WIXLIB

Fundamentals of UNIX System: Introduction about UNIX,differentiation between UNIX and other Operating systems, variousprograms in the UNIX System, structure of the UNIX system,applications of the UNIX systems, basic UNIX commands, fileaccess permissions, the file system hierarchy, terminating process,running jobs at background, controlling running programs, overviewof system administration, managing deisk space, shutting downUNIX system.Unit- III3Molecular modeling and Molecular mechanics15Molecular modelingIntroduction, force field, quantum chemistry, Schrödinger equation,potential energy functions, energy minimization, local and globalminima, saddle point, grid search, , various approximations; LCAO,HF, semi-empirical calculations; single point calculations, fullgeometry optimization methods, ZDO, MNDO, CNDO, NDDO,AM1, PM3, RM1, conformational search, Z-matrix, docking,molecular modeling packages.Molecular mechanicsDefinition, balls and springs, force fields, bond-stretching, bondbending, dihedral motions, out of plane angle potential, non-bondedinteraction, coulomb interactions, conformational search, unitedatoms and cut-offs, Derivative methods; First-order methods;Steepest descent, conjugate gradient, Second order methods;Newton-Raphson method.Unit- IV4Molecular dynamics and Bioinformatics applicationsMolecular dynamicsIntroduction, Newton’s equation of motion, equilibrium point, watermodels, thermodynamic ensembles, quilibration, radial distributionfunction, pair correlation functions, MD methodology, periodic box(PBC), algorithm for time dependence; leapfrog algorithm, Verletalgorithm, Boltzman velocity, time steps, basic steps in moleculardynamics simulations; starting structures, duration of the MD run,final MD simulation structure. Visualization and analysis oftrajectories.Bioinformatics applications915

Agriculture, Molecular biology, Environment, Biotechnology, FoodScience Neurobiology, Drug Designing, Biomedical genomemedicines.Suggested readings:1. Bioinformatics Sequence and Genome Analysis (David Mount) CBS Publishersand Distributors.2. Bioinformatics Methods and Applications Genomics, Proteomics, and DrugDiscovery (S. C. Rastogi, N. Mendiratta, and P. Rastogi).3. Introduction to Bioinformatics, (Atwood, T. K. and Parry-Smith, D. J).4. An introduction to Computational Biochemistry. (C. Stain Tsai, AJohn Wiley and Sons, Inc., publications).5. Developing Bioinformatics Computer Skills. (Cynthia Gibas and Per Jambeck).6. Molecular Modelling for Beginners (Alan Hinchliffe).7. Molecular Modelling by Alxander Rich8. A user guide to the UNIX system (Rebecca Thomas and Jean Yates)9. http://www.ncbi.nlm.nih.govRequired Financial Support10

Annexure-IBudget: Non-recurring (e.g. Equipments, software, accessories, Books/Journals etc.)(Rupees in Lacs)A) Equipments/Computer and Accessories:Sr.Item NameRequiredNos.Nos.Cost(Rupees in Lacs)1.Desktop PC4016.02.LINUX – Rack/Blade Servers0110.0with multiple cores3.Quard Core PC’s207.004.UPS (3 KVA) with batteries012.0-5.00021.0010.50(12 hrs backup)5.Other computer accessories6.Air Conditioners(Server Cooling System)7.LCD ProjectorTotal41.50Justification:This facility would be useful for all the faculties of this university who wish todo computational biology related work. This would also be useful to provideadvanced training in bioinformatics to students and teachers of our university as wellas affiliated colleges.1.Desktop PC: Desktop computers are necessary to carry out routinebioinformatics practicals.2.LINUX Blade Server: It has planned to use Linux Blade Server with multiplenodes to install various bioinformatics software (commercial and freely availablesoftware), molecular modeling software and also to run molecular dynamicssimulations practicals for longer time duration by MD simulation packages ,SPARTAN, etc.3.Quard Core PC’s: These 20 QC PC’s are required for training students from ouruniversity as well as affiliated colleges to conduct regular bioinformaticsworkshops, seminars, practicals and for research11

