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Computational Biology
Dr. U S Raghavender
SERB-DST Young Scientist

I am a trained Peptide Crystallographer (Ph.D. under the supervision of Prof. N. Shamala from Indian Institute of Science in a collaborative project with Prof. P. Balaram). I made my transition into the field of Bioinformatics and Computational Biology under Prof. R. Sowdhamini at National Center for Biological Sciences (NCBS). I had brief stints abroad and have learnt a lot from scientists, which has also helped me in shaping up my research. My research proposal is an amalgamation of my training in the field of peptides till now and intersects with basic and applied research areas in peptide biology and chemistry.

Project : Computational Approaches to Understanding Peptide-Protein Interactions Involved in the Regulatory Events in the Cell.

I am trying to understand protein-peptide interactions using computational approaches. I am analyzing protein sequences for the presence of regulatory motifs specifically at termini. Computational motif identification followed by studying their enrichment in proteomic sequences will help identify core players in transient protein-protein interactions. Peptidic regions which harbor a regulatory motif with high confidence will be studied further by modeling approaches. Conformational libraries for computational modeling are under development utilizing the structural information on peptide structures from Cambridge Structural Database and Protein Databank. Disease implied protein-protein complexes will be invoked as case studies.

Publications (before joining LCB)
  1. Raghavender US*. Analysis of Residue Conformations in Peptides in CSD and Protein-peptide Structural Complexes (Revised manuscript submitted, Under Review).

  2. Gandhimathi A, Margaret Sunitha S, Pritha Ghosh, Harini K, Hariprasanna, Meenakshi Iyer S, Adwait Joshi G, Snehal Karpe D, Mahita J, Manoharan Malini, Oommen Mathew K, Eshita Mutt, Mahantesha Naika, Nithin Ravooru, Sathyanarayanan Nitish, Shaik Naseer Pasha, Raghavender US, Rajas Rao M, Mohamed Shafi K, Prashant Shingate N, Anshul Sukhwal, Atul Upadhyay K, Rithvik Vinekar S and Ramanathan Sowdhamini. Draft Genome of Cissus quadrangularis to Elucidate the Medicinal Values. Herbal Medicine 2016; 2:1-7.

  3. Upadhyay AK, Chacko AR, Chandana S, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Mahita J, Malarini R, Malhotra S, Manoharan M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha N, Raghavender US, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Anantharaman R , Gowda M and Sowdhamini R. Genome sequencing of a herbal plant, Tulsi (Ocimum tenuiflorum), unravels key genes behind its strong medicinal properties. BMC Plant Biology 2015; 15:212-232.

  4. Raghavender US* and Sowdhamini R. Mechanistic basis of peptide-protein interaction in AtPep1-PEPR1 complex in Arabidopsis thaliana by computational studies. Protein and Peptide Letters 2015; 22:618-627.
    * corresponding author

  5. Metri R, Hariharaputran S, Ramakrishnan G, Anand P, Raghavender US, Ochoa-Montaño B, Ochoa-Montaño B, Higueruelo AP, Sowdhamini R, Chandra NR, Blundell TL, Srinivasan N. SInCRe - Structural Interactome Computational Resource for Mycobacterium tuberculosis. Database 2015; bav060.

  6. Ramakrishnan G, Ochoa-Montaño B, Raghavender US, Mudgal R, Joshi AG, Chandra NR, Sowdhamini R, Blundell TL, Srinivasan N. Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function. (Review)Tuberculosis (Edinb). 2015; 95(1):14-25.

  7. Aravinda S, Raghavender US, Rai R, Harini VV, Shamala N, Balaram P. Analysis of designed beta-hairpin peptides: molecular conformation and packing in crystals. Org Biomol Chem 2013; 11(25):4220-4231.

  8. Cupp ME, Song B, Kibler P, Raghavender US, Nayak SK, Thoen W, Galande AK. Investigating hydrophobic ligand-receptor interactions in parathyroid hormone receptor using peptide probes. J Pept Sci 2013; 19(6):337-344.

  9. Joshi AG, Raghavender US, Sowdhamini R. Improved performance of sequence search approaches in remote homology detection. F1000Res. 2013; 2:93.

  10. Raghavender US*. Ultrafast folding and molecular dynamics of a linear hydrophobic beta-hairpin. J Biomol Struct Dyn. 2013; 31(12):1404-1410.
    * corresponding author

  11. Bomar MG, Raghavender US, Spindel AW Kodukula K, Galande AK. The ST Pinch: A side chain-to-side chain hydrogen-bonded motif. Proteins 2012; 80(5):1259-1263.

  12. Raghavender US, Chatterjee B, Saha I, Rajagopal A, Shamala N, Balaram P. Entrapment of a water wire in a hydrophobic peptide channel with an aromatic lining. J Phys Chem B 2011; 115(29):9236-9243.

  13. Raghavender US, Aravinda S, Rai R, Shamala N, Balaram P. Peptide hairpin nucleation with the obligatory Type I' beta-turn Aib-DPro segment. Org Biomol Chem 2010; 8(14):3133-3135.

  14. Raghavender US, Kantharaju, Aravinda S, Shamala N, Balaram P. Hydrophobic peptide channels and encapsulated water wires. J Am Chem Soc. 2010; 132(3):1075-1086.

  15. Raghavender US, Aravinda S, Shamala N, Kantharaju, Rai R, Balaram P. Characterization of water wires inside hydrophobic tubular peptide structures. J Am Chem Soc. 2009; 131(42):15130-15132.

  16. Kantharaju, Raghothama S, Raghavender US, Aravinda S, Shamala N, Balaram P.Conformations of heterochiral and homochiral proline-pseudoproline segments in peptides: context dependent cis-trans peptide bond isomerization. Biopolymers (Pept Sci). 2009; 92(5):405-416.

Book Chapter
  1. Shingate PN, Upadhyay AK, Raghavender US, Sowdhamini R. Identification and Conformational Analysis of Hinge Regions in Proteins that Undergo Domain Swapping. In Biomolecular Form and Functions – A Celebration of 50 Years of the Ramachandran Map (Editors: Dr. Manju Bansal and Dr. N. Srinivasan)(IISc Press – WSPC Publication) (2013)
  1. SERB-DST StartUp Research Grant for Young Scientists (2015).

  2. NCBS Bridge Fellowship (2013).

  3. First all Indian authors Coverpage article in the internationally acclaimed journal Journal of American Chemical Society. October 28, 2009. Research communication highlighted in NEWS section of Chemistry World magazine of Royal Society of Chemistry.

  4. CSIR-UGC NET Fellowship (2004).

  5. JEST Fellowship (2004).

  6. University 5th in School of Physics, University of Hyderabad (2004).

  7. State First in Youth Parliament Competition held by K.V Sangathan (1997).

Contact Information
Email: usr<at>cdfd.org.in
Phone: +91-40-24749368
Fax: +91-40-24749448
Last updated on: Monday, 8th August, 2016.

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