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Vision Research Foundation

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Centre For Bioinformatics



Overview

Bioinformatics has become an essential component of computationally intensive functional genomics, comparative genomics, gene discovery, transcriptional regulatory networks, biochemical pathway analysis, molecular modeling, proteomics and rational drug design. It helps to analyze genes on a massive scale to dissect the precise understanding of the biological processes at the molecular level. Bioinformatics is widely regarded as the key to decipher the staggering functional genomics and genotyping data in the 21st century.

Envisaging the potential of bioinformatics in modern biological research, KBIRVO, Sankara Nethralaya established Centre for Bioinformatics by 2010, to provide a platform for education and research in bioinformatics and its application to Vision Science. The ultimate goal of this multidisciplinary centre is to focus on research and education in the rapidly emerging fields of bioinformatics and computational biology which deal with the analysis, integration and management of biological or biomedical data generated by high-throughput techniques in genomics, transcriptomics and proteomics (with potential application to ocular diseases). The Department was established and led by Dr.V.Umashankar since 2010.


Bioinformatics & its applications in Vision Research

Next Generation Sequencing Data analysis, Protein structure prediction, protein- drug interactions, Molecular Dynamics Simulation studies, evolutionary analysis, Systems Biology based Drug Target Identification and Drug design for ophthalmic ailments are the major bioinformatics areas of focus serving the Vision Research Community.


Vision & Missions

  • The primary goal of Centre for Bioinformatics is to increase our understanding of biological processes pertaining to Vision Research.

  • To develop the capacity for leadership in applying modern bioinformatics tools to the study and treatment of ocular diseases and make the facility as a hub for ophthalmic investigators all over India.

  • To develop core competencies, analytical and informatics tools and methodologies for the acquisition, storage, analysis, interpretation and integration of staggering amounts of biomedical data, generated from genomic, transcriptomic, proteomic and metabolomic studies, using high performance computational systems with the ultimate goal of elucidating differences between health and disease.

  • To provide personalized training and enhance the skills of ophthalmic investigators in bioinformatics.

  • To conduct workshops, training programs and seminars for ophthalmic researchers and investigators from other disciplines of biology on the potential application of bioinformatics tools in modern biology.


Research Heads

Incharge Dr Srujana Chitipothu
drsrujana@snmail.org

Research Fellows

Senior Research Fellow(DST-INSPIRE) Ms. Hemavathy Nagarajan, M.Tech
Project Fellow(ICMR) Ms. L. Barathi, M.Sc

Past Doctoral Fellows

Dr. Arun John
Dr. S.Muthukumaran
Dr. A.Samdani

Past Research Fellows

Project Fellow (DST-SERB) Ms. S.Anupriya, M.Sc
Junior Research Fellow (DBT) Ms. K.Dhivya, M.Tech
Research Assistant (ICMR) Ms. C.Swathine, M.Tech
Ongoing projects

Principal Investigator: Dr Srujana Chitipothu

Project Funding Agency
Rational Design of novel peptide inhibitors targeting DNA-Topoisomerase- II-Beta through virtual screening of combinatorial peptide libraries and in vitro validation of anticancer efficacies ICMR

Completed Projects

S.No Project Name Funding Agency
1 Insilco drug target identification in Chlamydia species through systems biology and molecular modelling approaches pertaining to the development of potential drug molecules DST-SERB
2 Genome wide Transcriptome profiling of Human Retinal Cells under diabetic mielieu under the context of Egr-1 expression towards deciphering alternative pathways mediating Retinal Angiogenesis. ICMR
3 In silico Design and Development of novel peptide inhibitors targeting CD147 through virtual screening and biopanning of peptide libraries and in vitro validation of anticancer efficacies. DBT
4 Design and development of novel Anti-Angiogenic molecules by targeting polysaccharide binding domain of Carbonic Anhydrase IX through structural bioinformatics methods and studies on cell culture models ICMR - PI
5 Molecular modelling and Docking, simulation studies of functional domains of Toxoplasma gondii RON4, RON2 & RON5 to understand the moving junction complex formation towards design of novel peptide and chemical inhibitors and validation through invitro studies DBT-RGYI
6 Development of therapeutic molecules for diabetic retinopathy from studies on structure/function relationship of PON2 by cloning CSIR
7 Peripheral Blood Gene Expression Profiling In Eales Disease ICMR
8 Regulation of Lysyl Oxidase expression in Lens Epithelial Cells and trabecular endothelium ICMR
9 Molecular modelling and Docking, simulation studies of functional domains of Toxoplasma gondii RON4, RON2 & RON5 to understand the moving junction complex formation towards design of novel peptide and chemical inhibitors and validation through in vitro studies DBT-RGYI
10 Development of modulators Ornithine decarboxylase (ODC) for the therapeutic application in retinoblastoma CSIR
11 Application of Next Generation Sequencing technique to determine the whole genome sequence of laboratory isolates of Enterococcus fealias, P.aeruginosa, B.cervus (both sensitive and resistant strains) And application of bioinformatics approaches to identify the vulnerable area of drug targets in genome ICMR
12 Biomarker pattern discovery of graded changes in the opacity of human lens in age-onset cataract: a proteomic approach ICMR
13 Fuch’s endothelial corneal Dystrophy (FCD)– Fine mapping and identifying candidate gene for the novel loci 20p12.1- q13.2 in early onset family and study the association of TCF4 gene in sporadic late onset FCD cases in our population ICMR
14 FASN Structure and inhibition: Design of catalytic domains. Identification of novel inhibitors and characterisation of enzyme-inhibitor dynamics using insilico tools and experimental validation in Y79 retinoblastoma cells. DBT
15 Development of therapeutic peptide from proteoglycan LRR-angiogenesis DBT
16 Identification of novel interacting partners for PEDF in angiogenesis and obesity DST

