PUBLICATIONS



[1] C.Ramakrishnan, N.Srinivasan & D.Prashanth (1987) Conformation of glycyl residues in globular proteins. Int. J. Pept. Prot. Res., 29, 629-637.


[2] R.Sowdhamini, N.Srinivasan, B.Shoichet, D.V.Santi, C.Ramakrishnan & P.Balaram (1989) Stereochemical modeling of disulfide bridges: Criteria for introduction into proteins by site-directed mutagenesis. Prot. Engng., 3, 95-103.


[3] C.Ramakrishnan & N.Srinivasan (1990) Glycyl residues in proteins and peptides - An analysis. Curr. Sci., 59, 851-861.


[4] N.Srinivasan, R.Sowdhamini, C.Ramakrishnan & P.Balaram (1990)Conformations of disulfide bridges in proteins. Int. J. Pept. Prot. Res., 36, 147-155.


[5] N.Srinivasan, R.Sowdhamini, C.Ramakrishnan & P.Balaram (1991) Analysis of short loops connecting secondary structural elements in proteins. In Molecular conformation and biological Interactions, (Eds. P.Balaram & S.Ramaseshan) Indian Academy of Sciences, Bangalore. pp 59-73.


[6] R.Sowdhamini, N.Srinivasan, C.Ramakrishnan & P.Balaram (1992) Orthogonal bb motifs in proteins. J. Mol. Biol., 223, 845-851.


[7] C.Ramakrishnan & N.Srinivasan (1992) Conformational preference of glycyl residues in proteins. A further confirmation. Proc. Ind. Natl. Acad. Sci., B59, 45-54.


[8] N.Srinivasan (1993) Conformational studies on globular proteins: Data analysis. (A paper on the Ph.D thesis work). J. Ind. Inst. Sci., 73, 114-120.


[9] N.Srinivasan & T.L.Blundell (1993) An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. Prot. Engng., 6, 501-512.


[10] M.S.Johnson, N.Srinivasan, R.Sowdhamini & T.L.Blundell (1994) Knowledge-based protein modelling. CRC Crit. Rev. Biochem. Mol. Biol., 29, 1-68.


[11] J.Emsley, H.E.White, B.P.O'Hara, G.Oliva, N.Srinivasan, I.J.Tickle, T.L.Blundell, M.B.Pepys & S.P.Wood (1994) Structure of pentameric human serum amyloid P component. Nature, 367, 338-345.


[12] A.C.W.May, M.S.Johnson, S.D.Rufino, H.Wako, Z.-Y.Zhu, R.Sowdhamini, N.Srinivasan, M.A.Rodionov & T.L.Blundell (1994) The recognition of protein structure and function from sequence: adding value to genome data. Phil. Trans. Roy. Soc. (London) 344, 373-381.


[13] C.M.Topham, N.Srinivasan, C.J.Thorpe, J.P.Overington & N.A.Kalsheker (1994) Comparative modelling of major dust mite allergen Der p I. Structure validation using an extended environmental amino acid propensity table. Prot. Engng. 7, 869-894.


[14] N.Srinivasan, V.S.Anuradha, C.Ramakrishnan, R.Sowdhamini & P.Balaram (1994) Conformational characteristics of asparaginyl residues in proteins. Int. J. Pept. Prot. Res. 44, 112-122.


[15] S.Zarina, C.Slingsby, R.Jaenicke, Z.H.Zaidi, H.Driessen & N.Srinivasan (1994) Three dimensional model and quaternary structure of the human eye lens protein -s crystallin based on and -crystallin X-ray coordinates and ultracentrifugation. Prot. Sci. 3, 1840-1846.


[16] N.Srinivasan, H.E.White, J.Emsley, S.P.Wood, M.B.Pepys & T.L.Blundell (1994) Comparative analyses of pentraxins: implications for protomer assembly and ligand binding. Structure. 2, 1017-1027.


[17] L.E.Donate, E.Gherardi, N.Srinivasan, R.Sowdhamini, S.Aparicio & T.L.Blundell (1994) Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGFl/MSP). Prot. Sci. 3, 2378-2394.


[18] R.Sowdhamini, N.Srinivasan, K.Guruprasad, S.D.Rufino, V.Dhanaraj, S.P.Wood, J.Emsley, H.E.White & T.L.Blundell (1995) Protein three-dimensional structure and molecular recognition: A story of soft locks and keys. Pharmaceutica Acta Helvetiae., 69, 185-192.


[19] S.D.Rufino, N.Srinivasan, R.Sowdhamini, J.Murray-Rust, L.E.Donate, A.C.W.May, K.Guruprasad, V.Dhanaraj, B.L.Sibanda & T.L.Blundell (1995) Structure-based design of proteins. Learning from evolution by comparative analyses of protein families. In Proceedings of the Annual Symposium on Protein Engineering, September 1994, Oxford, U.K. pp. 1-8.


[20] D.V.Nataraj, N.Srinivasan, R.Sowdhamini & C.Ramakrishnan (1995) Alpha-turns in protein structures. Curr. Sci., 69, 434-447.


[21] N.Srinivasan, M.D.Waterfield & T.L.Blundell (1995) Regions binding subunits in Ga and PH domains have common structural motifs. Proceedings of the International conference on Molecular Structural Biology, 17-20 Sep. 1995, Vienna. (Eds. A.J.Kungl, P.J.Andrew & H.Schreiber) pp. 27-39.