4.Uninterrupted Power Supply (UPS): UPS is must to avoid fluctuations ofelectricity and thereby increase durability of Rack/Blade servers, computer PC’sand workstations.5. LCD Projector: Department needs one LCD projector to arrange seminars /workshops / guest lectures.6. Other accessories: For upgradation and maintenance of Blade server and othercomputers.7. Air Conditioners: Required to maintain cold temperature for Blade server andother computers.B) REQUIRED SOFTWARES:Sr.NameRequiredNo.Amount(Rupees in lacs)Nos.1.Insight II0110.02.Maestro0110.03.Discovery Studio0110.04.PC Pro SPARTAN023.05.MATLAB014.06.GENO-CLUSTER015.07GCG Winsconsin : Following points justifies our need for particular software:1. Insight II: This software for energy minimization and MD simulations ofvarious biomolecules. This would also be useful to do graphical visulalizationof proteins, nucleic acids, carbohydrates, lipids, drug molecules, etc. duringregular bioinformatics practicals.2. Maestro: This software would be useful for energy calculations and moleculardocking process.3. Discovery Studio: Particularly to use graphical version of MODELLER andCHARMM through which sequence alignments, model building, energyminimization, protein-ligand interactions and refinement could be done.12

4. PC Pro SPARTAN: Would be useful for each and every student to doquantum chemical, molecular mechanical, ab-intio, and density functionalcalculations of drug molecules.5. MATLAB: For biostatistics purpose.6. GENO-CLUSTER: Would be useful in identifying various gene functions,sequence analysis, vaccine designing, drug receptors and to do somebioinformatics related activities by assigning project work to the students atthe time of workshops and seminars.7. GCG Winsconsin package: For sequence analysis, conversion of DNAsequence to protein and vice versa, phylogenetic tree construction andanalysis, primer designing, etc.8. GUASSIAN: For charge calculations and molecular modeling studies.C) Building/Books/Journals:Sr. Nos.Item NamesRequired urnals2500 sp.constructionAs per need1.2.Cost(Rupees in lacs)ft.50.00As per needTotal3.02.055.0Justification: Proposed Department of Bioinformatics requires separate building.Department would also require some library materials and journal subscription fee forthe students.A B C Total Non Recurring Grant(44.50 50.0 55.0 146.50 LacsAnnexure- II13

(Rupees in lacs)Recurring Grants:1. Man Power:Sr.Nos.2.3.4.5.5.NameRequiredNumbers(for 5 years)Assistant Professor04Technician-2 @ Rs.10,000/01per month.Clerk @ Rs.4,000/- per01month.Peon @ Rs.3,000/- per01month.Laboratory Assistant01TotalCost(Rupees in lacs)(for 5 years)188.006.003.01.802.10200.90Justification:At present Department of Biochemistry has one faculty (Dr. K. D. Sonawane,Asso. Prof. and Coordinator Post Graduate Diploma in Bioinformatics; BiodataAttached) working in Bioinformatics area, but department would require four morefaculties for teaching and practical purposes and also to conduct regular workshopsand seminars, etc. The technical assistant has to support the system and keep themachinery in working condition. He has to attend the minor repairs and look after theoverall maintenance of the unit. An office clerk, peon and laboratory assistant areneeded to look after the day-to-day office and lab work. They will assist the Coordinator or Head (I/c) in maintaining office record, purchase of the goods andgeneral administration of the department.Annexure-III14

Budgetary Provision/year:Sr.No.Budget HeadAmount(Rs. in Lacs)1.Laboratory expenses2.Purchase of teaching aids, computer hard wares, 10.00software, etc.3Honorarium to contributory teachers and T. A. to 0.50visiting professors4Internet 3Total Budgetary Provision for the department:Sr.No.Budgetary ProvisionAmount(Rs. in Lacs)1.Total of Annexure I (Non-recurring):146.502.Total of Annexure II (Recurring):200.903.Total of Annexure III15.53(Budgetary Provision/ year):Total Budgetary Amount:362.93CURRICULUM VITAE15