Collaborative research as a Core Facility serving other Departments

  • Design of peptide carrier molecules targeting fungal keratitis (Nanobiotechnology)

  • Structure Function relationship studies of PRR4 protein (Biochemistry)

  • Binding mode analysis of Fatty acids with therapeutically important proteins (Biochemistry)

  • Molecular modeling and Simulation studies of Aptamers and its molecular interactions (Nanobiotechnology& Pathology)

  • NGS based Variant Analysis of different ocular genetic disorders (Genetics)

  • Structure-function relationship studies of mutational impact on Retinoschisin- 1 (Genetics)

  • NGS Data Analysis of Ocular Pathogens& Mycobacterium tuberculosis (Microbiology)

  • Structure prediction of Lysyl oxidase using Insilico modeling techniques (Biochemistry)

  • Comparative study of LOX and other amine oxidases (Biochemistry)

  • Insilico mutation impact analysis in UL54 gene of hCMV (Microbiology)

  • Diabetic Retinopathy Microarray Analysis Project ( Genetics)

  • Glaucoma Genome-wide Association Studies (GWAS) (Genetics)

  • Structural studies on proteins of Ocular therapeutic interest(Biochemistry)

  • Structure-function studies of the impact of mutations in Mycobacterium tuberculosis proteins (microbiology)

  • Rule based siRNA&Primer design of SPARC and Copper Transporter Receptor 1.(Biochemistry)

  • Mutational analysis of Pyrazinamide (PZA) of Mtb using structural bioinformatics approaches (Microbiology)

  • Structural analysis of CYP4V2 mutations (Genetics)

  • Structural analysis of SLC4A11mutations (Genetics)

  • Functional characterization of novel mutations in UL54 of ganciclovir resistant HCMV strain using structural analysis (Microbiology)

  • Design of SiRNA for copper binding proteins using Bioinformatics tools (Biochemistry)

  • Structure function analysis of 88KDa protein (Biochemistry)

  • Characterization of Hypothetical proteins present in tear (Biochemistry)

  • Insilico modeling and docking studies of Glutamate cysteine ligase (Biochemistry)

  • Identification of various binding regions/ residues in Osteonectin, PEDF and Decorin (Biochemistry)

  • Structural and functional analysis of Serum paraoxonase 2 using Insilico strategies (Biochemistry)

  • Identification of anti-angiogenic peptides in small Leucine rich repeats (Biochemistry)

  • Identification of Transcription factor Binding sites (CellBiology)

  • Structural Domain analysis of RIM protein (Genetics)

  • Structural analysis of RPE 65 mutations(Genetics)

INVITED BOOK CHAPTERS


  • Insilico Tools of Molecular Modeling, in Handbook of Systems Toxicology, V.Umashankar and S.Gurunathan, edited by Daniel A. Casciano and Saura C.Sahu. Chichester, UK: John Wiley & Sons, Ltd, pp 579-590. (2011)

  • Cheminformatics and its Applications, in Handbook of Systems Toxicology, edited by Daniel A. Casciano and Saura C.Sahu. Chichester, V.Umashankar and S.Gurunathan, UK: John Wiley & Sons, Ltd,pp 347-360. (2011)

  • Databases and Tools for Computational Epigenomics for Computational Epigenomics, Toxicology and Epigenetics, Edited by Saura C.Sahu. Chichester, V. Umashankar and S. Gurunathan, UK: John Wiley & Sons, Ltd,pp. 595-614. (2011)

LIST OF RESEARCH PUBLICATIONS

    2022
  • Joshi, R. K., Pai, S. R., Nagarajan, H., & Vetrivel, U. (2022). Identification of potentially bioactive compounds from Blumea lacera essential oil by gas chromatography-mass spectroscopy and molecular docking studies for targeting inflammatory bowel disease. Natural Product Research, 1-5.

    2021
  • Nagarajan, H., & Vetrivel, U. (2021). Deciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach. Journal of Biomolecular Structure and Dynamics, 1-13.

  • Rajendran, R., Sudha, D., Chidambaram, S., Nagarajan, H., Vetrivel, U., & Arunachalam, J. P. (2021). Retinoschisis and Norrie disease: a missing link. BMC research notes, 14(1), 1-7.

  • Ansar, S., & Vetrivel, U. (2021). Structure-based design of small molecule and peptide inhibitors for selective targeting of ROCK1: an integrative computational approach. Journal of Biomolecular Structure and Dynamics, 1-19.

  • Nagarajan, H., & Vetrivel, U. (2021). Membrane dynamics simulation and virtual screening reveals potential dual natural inhibitors of endothelin receptors for targeting glaucomatous condition. Life Sciences, 269, 119082.

    2020
  • Nagarajan, H., & Vetrivel, U. (2020). Microsecond scale sampling of Egr-1 conformational landscape to decipher the impact of its disorder regions on structure–function relationship. Molecular Simulation, 46(16), 1255-1264.

  • Nagarajan, H., Lakshmi, P. D., & Vetrivel, U. (2020). Deciphering potential inhibitors targeting THI4 of Fusarium solani sp. to combat fungal keratitis: An integrative computational approach. Computational Biology and Chemistry, 88, 107350.

  • Ansar, S., & Vetrivel, U. (2020). KinomeRun: An interactive utility for kinome target screening and interaction fingerprint analysis towards holistic visualization on kinome tree. Chemical Biology & Drug Design, 96(4), 1162-1175.

  • Sadhasivam, A., Nagarajan, H., & Umashankar, V. (2020). Structure-based drug target prioritisation and rational drug design for targeting Chlamydia trachomatis eye infections. Journal of Biomolecular Structure and Dynamics, 38(11), 3131-3143.

