development toolsSwaroopa MarallaS26Molecular modelling and docking studies on histamine 4 receptor (H4R) forhistamine mediated allergic diseasesShobana S,Gopinath SS27Computational approaches for aflatoxin and their analogs bind to cyprinuscarpio(common carp) liver x receptorPradeepkiran JA, Madhuri E, Bhaskar MS28In silico approach of drug discovery processNaga Jyothi P, Praveenkumar KS29In silico gene prediction for autosomal recessive essential fructosuriaSreekanth M, Jacob Doss PS30Termina liatomentosa crude extract regulates adipogenesis and body weights inHFD-fed obese ratsMuniswamy G, Ramgopal M, Padmaja TK,Balaji MerigaS31Green synthesis of Zinc oxide Nanoparticles for cell proliferation synthesizedthrough Adhatoda vasica NeesBhumi G, Yugandhar P, Savithramma NS32βE-Pharmacophore based virtual screening to identify lead molecules for GSK-3βinduced Alzheimer’s diseaseNatarajan Pradeep, Swargam Sandeep, Kanipakam Hema, Umamaheswari AS33Delta CT, norm finder, genorm and best keeper programming for the validationof reference genes for the quantitative gene expression studies by in the ovarianfollicles of sheepSivakumar AVN, Praveen Chakravarthi V, Bhaskar M , Rao VHS34Poster Presentations2D-QSAR, pharmacophore modelling and molecular docking studies ofC-phycocyanin with human Rad9 proteinRajasekhar Avula, Mallikarjuna Thippana, Dakshayani Lomada, Madhava C ReddyS35Identification of potent inhibitors for RuvA through different docking strategiesManne Munikumar, Vani Priyadarshini, Dibyabhaba Pradhan, Umamaheswari AS36v

Design, synthesis and in vitro antifungal evaluation of novel ciprofloxacin derivativesMahalakshmi Naidu K, Suresh A, Suresh N, Nagesh HN, Chandra Sekhar KVGS37Homology modelling, molecular dynamics and drug docking studies of ATP-sensitiveK channel (KATP)Peddanna Kotha, Chippada Appa RaoS38Structured based drug designing approach on BerberisaristataValentina P, Sushrut SharmaS39Molecular dynamics study of the TSH receptor with small molecule antagonistsLavanya S, Kavya Kannan, Shalini DasguptaS40Docking studies to explore novel inhibitors against human beta-site APP cleavingenzyme (BACE-1) involved in Alzheimer’s diseaseAnjum Mobeen S, Manne Munikumar, Umamaheswari AS41Prediction and analysis of endocrine disruptors interacting with humanGonadotropin-releasing hormone (GnRH)Kranthi Kumar K, Kumaraswamy Naidu C, Suneetha YS42Virtual screening of selected endocrine disrupting chemicals against StAR proteinTrinath D, Kumara Swamy Naidu C, Suneetha YS43Polycystic ovary syndromeDevagudi Pujitha, Dubbaka Nidhi, Maanthula Jhansi ReddyS44In silico design of novel leads against p55 protein domain of VacA toxinPasala Chiranjeevi, Sandeep Swargam, Dibyabhaba Pradhan, Umamaheswari AS45Application of bioinformatics in peanut genomicsAmaravathi Y, SaiShruthi, Vasanthi RPS46Manganese induced changes in cholinergic system and energy metabolism in specificregions of rat brain: reversal effect of Vitamin EBhuvaneswari Devi C, Kiran Kumari K, Indravathi GS47Biological synthesis of silicon nanoparticles from leaf extracts of Cynodondactylonand Cymbopogon coloratusHaribabu R, Savithramma NS48vi