1.Name of the ApplicantDr. Kailas Dashrath Sonawane2.Present Position andAssociate Professor and Coordinator,Address:Post Graduate Diploma in BioinformaticsDepartment of Biochemistry,Shivaji University, Vidyanagar,Kolhapur – 416 004, India, (MS).Telephone 91–231-2609153, Mobile: 9881320719Fax. 91-231-2692333, 2691523E-mailkds biochem@unishivaji.ac.in, kds19@rediffmail.com3.Date of Birth19th March, 19734.NationalityIndian5.Educational Qualification (Starting from Graduate . Sc.Shivaji University, Kolhapur1994ChemistryIstii.iii.M. Sc.Ph. D.Shivaji University, KolhapurUniversity of Pune19962003BiochemistryBiochemistryIst-Ph.D. Thesis title: “Structural Significance of the 3’– adjacent N6-(Δ2-isopentenyladenosine) and related modifications in tRNA”.Work place: National Chemical Laboratory (NCL), Pune, India.POST DOCTORAL FELLOWSHIPDURATIONINSTITUTIONDESIGNATIONNATURE OF WORK DONEMarch 2003Oct. 2005National Instituteof Health (NIH),Bethesda, MD,USA.Post DoctoralFellowHomology modeling, sequenceanalysis, molecular docking andmolecular dynamics simulationstudies on K ion channels.DOCTORAL/ FELLOWSHIP16

1999-2003National ChemicalLaboratory, Pune,IndiaSenior ResearchFellow (CSIR,New Delhi).Molecularmodeling;Quantum chemical, molecularmechanics,moleculardynamics simulations study ofhypermodifiednucleosidespresent in anticodon loop oftRNA.1996-1999National ChemicalLaboratory (NCL),Pune, IndiaProject AssistantII, (Indo-FrenchProject),IFCPAR, NewDelhiConformational preferences ofhypermodified bases, i6A,ms2i6A. Protonation inducedconformational preferences ofhypermodifiednucleosides(g6A, t6A, ms2t6A) present inanticodon loop of tRNA usingvarious modeling techniques.ii. Research student working under the guidance for their Ph. D. programme:- 01 Thesis Submitted.- 08 Working.iii. Research Schemes/Projects: (Ongoing/Completed)Title of lecular modeling DST,18,32,000/studyofhypermodified New Delhinucleoside lysidine present atwobble position in anticodonloop of E. coli tRNAIle andits role in proper codonanticodon recognition”SERC - Fast Track YoungScientist Scheme.1.Date ofstartingDate ofendingWorked pril,2011PrincipalInvestigator2.UGC SAP DRS I UGC SAPInfrastructureGrant DRS ISanctioned to Department ofBiochemistry,ShivajiUniversity, Kolhapur32,00,000/- April, 2 Project 2009FellowsMarch, Dy.2013Coordinator3. “Structural Significance of UGC,10,41,800/- July,March, Principal17

hypermodified nucleosides 5- New Delhitaurinomethyluridine e,(τm5s2U) present at ‘wobble’position in anticodon loop oftRNA”20112014InvestigatorResearch Specialization:Bioinformatics/Computational Biology:- Molecular modeling. Structural biology of hypermodified nucleic acids, Molecular modeling,homology modeling. RNA-Protein interactions, Prediction of three-dimensional structures ofenzymes involved in Alzheimer’s disease; molecular docking, and drugdesigning.Antimicrobial activity and EnzymologyResearch Experience: (16 Years) Post-Doctoral Fellow at the National Institutes of Health (NIH), Bethesda,MD, USA from March 2003 to Oct. 2005. During this period worked onsequence analysis, homology modeling and molecular dynamics (MD)simulations of potassium ion Channels. Software used during the period:Modeler (Insight-II), CHARMM, GROMACS (MD Simulations using dual xeonprocessor and Helix NIH supercomputer system), BLAST, FASTA, Sequencealignment using ClustalW & GCG Wisconsin package, DS viewer Pro(Accelrys), Chimera, programming languages; PERL, HTML. Java, Java Scriptetc.National Chemical Laboratory (NCL), Pune, India, from 1996 to 2003 duringPh.D. During this period got an opportunity to learn: UNIX; Molecular modelingtechniques such as, ab-initio; Semi-empirical quantum chemical calculationsusing PCILO, PM3, MNDO, AM1; Molecular mechanics (MMFF) and MolecularDynamics (MD) Simulations. Professional software: SYBYL, SPARTAN,HYPERCHEM, WINMOPAC; programming languages; FORTRAN, C, etc.Structural significance of hypermodified nucleosides present in the anticodonloop of tRNA. Transfer RNA sequence analysis.Research Guidance: U.G.:- Guidance to graduate student for his project work during the post-doctoralfellowship period from March 2003 to Oct. 2005 at National Institutes ofHealth, Bethesda (NIH), MD, USA. During this period worked on sequenceanalysis, homology modeling and molecular dynamics (MD) simulations of K ion Channels (Protein folding). P.G.:- Guidance to M. Sc (Bioinformatics) student for his project work at NCL,Pune, India (2000).18