  • Jonnalagadda, B., Arockiasamy, S., Vetrivel, U., & PA, A. (2021). In silico docking of phytocompounds to identify potent inhibitors of signaling pathways involved in prostate cancer. Journal of Biomolecular Structure and Dynamics, 39(14), 5182-5208.
  • Muthukumaran, S., Sulochana, K. N., & Umashankar, V. (2021). Structure based design of inhibitory peptides targeting ornithine decarboxylase dimeric interface and in vitro validation in human retinoblastoma Y79 cells. Journal of Biomolecular Structure and Dynamics, 39(14), 5261-5275.

  • Chatterjee, A., Nagarajan, H., Padmanabhan, P., Vetrivel, U., Therese, K. L., & Janakiraman, N. (2020). Understanding the Uptake Mechanism and Interaction Potential of the Designed Peptide and Preparation of Composite Fiber Matrix for Fungal Keratitis. ACS omega, 5(21), 12090-12102.

  • John, A., Vetrivel, U., Sivashanmugam, M., & Natarajan, S. K. (2020). Microsecond simulation of the proteoglycan-like region of carbonic anhydrase IX and design of chemical inhibitors targeting pH homeostasis in cancer cells. ACS omega, 5(8), 4270-4281.

  • Nagarajan, H., Narayanaswamy, S., & Vetrivel, U. (2020). Mutational landscape screening of methylene tetrahydrofolate reductase to predict homocystinuria associated variants: An integrative computational approach. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 819, 111687.

    2019
  • Amit, C., Muralikumar, S., Janaki, S., Lakshmipathy, M., Therese, K. L., Umashankar, V., ... & Narayanan, J. (2019). Designing and enhancing the antifungal activity of corneal specific cell penetrating peptide using gelatin hydrogel delivery system. International Journal of Nanomedicine, 14, 605.

  • Ansar, S., Sadhasivam, A., & Vetrivel, U. (2019). PocketPipe: A computational pipeline for integrated Pocketome prediction and comparison. Bioinformation, 15(4), 295.

  • Kumar, D., Vetrivel, U., Parameswaran, S., & Subramanian, K. K. (2019). Structural insights on druggable hotspots in CD147: A bull's eye view. Life sciences, 224, 76-87.

  • John, A., Sivashanmugam, M., Natarajan, S. K., & Umashankar, V. (2019). Computational modeling of novel inhibitory peptides targeting proteoglycan like region of carbonic anhydrase IX and in vitro validation in HeLa cells. Journal of Biomolecular Structure and Dynamics.

  • Ansar, S., & Vetrivel, U. (2019). PepVis: An integrated peptide virtual screening pipeline for ensemble and flexible docking protocols. Chemical Biology & Drug Design, 94(6), 2041-2050.

    2018
  • Rao, B. S., Ansar, S., Arokiasamy, T., Sudhir, R. R., Umashankar, V., Rajagopal, R., & Soumittra, N. (2018). Analysis of candidate genes ZEB1 and LOXHD1 in late-onset Fuchs’ endothelial corneal dystrophy in an Indian cohort. Ophthalmic Genetics, 39(4), 443-449.

  • Umashankar Vetrivel, Nagarajan H. Deciphering ophthalmic adaptive inhibitors targeting RON4 of Toxoplasma gondii: An integrative in silico approach. Life Sciences. 2018 Oct 13. pii: S0024-3205(18)30639-8. doi: 10.1016/j.lfs.2018.10.022. PubMed PMID: 30326220.

  • Sadhasivam A, Vetrivel U. Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach. Journal of Cellular Biochemistry 2018 Oct 10. doi:10.1002/jcb.27553. PubMed PMID: 30302805.

  • Nagarajan H, Vetrivel U. Demystifying the pH dependent conformational changes of human heparanase pertaining to structure-function relationships: an in silico approach. Journal of Computer Aided Molecular Design. 2018 Jul 6. doi: 10.1007/s10822-018-0131-0. PubMed PMID: 29980923.

  • Sudha D, Neriyanuri S, Sachidanandam R, Natarajan SN, Gandra M, Tharigopala A,Sivashanmugam M, Alameen M, Vetrivel U, Gopal L, Khetan V, Raman R, Sen P,Chidambaram S, Arunachalam JP. Understanding variable disease severity in X-linked retinoschisis: Does RS1 secretory mechanism determine disease severity? PLoS One. 2018 May 31;13(5):e0198086. doi: 10.1371/journal.pone.0198086. eCollection 2018. PubMed PMID: 29851975; PubMed Central PMCID: PMC5978886.

  • Samdani, A., and Umashankar Vetrivel. "POAP: A GNU Parallel based multithreaded pipeline of Open Babel and AutoDock suite for boosted High Throughput Virtual Screening." Computational Biology and Chemistry (2018).

  • Muthukumaran S, Sulochana KN, Umashankar V. Virtual screening of Natural inhibitors targeting Ornithine Decarboxylase with pharmacophore scaffolding of DFMO and validation by molecular dynamics simulation studies. J Biomol Struct Dyn. 2018 Feb 13:1-30. doi: 10.1080/07391102.2018.1439772. [Epub ahead of print] PubMed PMID: 29436980


    2017
  • Muthukumaran S, Bhuvanasundar R, Umashankar V, Sulochana KN. Insights on ornithine decarboxylase silencing as a potential strategy for targeting retinoblastoma. Biomed Pharmacother. 2018 Feb;98:23-28. doi:10.1016/j.biopha.2017.12.030. Epub 2017 Dec 11. PubMed PMID: 29241071.

  • Vetrivel U, Nagarajan H, Thirumudi I. Design of inhibitory peptide targeting Toxoplasma gondii RON4-human β-tubulin interactions by implementing structural bioinformatics methods. J Cell Biochem. 2017 Nov 1. doi: 10.1002/jcb.26480. [Epub ahead of print] PubMed PMID: 29091310.

  • Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification. Anupriya Sadhasivam & Umashankar Vetrivel. Article in Journal of Biomolecular Structure and Dynamics. Published online on Jul 4 2017, page number 1-25. PMID: 28627970 DOI: 10.1080/07391102.2017.1343685

  • Polymorphism of the PAI-1gene (4G/5G) may be linked with Polycystic Ovary Syndrome and associated pregnancy disorders in South Indian Women. Maniraja Jesintha Mary, Lakshmanan Saravanan, Munuswamy Deecaraman, Melantharu Vijayalakshmi, Vetrivel Umashankar, Jaigopal Sailaja. Article in Bioinformation. 13(5): 149-153 May 2017. http: //www.bioinformation.net / 013 /97320630013149.htm.

  • Ornithine and its role in metabolic diseases: An appraisal. Muthukumaran Sivashanmugam, Jaidev Ja, Umashankar V., Sulochana K.N. Article in Biomedicine & Pharmacotherapy 86:185–194 • February 2017 DOI: 10.1016/j.biopha.2016.12.024

  • Inhibition of IKKβ by celastrol and its analogues – an in silico and in vitro approach. Karpagam Veerappan, Sathishkumar Natarajan, Purushoth Ethiraj, Umashankar Vetrivel& Shila Samuel. Article in Pharmaceutical Biology 55(1): 368-373. January 2017. DOI: 10.1080/13880209.2016.1241809

  • Virulence genome analysis of Pseudomonas aeruginosa VRFPA10 recovered from patient with scleritis. Murugan N, Malathi J, Umashankar V, Madhavan HN. Genom Data. 2017 Feb 6;12:1-3. doi: 10.1016/j.gdata.2017.02.007. eCollection 2017 Jun. PubMed PMID: 28217443; PubMed Central PMCID: PMC5302140.

  • Probing the intermolecular interactions of PPAR?-LBD with polyunsaturated fatty acids and their anti-inflammatory metabolites to infer most potential binding moieties. Shalini Muralikumar, Umashankar Vetrivel, Angayarkanni Narayanasamy and Undurti N. Das. Lipids Health Dis. 2017; 16: 17. DOI: 10.1186/s12944-016-0404-3.


    2016
  • Unraveling Genomic and Phenotypic nature of Multidrug-Resistant (MDR) Pseudomonas aeruginosa VRFPA04 Isolated from Keratitis Patient. N. Murugan, J. Malathi, V. Umashankar, H.N. Madhavan. MicrobiologicalResearch. 2016; 193. DOI:10.1016/j.micres.2016.10.002. PMID: 27825482

  • In Silico Structure Prediction of Human Fatty Acid Synthase–Dehydratase: A Plausible Model for Understanding Active Site Interactions. Perinkulam Ravi Deepa, John Arun, Vetrivel Umashankar, A Samdani, Manoharan Sangeetha, Subramanian Krishnakumar. Bioinformatics and biology insights 2016; DOI:10.4137/BBI.S38317.2016. PMID: 27559295

  • Virtual Screening, Molecular dynamics and binding free energy calculations on Human Carbonic Anhydrase IX catalytic domain for deciphering potential leads. Arun John, Muthukumaran Sivashanmugam, Vetrivel Umashankar, Sulochana Konerirajapuram Natarajan. Journal of Biomolecular Structure & Dynamics. 2016; DOI:10.1080/07391102.2016.1207565. PMID: 27373313

  • Multilevel Precision-Based Rational Design of Chemical Inhibitors Targeting the Hydrophobic Cleft of Toxoplasma gondii Apical Membrane Antigen 1 (AMA1). Umashankar Vetrivel, Shalini Muralikumar, B Mahalakshmi, K Lily Therese, HN Madhavan, Mohamed Alameen, Indhuja Thirumudi. Genomics & Informatics. 2016; 14(2). DOI:10.5808/GI.2016.14.2.53. PMID: 27445648

  • Comparative docking of dual conformations in human fatty acid synthase thioesterase domain reveals potential binding cavity for virtual screening of ligands. Arun John, Umashankar Vetrivel, Krishnakumar Subramanian, Perinkulam Ravi Deepa. Journal of Biomolecular Structure & Dynamics 2016; DOI:10.1080/07391102. PMID: 27145135

  • Targeting CD44, ABCG2 and CD133 markers using aptamers: in silico analysis of CD133 extracellular domain 2 and its aptamer. Subramanian N, Akilandeswari B, Bhutra A, Alameen M, Vetrivel U, Khetan V et al,. RSC Advances. 2016; 6(38): 32115-32123. DOI: 10.1039/C5RA27072C

  • Resistome and pathogenomics of multidrug resistant (MDR) Pseudomonas aeruginosa VRFPA03, VRFPA05 recovered from alkaline chemical keratitis and post-operative endophthalmitis patient. Murugan N, Malathi J, Umashankar V, Madhavan H. Gene. 2016; 578(1):105-111. PMID: 26692145

  • Bio-conjugation of antioxidant peptide on surface-modified gold nanoparticles: a novel approach to enhance the radical scavenging property in cancer cell. Kalmodia S, Vandhana S, Tejaswini Rama B, Jayashree B, Sreenivasan Seethalakshmi T, Umashankar V et al,. Cancer Nanotechnology. 2016; 7(1). PMID: 26900409

  • Probing the biophysical interaction between Neocarzinostatin toxin and EpCAM RNA aptamer. Athyala PK, Kanwar JR, Alameen M, Kanwar RK, Krishnakumar S, Watson J, Vetrivel U, Narayanan J. Biochem Biophys Res Commun. 2016; 469(2):257-62. PMID: 26642954


