Chandra:Publications

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2007

  • Ketki Verkhedkar, Karthik Raman, Nagasuma Chandra and Saraswathi Visheveshwara (2007, In Press) "Metabolome based reaction graphs of M. tuberculosis and M. leprae: A comparative network analysis" PLoS ONE
  • Kanade S. R., Suhas V. L., Chandra N. & Gowda L. R. (2007). Functional interaction of diphenols with polyphenol oxidase. FEBS J. 274, 4177-87.
  • Singh D. D., Chandran D., Jeyakani J. & Chandra N. (2007). Scanning the Genome of Mycobacterium Tuberculosis to Identify Potential Lectins. Protein. Pept. Lett. In Press
  • Sivapriya K., Hariharaputran S., Suhas V. L., Chandra N. & Chandrasekaran S. (2007). Conformationally locked thiosugars as potent alpha-mannosidase inhibitors: Synthesis, biochemical and docking studies. Bioorg. Med. Chem. 15, 5659-65.
  • Dash B. P., Mukherjee S., Suhas V. L. & Chandra N. (2007). Interaction Profiling of T-Cell Epitopes with MHC-Class I Molecules. Protein Pept Lett. 14, 557-64.
  • Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2007) "Hallmarks of Mycolic Acid Biosynthesis: A Comparative Genomics Study" Proteins: Structure, Function and Bioinformatics. 69:358--368 PMID 17600834
  • Vani J., Jeyakani J., Chandra N. R., Nayak R. & Shaila M. S. (2007). Peptidomimetics of antigen are present in variable region of heavy and light chains of anti-idiotypic antibody and function as surrogate antigens for perpetuation of immunological memory. Mol. Immunol. 44, 3345-3354
  • Sriharsha S. N., Pai K. S. R., Suhas V. L., Shashikanth S. & Chandra N. R. (2007). Synthesis, Docking and anti-tumor activity of -L-1,3-Thiazolidine pyrimidine nucleoside analogues. Curr. Med. Chem., In Press
  • Poddar P., Chandra N., Ganapathiraju M., Sekar K., Klein-Seetharaman J., Reddy R. & Balakrishnan N. (2007). Genome sequence analysis using suffix arrays: Application leading to evolutionary insights. J. BioSci. 2007, (Special issue, InCoB `06).
  • Khodade P., Prabhu R, Chandra N., Raha S. & Govindarajan R. Parallel Implementation of Autodock. J. Appl. Cryst (2007). J. Appl. Crystallogr. 40, 598-599
  • Khodade P., Malhotra S., Kumar N., Iyengar M. S., Balakrishnan N. & Chandra N. (2007) Cytoview: Development of a Cell modeling framework

J. Biosci., In Press

  • Bhattacharya S., Bhattacharyya C. & Chandra N. R. (2007). Comparison of protein structures by growing neighborhood alignments. BMC Bioinformatics 8, 77.
  • Konkimalla V. B., Suhas V. L., Chandra N. R., Gebhart E. & Efferth T. (2007). Diagnosis and therapy of oral squamous cell carcinoma. Expert. Rev. Anticancer Ther. 7, 317-29.
  • Krishna R., Prabu J. R., Manjunath G. P., Datta S., Chandra N. R., Muniyappa K. & Vijayan M. (2007). Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA. J. Mol. Biol. 367, 1130-44.
  • Vidyasagar, … Chandra N. R., … et al (NMITLI consortium for BioSuite) (2007). BioSuite: A comprehensive bioinformatics software package (a unique-industry- academia collaboration). Curr. Sci. 92, 29-38.

2006

  • Bhattacharya S., Bhattacharyya C. & Chandra N. R. (2006). Projections for fast protein structure retrieval. BMC Bioinformatics 7 Suppl 5:S5.
  • Ramesha K. P., Gowda S., Chandra N. R. & Rao M. R. S. (2006). Single nucleotide polymorphisms in -lactalbumin gene in cattle and their effect on the mature protein. Indian J. Anim Sci. 76, 816-820
  • Bhavani S., Nagargadde A., Thawani A., Sridhar V. & Chandra N. (2006).

Substructure-Based Support Vector Machine Classifiers for Prediction of Adverse Effects in Diverse Classes of Drugs J. Chem. Inf. Model. 46, 2478 -2486.