P.G.:- Guidance to M. Sc Biochemistry, Biotechnology and PG Diploma inBioinformatics students for their project work in the Department of Biochemistry,Shivaji University, Kolhapur, since (2006). Ph. D:- Guidance to Ph. D. students in the subject of Biochemistry,Biotechnology and Microbiology, (Total no. of Ph.D. students working; 06).Membership/Other Charge: Presently working as a Head (I/c), Department of Microbiology, ShivajiUniversity, Kolhapur since August 2007. Co-ordinator, PG Diploma in Bioinformatics, Department of Biochemistry,Shivaji University, Kolhapur since 2008.Dy. Coordinator; UGC SAP DRS-I, sanctioned to Department of Biochemistry,Shivaji University, Kolhapur (2009-2014).Worked as Director, CAP (Microbiology Examination; Kolhapur, Karad andSatara centers), since August 2007, Department of Microbiology, ShivajiUniversity, Kolhapur.Life member, Association of Microbiologist of India (AMI).Reviewer: Biochimica et Biophysica ActaEditorial Board Member, Journal of Microbial WorldMember, Editorial Board “SHIVSANDESH” an E-Bulletin of ShivajiUniversity, Kolhapur.Chairman, B.Sc. Bioinformatics Syllabus Sub-Committee, under BOSBiotechnology, Shivaji University, Kolhapur.Member BUTR, Shivaji University, KolhapurBOS member, Biotechnology, Solapur University, Solapur.BOS member, Biotechnology, Dr. Babasaheb Ambedkar MarathwadaUniversity, Aurangabad. iv. Administrative experience:a) Head (I/c) Department of Microbiology,Shivaji University, Kolhapur, India(Since August, 2007).b) Coordinator; Post Graduate Diploma in BioinformaticsDepartment of Biochemistry,Shivaji University, Kolhapur, India(Since August, 2008).v. Teaching and Research Experience:a) Teaching experience: Since April, 2006.b) Research experience:16 yearsvi. Publications:A) List of Research Publications: Total (17)19