    2015
  • Homozygosity mapping in Leber congenital amaurosis and autosomal recessive retinitis pigmentosa in South Indian families. Sundaramurthy Srilekha, Tharigopala Arokiasamy, Natarajan N. Srikrupa, Vetrivel Umashankar, Swaminathan Meenakshi, Parveen Sen, Suman Kapur, Nagasamy Soumittra. PLOS ONE. 2015. PMID: 26147992

  • Draft genome sequence of blaVeb-1, blaoxa-10producing multi-drug resistant (MDR) Pseudomonas aeruginosastrain VRFPA09 recovered from bloodstream infection. Nandagopal Murugan, Jambulingam Malathi, Vetrivel Umashankar, Hajib Narahari Rao Madhavan. Brazilian Journal of Microbiology. 2015; vol.46, n.3, pp. 639-640. PMID: 26413042

  • Comparative Modeling and Molecular Dynamics Simulation of Substrate Binding in Human Fatty Acid Synthase: Enoyl Reductase and β-Ketoacyl Reductase Catalytic Domains. Arun John, Vetrivel Umashankar, Subramanian Krishnakumar, and Perinkulam Ravi Deepa. Genomics & Informatics. 2015; 13(1): 15-24. PMID: 25873848

  • Insights on Drug Targeting of Toxoplasma gondii Host Invasion Proteins: A Review. Indhuja Thirumudi, Umashankar Vetrivel, Mahalakshmi B, Lily Therese K, Madhavan HN. Asian Journal of Pharmaceutical and Clinical Research. 2015; 8:3

  • Drug Discovery: an appraisal. Umashankar, V., and S. Gurunathan. International Journal of Pharmacy and Pharmaceutical Sciences. 2015; 7.4.

  • Virtual screening studies of seaweed metabolites for predicting potential pparγ agonists. Gurula, H., Loganathan, T., Krishnamoorthy, T., Vetrivel, U., & Samuel, S. International Journal of Pharmacy and Pharmaceutical Sciences. 2015 7(11).


    2014
  • Mutation spectrum in BBS genes guided by homozygosity mapping in an Indian cohort. Sathya Priya C, P. Sen, V. Umashankar, N. Gupta, M. Kabra, G. Kumaramanickavel, C. Stoetzel, H. Dollfus and S. Sripriya. Clin Genet. 2014. doi: 10.1111/cge.12342. PMID: 24400638

  • In Silico analysis and prioritization of drug targets in Fusarium solani. Muthukumaran Sivashanmmugam, Hemavathy Nagarajam, Umashankar Vetrivel, Gayathri Ramasubban, KL therese, Madhavan HN, Umashankar Vetrivel. Medical Hypotheses, Elsevier. 2014; 84(2). PMID: 25555413

  • Computational docking studies reveal the potential inhibitory binding mode of Curcumin and its analogues on Lung Resistance Protein. Seethalakshmi Sreenivasan, Mohamed al ameen, Subramanian Krishnakumar and Umashankar Vetrivel. International Journal of Pharmacy and Pharmaceutical Sciences. 2014

  • Whole-Genome Sequencing and Mutation Analysis of Two Extensively Drug-Resistant Sputum Isolates of Mycobacterium tuberculosis (VRFCWCF XDRTB 232 and VRFCWCF XDRTB 1028) from Chennai, India. Kulandai LT, Lakshmipathy D, Ramasubban G, Vetrivel U, Rao MH, Rathinam S, Narasimhan M.. Genome Announcements, American Society of Microbiology. 2014; 2(6).PMCID: PMC4241668

  • Whole genome sequence of polyresistant Mycobacterium tuberculosis CWCFVRF PRTB 19 sputum isolate from Chennai, India, closely clustering with East African Indian 5 genogroup. Lakshmipathy D, Vetrivel U, Ramasubban G, Kulandai LT, Madhavan HN, Sridhar R, Meenakshi N.Genome Announcements, American Society of Microbiology.2014; 2(4):e00702-14. PMCID: PMC4102868

  • Draft Genome Sequence of sputum isolate of Multidrug resistant Mycobacterium tuberculosis CWCFVRF MDRTB 670 strain from Chennai, India with Clinically Suspected Tuberculosis. Gayathri Ramasubban, Dhanurekha Lakshmipathy, Umashankar Vetrivel, Lily Therese Kulandai, Hajib Narahari Madhavan, R Sridhar, N Meenakshi. Genome announcements, American Society of Microbiology. 2014; Vol 2. Issue 3. PMID: 24855307

  • Importance of ABC transporters in different tissues. Umashankar Vetrivel and Gurunathan Subramanian. Drug metabolism and drug interactions 29.2 2014; 65-66.

  • Comparative genomic analysis of multidrug-resistant Pseudomonas aeruginosa clinical isolates VRFPA06 and VRFPA08 with VRFPA07.Murugan, Nandagopal, Jambulingam Malathi, Vetrivel Umashankar, and Hajib Narahari Rao Madhavan. Genome announcements, American Society of Microbiology. 2014; no. 2 (2014): e00140-14. PMCID: PMC3945505

  • Whole-Genome Sequencing of Streptomycin-Resistant Mycobacterium tuberculosis Isolate VRFCWCF MRTB 180 Reveals Novel and Potential Mutations for Resistance. Gayathri Ramasubban, Dhanurekha Lakshmipathy, Umashankar Vetrivel, Lily Therese Kulandai, Hajib Narahari Madhavan, R. Sridhar, N. Meenakshi. Genome announcements, American Society of Microbiology. 2014 2(5): pii: e00919-14. PMID: 25212629

  • A molecular model of human Lysyl Oxidase (LOX) with optimal copper orientation in the catalytic cavity for induced fit docking studies with potential modulators. Bhuvanasundar R, John A, Sulochana KN, Coral K, Deepa PR4, Umashankar V. Bioinformation. 2014 10(7):406-412. PMID: 25187679


    2013
  • Identification and In silico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets Towards Prediction of Novel Serum Biomarkers. Madhu Beta, Nalini Venkatesan, Madavan Vasudevan, Umashankar Vetrivel, Vikas Khetan, Subramanian Krishnakumar, Bioinformatics and Biology Insights. 2013; Vol 7, 21-34, PMID: 23400111.