  • Ramesh S, Bharath MM, Chandra NR, Rao MR. A K52Q substitution in the globular domain of histone H1t modulates its nucleosome binding properties. FEBS Lett 580(25):5999-6006. PMID 17052712
  • Vinod PK, Konkimalla B, Chandra N. In-silico pharmacodynamics: correlation of adverse effects of H2-antihistamines with histamine N-methyl transferase binding potential. Appl Bioinformatics 2006;5(3):141-50. PMID 16922595
  • Prabu JR, Thamotharan S, Khanduja JS, Alipio EZ, Kim CY, Waldo GS, Terwilliger TC, Segelke B, Lekin T, Toppani D, Hung LW, Yu M, Bursey E, Muniyappa K, Chandra NR, Vijayan M. Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination. Acta Crystallograph Sect F Struct Biol Cryst Commun 2006 Aug 1;62(Pt 8):731-4. PMID 16880543
  • Chandra N. Common scaffolds, diverse recognition profiles. Structure 2006 Jul;14(7):1093-4. PMID 16843888
  • Chandra NR, Kumar N, Jeyakani J, Singh DD, Gowda SB, Prathima MN. Lectindb: a plant lectin database. Glycobiology 2006 Oct;16(10):938-46. PMID 16782824
  • Krishna R, Manjunath GP, Kumar P, Surolia A, Chandra NR, Muniyappa K, Vijayan M. Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery. Nucleic Acids Res 2006 Apr 28;34(8):2186-95. PMID 16648362
  • Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2006) "Principles and Practices of Pathway Modelling" Current Bioinformatics 1(2):147—160 Abstract
  • Vani J, Shaila MS, Chandra NR, Nayak R. A combined immuno-informatics and structure-based modeling approach for prediction of T cell epitopes of secretory proteins of Mycobacterium tuberculosis. Microbes Infect, 2006 Mar; 8(3):738-46. PMID 16476561
    • TABLES "Combined in silico approach for defining T-cell epitopes from secretory proteins of M. tuberculosis"
    • Table I - M. tuberculosis peptide sequences showing homology with human proteins
    • Table II - Peptides from selected secretory proteins of M. tuberculosis foreign to human
  • Rajan Prabu , Vetriselvi Rangannan and Nagasuma Chandra. Carbohydrate based drug design: Recognition fingerprints and their use in lead identification. Indian Journal of Chemistry: Special issue on Structure based drug design, Jan 2006

2005

  • K. Raman, P. Rajagopalan, and N. Chandra. Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs. PLoS Comput Biol, 1(5):e46, Oct 2005 PMID 16261191
  • MG. Chaitra, S. Hariharaputran, NR. Chandra, MS. Shaila, and R. Nayak. Defining putative T cell epitopes from PE and PPE families of proteins of Mycobacterium tuberculosis with vaccine potential. Vaccine, 23(10):1265-1272, Jan 2005 PMID 15652669.

2004

  • S. Raval, SB. Gowda, DD. Singh, and NR. Chandra. A database analysis of jacalin-like lectins: sequence-structure-function relationships. Glycobiology, 14(12):1247-1263, Dec 2004. PMID 15329359
  • P. Kumar, AG. Rao, S. Hariharaputran, N. Chandra, and LR. Gowda. Molecular mechanism of dimerization of Bowman-Birk inhibitors. Pivotal role of ASP76 in the dimerzation. J Biol Chem, 279(29):30425-30432, Jul 2004. PMID 15123729
  • T. Prasad, T. Subramanian, S. Hariharaputran, HS. Chaitra, and N. Chandra. Extracting hydrogen-bond signature patterns from protein structure data. Appl Bioinformatics, 3(2-3):125-135, 2004. PMID 15693738
  • S. Dhanasekaran, NR. Chandra, BK. Chandrasekhar Sagar, PN. Rangarajan, and G. Padmanaban. Delta-aminolevulinic acid dehydratase from Plasmodium falciparum: indigenous versus imported. J Biol Chem, 279(8):6934-6942, Feb 2004. PMID 14638682
  • Muniyappa K., Ganesh N., Guhan N., Singh P., Manjunath G. P., Datta S., Chandra N. and Vijayan M. Homologous recombination in mycobacteria. Curr. Sci. 86:141-148, 2004

2003

  • G. Ramachandraiah, NR. Chandra, A. Surolia, and M. Vijayan. Computational analysis of multivalency in lectins: structures of garlic lectin-oligosaccharide complexes and their aggregates. Glycobiology, 13(11):765-775, Nov 2003. PMID 12851290
  • VB. Konkimalla and N. Chandra. Determinants of histamine recognition: implications for the design of antihistamines. Biochem Biophys Res Commun, 309(2):425-431, Sep 2003. PMID 12951067
  • S. Datta, R. Krishna, N. Ganesh, NR. Chandra, K. Muniyappa, and M. Vijayan. Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes. J Bacteriol, 185(14):4280-4284, Jul 2003. PMID 12837805
  • MM. Bharath, NR. Chandra, and MR. Rao. Molecular modeling of the chromatosome particle. Nucleic Acids Res, 31(14):4264-4274, Jul 2003. PMID 12853645
  • J. Shobini, AK. Mishra, and N. Chandra. Conformation of gramicidin-A in CTAB micellar media. J Photochem Photobiol B, 70(2):117-124, May-Jun 2003. PMID 12849702
  • S. Datta, N. Ganesh, NR. Chandra, K. Muniyappa, and M. Vijayan. Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition. Proteins, 50(3):474-485, Feb 2003. PMID 12557189
  • T. Prasad, MN. Prathima, and N. Chandra. Detection of hydrogen-bond signature patterns in protein families. Bioinformatics, 19(1):167-168, Jan 2003. PMID 12499314