1. Rohit S. Bavi, Asmita D. Kamble, Navanath M. Kumbhar, Bajarang V.Kumbhar and Kailas D. Sonawane, “Conformational preferences of modifiedits derivative N2, N2nucleoside N2-methylguanosine (m2G) and2thdimethylguanosine (m 2G) occur at 26 position (hinge region) in tRNA”Cell Biochemistry and Biophysics, 507-521, 61, 2011.(Impact Factor 4.321)2. Navanath M. Kumbhar and Kailas D. Sonawane “Iso-energetic multipleconformations of hypermodified nucleic acid base Wybutine (yW) which occurat 37th position in anticodon loop of tRNAPhe”.J. of Molecular Graphics and Modelling, 29, 935-946, 2011(Impact Factor 2.033)3. Bajarang V Kumbhar1 and Kailas D Sonawane1* “Molecular modeling study ofhypermodified nucleic acid base 3-hydroxynorvalylcarbamoyl adenine, hn6Adepresent at 3’-adjacent position in anticodon loop of hyperthermophilic tRNAs”IRSAPS Bulletin (1) 3, 2011, -8-15, 2011.4. R.T. Sapkal, S.S. Shinde, A.R. Babar, C.B. Jalkute ,K.Y. Rajpure , K.D.Sonawane ,C.H. Bhosale. Photoelectrocatalytic purification of fecal, tap andE.coli contained water using ZnO thin films: A comparative study.International Journal of Basic and Applied Research, 1, 42-49, 2011.5. Maruti J. Dhanawade, Chidamber B. Jalkute, Jai S. Ghosh and Kailas D.Sonawane “Study Antimicrobial Activity of Lemon (Citrus lemon L.) PeelExtract”British J. of Pharmacology and Toxicology, 2, 119-122, 2011.6. Sapkal, R. T., Shinde, S. S., Sapkal, M. R., Babar, A. R. Sakpal, D. M., Jalkute,C. B., Rajpure, K. Y., Patil, P. S., Sonawane, K. D. and Bhosale, C. B.“Photoelectrocatalytic Hydrolysis of Starch By Sprayed Zno Thin Film”Material Science, 7, 2011.7. Susmit B. Sambhare, Navanath M. Kumbhar, Asmita D. Kamble, Bajarang V.Kumbhar and Kailas D. Sonawane “Molecular modeling study to investigateconformational preferences and base stacking interactions of hypermodifiednucleoside lysidine (k2C) incorporated in the trinucleotide segment of anticodonloop of tRNAIle”Bionanofrontier, 4, 191-196, 2011.(Impact Factor 0.237)8. Kailas D. Sonawane, Bajarang V. Kumbhar, Navanath M. Kumbhar, Susmit B.Sambhare and Asmita D. Kamble. “Consequences of 5’ -3’ diphosphatebackbone on the conformation of hypermodified nucleotide lysidine (k2C) occurat wobble (34th) position in the anticodon loop oftRNAIle”, International JBioinformatics Research, 3, 148-160, 2011.9. Sonawane, K. D., Tewari, R. “Conformational preferences of hypermodifiednucleoside lysidine (k2C) occurring at ‘wobble’ position in anticodon loop oftRNAIle”.Nucleosides, Nucleotides and Nucleic Acids. 27, 1158-1174, 2008.(Impact Factor 1.3)10. Gea-Ny, Tseng., Sonawane, K. D., Korolkova, Y. V., Zhang, M., Liu, J.,Grishin, E. V., and Guy, H. R. “Probing outer mouth structure of hERG channelwith peptide toxin foot printing and molecular modeling.20

Biophysical J. 92, 3524-3540, 2007.(Impact Factor 4.8)11. Zhang, M., Liu, J., Jiang, M, Wu, D. M., Sonawane K., Guy, H. R. and Tseng,G. N. “Interactions between charged residues in the transmembrane segments ofvoltage-sensing domain in the hERG channel.J. Memb. Biol. 207, 169-181, 2005.(Impact Factor 2.8)12. Sonavane, U. B., Sonawane, K. D. and Tewari, R. Modified Nucleotides andacross the anticdon loop interaction in tRNA. Europ. Biophysics Lett., 34, 581581, 2005.13. Sonavane, U.B., Sonawane, K. D. and Tewari, R. “Conformational preferencesof the base substituent in hypermodified nucleoside queuisine 5’monophosphate‘pQ’ and protonated variant ‘pQH ’”. J. Biomol. Struct. Dyn. 20, 437-485,2002.(Impact Factor 4.923)14. Sonawane, K. D., Sonavane, U.B., and Tewari, R. “Conformational preferencesof anticodon 3’-adjacent hypermodified nucleic acid base cis- or trans-Zeatinand its 2-methylthio derivative, cis- or trans-ms2Zeatin”. J. Biomol. Struct.Dyn. 19, 637-648, 2002.(Impact Factor 4.923)15. Sonawane, K. D., Sonavane, U.B. and Tewari, R. “Conformational flipping ofthe N(6) substitutent in diprotonated N6-(N-glycylcarbonyl) adenines: The roleof N(6) H in purine ring protonat

M.Phil./Ph.D. Course Work (Introduced from June 2012 onwards) Syllabus for Bioinformatics i) Paper - I: (60 Lectures, 100 marks) ii) Title of the Paper: Research Methodology iii) Specific Objectives if any: To trend the research students in the analytical tools required during the M.Phil./Ph.D. Course and to develop computational skills.