  • Modulation of MDR1 expression and function in retinoblastoma cells by curcumin. Seethalakshmi Sreenivasan, Sathyabaarathi Ravichandran, UmashankarVetrivel, Subramanian Krishnakumar, Journal of Pharmacology and Pharmacotherapeutics.2013 doi: 10.4103/0976-500X.110882. PMCID: PMC3669568

  • In silico Analysis of Novel Mutation ala102pro Targeting pncA Gene of M. Tuberculosis. Dhanurekha Lakshmipathy, Gayathri Ramasubban, Lily Therese*, Umashankar Vetrivel, Muthukumaran Sivashanmugam, Sunitha Rajendiran, Sridhar R, Madhavan HN, and Meenakshi N. J Comput Sci Syst Biol. 2013, 6:2.

  • Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India. Malathi J, Murugan N, Umashankar V, Bagyalakshmi R, Madhavan HN. Genome Announc.American Society of Microbiology. 2013; 1(4). PMCID: PMC3703595

  • Elucidation Of IRON Binding Patterns Through Insilico Approaches In Human Iron Binding Proteins. Muthukumaran Sivashanmugam, Anusha Kuppuswamy, UmashankarVetrivel, K.N. Sulochana. International Journal of Therapeutic Applications, Volume 10, 2013, 11-18.

  • Structural studies on AIPL1 and its functional interactions with NUB1 to identify key interacting residues in LCA4. S. Muthukumaran,V. Umashankar, Meena Revathi Valliappan. Journal of Ocular Biology, Diseases, and Informatics. 2013 April. Springer. PMID: 24596939

  • Virtual screening studies reveal linarin as a potential natural inhibitor targeting cdk-4 in retinoblastoma. S. Muthukumaran & R. Chandana, V. Umashankar. Journal of Pharmacology and Pharmacotherapeutics. 2013. PMID: 24250202

  • Novel Mutations in the thymidne kinase gene of ocular herpes simplex virus isolate responsible for acyclovir resistance by in silico analysis. Samson Moses Y, Malathi J, UmashankarV, Sherlin and Madhavan H.N, International Journal of Computational Bioinformatics and In Silico Modeling.2013 2(4): 158-165


    2012
  • ICAM-1 K469E polymorphism is a genetic determinant for the clinical risk factors of T2D subjects with retinopathy in Indians: a population-based case–control study. Kumari Vinita1, Sarangapani Sripriya1, Krishnamurthy Prathiba, Kulothungan Vaitheeswaran, Ravichandran Sathyabaarathi, Mahendran Rajesh, John Amali, Vetrivel Umashankar, Govindasamy Kumaramanickavel, Swakshyar Saumya Pal, Rajiv Raman, Tarun Sharma, British Medical Journal Open. 2012; 2:e001036. PMID: 22904330.

  • Agonistic effect of polyunsaturated fatty acids (PUFAs) and its metabolites on brain-derived neurotrophic factor (BDNF) through molecular docking simulation. Umashankar Vetrivel et al., BMCLipids in Health and Disease.2012 11:109. PMCID: PMC3477081.

  • In vitro and In silico studies on inhibitory effects of curcumin on multi drug resistance associated protein (MRP1) in retinoblastoma cells. Seethalakshmi Sreenivasan, Sathyabaarathi Ravichandran, UmashankarVetrivel, and Subramanian Krishnakumar, Bioinformation. 2012; 8(1): 13–19. 2012. PMID: 22359429

  • Phylogenetic comparison of exonic US4, US7 and UL44 regions of clinical herpes simplex virus type 1 isolates showed lack of association between their anatomic sites of infection and genotypic/sub genotypic classification. Harishankar A, Jambulingam M, Gowrishankar R, Venkatachalam A, Vetrivel Umashankar, Ravichandran S, Yesupadam SM and Madhavan HN, Virology Journal, BMC. 2012; 9:65. PMID: 22416856

  • Studies on New Delhi Metallo-Beta-Lactamse-1 producing Acinetobacter baumannii isolated from donor swab in a tertiary eye care centre, India and structural analysis of its antibiotic binding interactions. Murali Sowmiya, VetrivelUmashankar, Sivashanmugan Muthukumaran, Hajib Narahari rao Madhavan, and Jambulingam Malathi, Bioinformation. 2012; 8(10): 445–452. PMID: 22715297

  • Elucidation Of Structure - Function Relationship In Families Of Copper Binding Proteins In Homo Sapiens – A Bioinformatics Approach. Mathangi Jayaraman & Sudarshana N, Vidya Natarajan, Umashankar Vetrivel, Sulochana. K.N. International Journal of Pharma and Bio Sciences. 2012 3(3): (B) 647 – 662


    2011
  • A novel in silico approach to identify potential therapeutic targets in human bacterial pathogens. Umashankar Vetrivel Gurunathan Subramanian Sudarsanam Dorairaj. HUGO Journal (Official Journal of Human Genome Organization). 2011; DOI 10.1007/s11568-011-9152-7. Springer. PMID: PMC3238024

  • Insilico Identification of Novel Inhibitors for Emphysema through Structure Based Drug Design Approaches. Raghavan rajashekaran, Charanya muralidharan, Sathyabaarthi ravichandran, Umashankarvetrivel. Journal of Biology and Life Sciences. 2011; Vol 2, No 1.