5th National Seminar on Bioinformatics (NSBI 2014)ORGANIZING COMMITTEEPresident:Dr B. VengammaDirector-cum VC, SVIMS, TirupatiVice-President:Dr B.C.M. PrasadDean, SVIMS, TirupatiChairman:Dr V.S.R. AnjaneyuluRegistrar, SVIMS, TirupatiWorking Chairpersons:Dr P.V.L.N. SrinivasaRaoHead, Department of Biochemistry, SVIMS, TirupatiDr M.M. SuchitraCo-ordinator, Department of Biotechnology & BioinformaticsSVIMS, TirupatiOrganizing Secretary:Dr A. UmamaheswariAssociate Professor, Co-ordinator of Bioinformatics InfrastructureFacility, Department of Bioinformatics, SVIMS, TirupatiJoint Secretaries:Dr P.V.G.K SarmaAssociate Professor, Department of Biotechnology,SVIMS, TirupatiDr C. Bhuvaneswari DeviAssistant Professor, Department of Biotechnology,SVIMS, TirupatiMembers:Mrs I. VaniPriyadarshiniMr DibyabhabaPradhanMr ManneMunikumarMr SandeepSwargamMr NatarajanPradeepMs KanipakamHemaMr Pasala Chiranjeevivii

Editors’ MessageBioinformatics is attributed to have profound impact in research on human health, agriculture andenvironment. Acknowledging the growing importance, the Department of Biotechnology (DBT),Ministry of Science and Technology, has approved a centre for Bioinformatics Infrastructure Facility(BIF) in the Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences (SVIMS),Tirupati, for the promotion of Biology Teaching through Bioinformatics. The BIF organizes Nationallevel seminar/workshop annually to foster bioinformatics skills of researchers. The 5th NationalSeminar on Bioinformatics was organized from 14th to 15th February 2014 at Sri VenkateswaraInstitute of Medical Sciences, Tirupati. This seminar mainly focussed on drug designing also coveringrelevant areas of genomics and proteomics.The Journal of Clinical and Scientific Research, in its endeavour to publish and highlight researchhas provided the scientific abstracts of the research papers (Invited lectures, oral presentations andposter presentations) presented at the 5th National Seminar on Bioinformatics to its readers as aSupplement to Vol. 3(2) of the journal.P.V.L.N. SrinivasaRaoExecutive Editor-in-ChiefB. VengammaHonorary Editor-in-Chiefviii

Scientific Programme5th National Seminar on Bioinformatics (NSBI 2014)Friday 14th, February 201409:30 AM – 10:00 AMRegistration10:00 AM - 10:45 AMInaugurationB. Vengamma,Director-cum-VC, SVIMS, TirupatiB.C.M. Prasad,Dean, SVIMS, Tirupati10:45 AM - 11:00 AMTea BreakSESSION – IChairpersons: P.V.L.N. Srinivasa Rao, P.V.G.K. Sarma11:00 AM - 12:00 noonA disorder induced domino-like destabilization mechanism governsαthe folding and functional dynamics of the repeat protein IKBαAthi Narayanan, IIT Madras, Chennai12:00 noon - 01:00 PMStructural Bioinformatics and protein foldingN. Gautam, University of Madras, Chennai1:00 PM - 2:00 PMLunch BreakSESSION – IIChairpersons: V. Jayaram, D.V.R. Sai Gopal2:00 PM - 3:00 PMAccelerating drug discovery using computational drug designR. Raghu, Vice-President, Schrodinger LLC3:00 PM - 4:00 PMOral Presentations4:00 PM - 4:15 PMTea Break4:15 PM - 5:00 PMPoster Presentationsix

Saturday 15th, February 2014SESSION – IIIChairpersons: Alladi Mohan, P. Uma Maheswari Devi09:30 AM - 10:30 AMViral proteomics: a novel approach for human therapeuticsD.V.R. Sai Gopal, Head, Dept. of Virology, S.V. University, Tirupati10:30 AM - 11:30 AMProteomic approaches in combination with systems biology to revealcancer relevant biomarkers and proteins from intracellular signalingpathwaysU. Ramesh, IICT, Hyderabad11:30 AM - 11:45 AMTea Break11:45 AM – 1:00 PMOral presentations1:00 PM - 2:00 PMLunch BreakSESSION – IVChairpersons: M.M. Suchitra, G. Rajitha2:00 PM – 3:00 PMA computational and experimental approach for design of Inhibitorsfor cell division proteinMukesh Doble, IIT Madras, Chennai3:00 PM - 3:20 PMAntibiotic resistance challenges and recent approachesV.V.Lakshmi, Dept. of Applied Microbiology, SPMVV, Tirupati3:20 PM - 3:40 PMIdentifying targets for common inhibitor design against strains ofbacterial leaf blight and bacterial leaf streak pathogens of riceM. Hemanthkumar, RARS, ANGRA University, Tirupati3.40 PM – 4.00 PMDown Regulation of NF-KB by α-Mangostin: autodock analysisP. Uma Maheswari Devi, Dept. of Applied Microbiology, SPMVV, Tirupati4:00 PM – 5:00 PMValedictory Session & Certificate Distributionx