2002

  • MM. Bharath, NR. Chandra, and MR. Rao. Prediction of an HMG-box fold in the C-terminal domain of histone H1: insights into its role in DNA condensation. Proteins, 49(1):71-81, Oct 2002. PMID 12211017
  • MM. Bharath, S. Ramesh, NR. Chandra, and MR. Rao. Identification of a 34 amino acid stretch within the C-terminus of histone H1 as the DNA-condensing domain by site-directed mutagenesis. Biochemistry, 41(24):7617-7627, Jun 2002. PMID 12056893
  • G. Ramachandraiah, NR. Chandra, A. Surolia, and M. Vijayan. Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin. Acta Crystallogr D Biol Crystallogr, 58(Pt 3):414-420, Mar 2002. PMID 11856826

2001

  • NR. Chandra, MM. Prabu, K. Suguna, and M. Vijayan. Structural similarity and functional diversity in proteins containing the legume lectin fold. Protein Eng, 14(11):857-866, Nov 2001. PMID 11742104
  • J. Shobini, AK. Mishra, K. Sandhya, and N. Chandra. Interaction of coumarin derivatives with human serum albumin: investigation by fluorescence spectroscopic technique and modeling studies. Spectrochim Acta A Mol Biomol Spectrosc, 57A(5):1133-1147, Apr 2001. PMID 11374572

2000

  • S. Datta, MM. Prabu, MB. Vaze, N. Ganesh, NR. Chandra, K. Muniyappa, and M. Vijayan. Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation. Nucleic Acids Res, 28(24):4964-4973, Dec 2000. PMID 11121488
  • G. Ramachandraiah and NR. Chandra. Sequence and structural determinants of mannose recognition. Proteins, 39(4):358-364, Jun 2000. PMID 10813817

1999—1995

  • M. Vijayan and N. Chandra. Lectins. Curr Opin Struct Biol, 9(6):707-714, Dec 1999. PMID 10607664
  • NR. Chandra, G. Ramachandraiah, K. Bachhawat, TK. Dam, A. Surolia, and M. Vijayan. Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity. J Mol Biol, 285(3):1157-1168, Jan 1999. PMID 9887270
  • R. Ravishankar, NR. Chandra, and M. Vijayan. X-ray studies on crystalline complexes involving amino acids and peptides XXXIV. Novel mode of aggregation, interaction patterns and chiral effects in the maleic acid complexes of DL- and L- arginine. J Biomol Struct Dyn, 15(6):1093-1100, Jun 1998. PMID 9669554
  • NR. Chandra, H. Muirhead, JJ. Holbrook, BE. Bernstein, WG. Hol, and RB. Sessions. A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme. Proteins, 30(4):372-380, Mar 1998. PMID 9533621
  • NR. Chandra, TK. Dam, A. Surolia, and M. Vijayan. Crystallization and preliminary crystallographic studies on the mannose-specific lectin from garlic. Acta Crystallogr D Biol Crystallogr, 53(Pt 6):787-788, Nov 1997. PMID 15299871
  • RA. Kumar, MB. Vaze, NR. Chandra, M. Vijayan, and K. Muniyappa. Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis. Biochemistry, 35(6):1793-1802, Feb 1996. PMID 8639660
  • RV. Kishan, NR. Chandra, C. Sudarsanakumar, K. Suguna, and M. Vijayan. Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme. Acta Crystallogr D Biol Crystallogr, 51(Pt 5):703-710, Sep 1995. PMID 15299799

Pre-1995

  • H. C. Joao, R.J.P. Williams, J.A. Littlechild, R. Nagasuma, and H.C. Watson. An investigation of large inhibitors binding to phosphoglycerate kinase and their effect on anion activation. European Journal of Biochemistry, 205(3):1077-1088, 1992. PMID 1349525
  • Vani Brahmachari, Nagasuma.R, and Samir K. Brahmachari. Preparation of megabase-size DNA from adult insects and mammalian spleen for Pulsed-Field Gel Electrophoresis. Journal of Genetics, 68(3):185-188, 1989.
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