  • Detection of novel coupled mutations in the katG gene (His276Met, Gln295His and Ser315Thr) in a multidrug-resistant Mycobacterium tuberculosis strain from Chennai, India, and insight into the molecular mechanism of isoniazid resistance using structural bioinformatics approaches. Gayathri Ramasubbana, Kulandai Lily Theresea, UmashankarVetrivel, Muthukumaran Sivashanmugamb, Parvathy Rajanc, R. Sridhard, Hajib N. Madhavana, N. Meenakshie. International Journal of Antimicrobial Agents. Elsevier. 2011 PMID: 21330112

  • Functional characterization of novel mutations in UL54 of ganciclovir resistant HCMV strain using structural analysis. Jambulingam Malathi, VetrivelUmashankar, Ravichandran Sathyabaarathi, Sivashanmugan Muthukumaran, Murali Ishwarya, Hajib Narahari Madhavan. Bioinformation.2011. PMID: 21383907

  • Molecular screening of the CYP4V2 gene in Bietti crystalline dystrophy that is associated with choroidal neovascularization. Gandra Mamatha, Vetrivel Umashankar, Nachiappan Kasinathan, Tandava Krishnan, Ravichandran Sathyabaarathi, Thirumalai Karthiyayini,1 John Amali,1 Chetan Rao,3 Jagadeesan Madhavan1. Molecular Vision.2011; 17:1970-1977. PMID: 21850171.

  • Chemical inhibition of Fatty Acid Synthase: molecular docking analysis and biochemical validation in ocular cancer cells. P. R. Deepa, S. Vandhana, S. Muthukumaran, V.Umashankar, U. Jayanthi, S. Krishnakumar, J Ocul Biol Dis Infor. Springer, 2011. PMID: 23181152

  • Comparative modeling of PON2 and analysis of its substrate binding interactions using computational methods. Subramanian Barathi & Muralidaran Charanya & Shivashanmugam Muthukumaran & Narayanasamy Angayarkanni &VetrivelUmashankar.J Ocul Biol Dis Infor,springer.2011; DOI 10.1007/s12177-011-9057-7. PMID: 22319641


    2010
  • Ab initio model of HIV’s Vif and simulation studies of APOBEC3G-Vif complex.UmashankarVetrivel. International Journal of Integrative Biology (IJIB). 2010, Vol. 10, No. 1, 29.

  • Homocysteinethiolactone and Paraoxonase: Novel markers of diabetic retinopathy. (2010). Barathi, S., Angayarkanni, N., Pasupathi, A., Natarajan, S. K., Pukraj, R., Dhupper, M., … Sivashanmugham, M. Diabetes Care, 33(9), 2031–2037. http://doi.org/10.2337/dc10-0132


POAP tool is a bash shell script based pipeline which can be used to optimize multiples ligands in a parallelized way using Open Babel and also to perform parallelized virtual screening using different flavours of Autodock Suite. POAP implements simple yet powerful GNU Parallel tool for efficient CPU usage in a multicore architecture. It was developed as in-house pipeline for performing ocular drug discovery research at Centre for Bioinformatics, Vision Research Foundation, Sankara Nethralaya, Chennai, India. The pipeline has undergone lots of fine tuning for optimal performance in terms of CPU usage, dynamic file handling and presentation of results. POAP is distributed freely under the terms of GNU GPL license. It can be modified and redistributed freely. We wish the pipeline will be useful for many of the scientists aspiring to use Virtual screening methods implementing Open Source tools.


POAP features

  1. Massive Parallelization of Ligand Preparation and Virtual screening using Open Babel and Autodock suite

  2. Dynamic File handling

  3. Seamless workflows & Guided text interface

  4. Well organized results

  5. Multi receptor Docking

  6. Visualization ready Docked complexes

  7. Offers the flexibility to modify the code

To download the Zip file containing the POAP pipeline, tutorial datasets and Operating manual click here


Usage:

unzip POAP.zip
cd POAP/
cd scripts/ #You will find two bash shell scripts#
POAP_lig.bash #is for ligand preparation module#
POAP_vs.bash #is for virtual screening module#


For detailed information on the POAP usage kindly refer the MANUAL
POAP can also be downloaded from github: https://github.com/inpacdb/POAP
POAP is available online since 21-7-2017


Reference:

POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening, A. Samdani, Umashankar Vetrivel, Computational Biology and Chemistry 74 (2018) 39–48.


Contact Info:

Dr.V.Umashankar
vumashankar@gmail.com

PepVis-Peptide Virtual Screening Pipeline
PepVis tool is a python based GUI pipeline which can be used to model and prepare large-scale peptide structure from the sequence and also to perform large-scale peptide virtual screening. PepVis integrates ModPep and Gromacs for modelling and structure optimization of the peptides, while it integrates AutoDock Vina,ZDOCK, AutoDock CrankPep(ADCP) for performing peptide virtual screening. The protein-peptide complexes can be rescored using ZRANK2 and the flexible refinement of the large protein-peptide complexes can also be performed using FlexPepDock. The parallel job execution have been implemented using GNU parallel and the user can provide inputs using GUI which will produce the bash script based on the customized input provided by the user and can be run in terminal.


PepVis can also be downloaded from github: https://github.com/inpacdb/PepVis


Reference:

Ansar, S., & Vetrivel, U. (2019). PepVis: An integrated peptide virtual screening pipeline for ensemble and flexible docking protocols. Chemical Biology & Drug Design, 94(6), 2041-2050.