Abstracts of Invited Lectures (NSBI 2014)A disorder induced domino-like destabilization mechanism governs theαfolding and functional dynamics of the repeat protein IKBαSrinivasan Sivanandan,1 Athi N. Naganathan2Department of Biotechnology, Indian Institute of Technology Kharagpur 721302, Kharagpur and2Department of Biotechnology, Indian Institute of Technology Madras, Chennai1The stability of IKBα, a transcription inhibitor, is critical for the functioning of the NF-KB signalingmodule implicated in an array of cellular processes including disease, immunity and apoptosis.Here, we provide a quantitative picture of the folding and dynamic behavior of IKBα repeat proteinemploying an structure-based Ising-like statistical mechanical model that is in agreement withexperimental ensemble thermodynamics and kinetics, and single-molecule measurements. Weidentify a unique mechanism at work in IKBα folding wherein disorder in one domain initiates adomino effect partially destabilizing neighboring domains thus resulting in a multi-- state and dynamicconformational landscape that is populated by increasingly partially folded ensembles upondestabilization. Our results provide a rationale to the promiscuous binding of IKBα, expands thefunctional repertoire of disordered regions in proteins and introduces a simple procedure to modeldisorder in systems that undergo binding-induced-folding guided by equilibrium experimentalobservables.Srinivasan S, Naganathan AN. A disorder induced domino-like destabilization mechanism governs the folding and functionalα. J Clin Sci Res 2014;3(Suppl 1):S1.dynamics of the repeat protein IKBαS1

Abstracts of Invited Lectures (NSBI 2014)Structural bioinformatics and protein foldingN. GauthamCAS in Crystallography and Biophysics, University of Madras, ChennaiThe central paradigm of biophysics, indeed of physics in general, is ‘Structure implies Function’.Thus, in order to understand and perhaps modify the behaviour of biomolecules, it is necessary toknow and understand their structure. One of the most dramatic illustrations of this principle camewith the discovery of the double-helical structure of DNA. It was immediately clear how DNAcould function as the storage and carrier of genetic information. Protein structure and virus structuresalso illustrate the truth of this principle.Proteins are an important class of biological polymers. They range in size from a few kilodaltons tohundreds of kilodaltons. All proteins are built up from 20 amino acids, which constitute themonomers. The sequence in which these amino acids are arranged differs from protein to proteinand is referred to as the primary structure of the protein. Some sequences of amino acids are knownto arrange themselves into regular three-dimensional structures that are referred to as the secondarystructure of the proteins. At the next level of structural organisation, the secondary structural unitsarrange themselves into globular shapes. This is called the tertiary structure and is stabilised mainlyby interactions between the amino acid side chains. Also discernible at this level are domainscorresponding to compactly arranged groups of secondary structural features. In the next higherlevel of structure, globular folded polypeptide chains come together in specific arrangements calledthe quartenary structure.Thermodynamic experiments by Anfinsen have shown that the functional three-dimensional structureof the protein is encoded in its primary amino acid sequence. Thus a polypeptide chain in solutionwill automatically fold into its three dimensional structure given only that the conditions oftemperature, ionic strength, pH, etc., are within a fairly wide range. The natu

Abstracting and indexing information Journal of Clinical and Scientific Research is indexed in Index Copernicus, Academic Index, Open J-gate, Directory of Open Access Journals (DOAJ), Journal Seek, Indian Science Abstracts, Geneva Foundation for Medical Education