KinomeRun
An interactive utility for kinome target screening and interaction fingerprint analysis towards holistic visualization on kinome tree


KinomeRun is a python based GUI pipeline which can be used for performing the target screening with the ligand of interest. It can be used to perform inverse screening against the kinome structures. KinomeRun integrates AutoDock Vina for performing the virtual screening and Protein-Ligand Interaction Profiler for calculation of the kinome-ligand interaction patterns at Largescale. The customized filteration analysis using KinomeRun will enable the user to specify the interaction filteraction pattern of their own for target prioritization and ranking for visualization in the Kinometree produced by KinomeRender.


KinomeRun can also be downloaded from github: https://github.com/inpacdb/KinomeRun


Reference:

Ansar, S., & Vetrivel, U. (2020). KinomeRun: An interactive utility for kinome target screening and interaction fingerprint analysis towards holistic visualization on kinome tree. Chemical Biology & Drug Design, 96(4), 1162-1175.


PocketPipe
A computational pipeline for integrated Pocketome prediction and comparison


PocketPipe with seamless integration of robust algorithms namely, P2Rank and PocketMatch, for pocketome generation and comparison, respectively. the pipeline proves to be efficient in terms of seamless operability, high scalability, dynamic file handling and optimal utilization of CPU for computationally demanding tasks. PocketPipe is distributed freely under GNU GPL license.


Pocketpipe can also be downloaded from github: https://github.com/inpacdb/PocketPipe


Reference:

Ansar, S., Sadhasivam, A., & Vetrivel, U. (2019). PocketPipe: A computational pipeline for integrated Pocketome prediction and comparison. Bioinformation, 15(4), 295.


For queries please contact:


vumashankar@gmail.com / samdani1593@gmail.com

  • Mr.Arun John was awarded SRF research fellowship for the project entitled “Virtual screening of natural compounds targeting human carbonic anhydrase ix validation of efficacy as anticancer agents through biochemical and in vitro assays” by ICMR (Indian Council of Medical Research)

  • Mr.S.Muthukumaran, (ICMR-SRF) was awarded First prize for Best oral presentation entitled “Dissecting the intermolecular interactions of Antizyme-Antizyme inhibitor complex reveals potential inhibitory peptides targeting synthesis in retinoblastoma cells” at International Conference on Emerging perspectives on Bioengineering and Biomedical Informatics with Special relevance to Ethnomedicine in Human Health" (ICBBI 2019) on March 25-27, 2019, Conducted by SATHYABAMA University.

  • Ms.Hemavathy Nagarajan was awarded Gyan fellowship to attend NGBT 2019 for presentation entitled “Structure-function relationship studies on Methylene tetrahydrofolatereductase mutational Landscape reveal unreferred pathogenic variants linked to homocystinuria”

  • Ms. Hemavathy Nagarajan was awarded DST-Inspire Fellowship for pursuing her Doctoral studies.

  • Mr. A. Samdani won 3rd prize in poster and oral presentation entitled “KinomeRun: An HPC compatible pipeline for kinome screening and comparative interaction fingerprint analysis” at Accelerating Biology 2020, organized by CDAC held at IISER Pune

  • Dr.V.Umashankar is a recipient of RGYI (Rapid Grant for Young Investigators) grant awarded by DBT (2013)

  • Dr.V.Umashankar is recipient of Early Career Research Award from SERB-DST (2016).

  • Mr.Samdani.A (DBT-SRF) has successfully cleared the highly competitive DBT-BINC-2018 (Bioinformatics National Certification) and also has secured All India Rank 8th position.

  • Mr.Muthukumaran, (ICMR-SRF), received the NextGen Genomics, Biology, and Bioinformatics and Technologies (NGBT) GYAN scholarship to attend the 7th NGBT conference-2018

  • Mr.Muthukumaran.S was awarded SRF research fellowship for the project entitled “Insilico Design and invitro validation of naturally occurring compounds as anticancer moieties for targeting Ornithine decarboxylase paralog (ODCp) protein.” by ICMR (Indian Council of Medical Research)

Training programmes

The department conducts training programmes for the benefit of students aspiring to learn and pursue research in bioinformatics:

  1. Short-term Internships

  2. Observership

  3. Workshops

  4. Summer training

So far more than 80 students have been trained in molecular modelling, dynamics simulation and Genome data analysis through the training programs


(For more information on training, kindly mail to: vibs@snmail.org, drsrujana@snmail.org)


The department also offers Ph.D program in Bioinformatics affiliated to SASTRA Deemed to be University and Alagappa university.


Supervisor: Dr Srujana Chitipothu
Current PhD scholar: 1


Supervisor: Dr.V.Umashankar
Completed PhD scholar: 3

Infrastructure and Facilities:

Computer Hardware:

  • Dedicated Linux Servers:

  • Multicore Clustered Workstations– NVIDIA-Tesla GPU Enabled

  • Dedicated broadband connection

Software:

CHARMM, AMBER for Molecular dynamics Simulations
Scrhodinger Drug Design suite
Opensource Bioinformatics Softwares


In-house Standardized protocols:

  • Next Generation Sequencing Analysis (customized RNA-Seq, SmallRNAand Variant Calling Pipelines)

  • Genome wide association studies (GWAS)

  • Rule based siRNA Design

  • In-house developed pipeline for High Throughput, Massively parallel Virtual screening (POAP)

  • Therapeutic peptide design

  • Customized pipeline for Molecular Modeling and Optimization

  • Small and Macromolecular Docking studies

  • Molecular dynamics & Simulation studies

  • Holisitic Identification of potential therapeutic targets based on Systems Biology approaches
Center for Bioinformatics
Vision Research Foundation,
18, College Road, Nungambakkam,
Chennai - 600 006.
Phone: 044-28271616 (Extn 1320)
Fax: 044-28254180
E-mail: drsrujana@snmail.org / bioinfo@snmail.org