[22] M.Introna, V.V.Alles, M.Castellano, G.Picardi, L.De Gioia, B.Bottazzi, G.Peri, F.Breviario, M.Salmona, L.De Gregorio, T.A.Dragani, N.Srinivasan, T.L.Blundell, T.A.Hamilton & A.Mantovani (1996) Cloning of mouse ptx3, a new member of the pentraxin gene family expressed in extrahepatic sites. Blood, 87, 1862-1872.


[23] N.Srinivasan, M.D.Waterfield & T.L.Blundell (1996) Comparative analysis of the regions binding bg-subunits in G alpha and PH domains. Biochem. Biophys. Res. Commn., 220, 697-702.


[24] N.Srinivasan, S.D.Rufino, M.B.Pepys, S.P.Wood & T.L.Blundell (1996) A superfamily of proteins with the lectin fold. Chemtracts Biochem. Mol. Biol., 6, 149-164.


[25] N.Srinivasan, K.Guruprasad & T.L.Blundell (1996) Comparative modelling of proteins. In Protein structure prediction - A practical approach. (Ed. M.J.E.Sternberg) Oxford University Press, Oxford. pp. 111-140.


[26] N.Srinivasan, B.Bax, T.L.Blundell & P.J.Parker (1996) Structural aspects of the functional modules in human protein kinase C-alpha deduced from comparative analyses. Proteins Str. Fn. Gen., 26, 217-235.


[27] T.L.Blundell & N.Srinivasan (1996) Symmetry, stability and dynamics of multidomain and multicomponent protein systems. Proc. Natl. Acad. Sci. (USA), 93, 14243-14248.


[28] C.Ramakrishnan, N.Srinivasan & D.V.Nataraj (1996) Motifs and conformational analysis of aminoacid residues adjoining beta-turns in proteins. Int. J. Pept. Prot. Res., 48, 420-428.


[29] N.Srinivasan & T.L.Blundell (1996) Insights on the structures of functional modules in protein kinase C family. In Molecular Biology Intelligence Unit - Protein kinase C. (eds. P.J.Parker & L.V.Dekker). R.G.Landes company, Texas. pp. 11-24.


[30] C.M.Topham, N.Srinivasan & T.L.Blundell (1997) Prediction of protein mutant stability based on three-dimensional structure dependent aminoacid substitution and propensity tables. Prot. Engng., 10, 7-21.


[31] C.Robinson, N.A.Kalsheker, N.Srinivasan, C.M.King, D.R.Garrod, P.J.Thompson & G.A.Stewart (1997) On the potential significance of the enzymatic activity of mite allergens to immunogenicity. Clues to structure and function revealed by molecular characterization. Clin. Exp. Allergy 27, 10-21.



[32] E.Gherardi, G.Hartmann, J.Hepple, D.Chirgadze, N.Srinivasan & T.Blundell (1997) Domain structure of hepatocyte growth factor / scatter factor (HGF/SF). CIBA Foundation symposia, 212. 84-98.


[33] A.Albert, T.L.Blundell, V.Dhanaraj, L.E.Donate, M.Groves, K.Guruprasad, P.G.Nugent, P.Orprayoon, J.E.Pitts, S.Rufino, N.Srinivasan, M.Williams & J.Wilsher (1998) Protein engineering of aspartic proteinases: Site-directed mutagenesis, biochemical characterisation and X-ray analysis of chymosins with substituted single aminoacid substitutions and loop replacements. Adv. Exp. Med. Biol., 436, 169-177.


[34] R.Sowdhamini, D.F.Burke, , J.-F.Huang, K.Mizuguchi, H.A.Nagarajaram, N.Srinivasan, R.E.Stewart & T.L.Blundell (1998) CAMPASS: A database of structurally aligned protein superfamilies. Structure 6, 1087-1094.


[35] R.Sowdhamini, D.F.Burke, C.M.Deane, J.-F.Huang, K.Mizuguchi, H.A.Nagarajaram, J.P.Overington, S.D.Rufino, N.Srinivasan, R.E.Stewart & T.L.Blundell (1998) Protein 3D structural databases: domains, structurally aligned homologues and superfamilies. Acta Cryst. D , 54, 1168-1177.


[36] N.Srinivasan, M.Antonelli, G.Jacob, I.Korn, F.Romero, A.Jedlicki, V.Dhanaraj, M.-F.Sayed, T.L.Blundell, C.C.Allende & J.E.Allende (1999) Structural interpretation of site-directed mutagenesis and specificity of the catalytic subunit of protein kinase CK2 using comparative modelling. Prot. Engng., 12, 119-127.


[37] I.Korn, S.Gutkind, N.Srinivasan, T.L.Blundell, C.C.Allende & J.E.Allende (1999) Interactions of protein kinase CK2 subunits. Mol. Cell. Biochem., 191, 75-83.


[38] A.R.Walker, P.A.Davison, C.Agnese, B-.Winfield, C.M.James, N.Srinivasan, T.L.Blundell, J.J.Esch, M.D.Marks & J.C.Gray (1999) The TTG1 (Transparent Testa, Glabra1) locus which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis encodes a WD40-repeat protein. Plant Cell 11, 1337-1349.


[39] N.Srinivasan & V.S.R.Rao (1999) Structural features of protein – carbohydrate interactions in galactose and mannose binding proteins complexes. (in Perspectives in Structural Biology. Eds. M.Vijayan, N.Yathindra & A.S.Kolaskar) Indian Academy of Sciences. pp. 355-366.


[40] L.A.Lindsey-Boltz, G.Chawla, N.Srinivasan, U.Vijayraghavan & M.A.Garcia-Blanco (2000) The Carboxy Terminal WD Domain of the pre-mRNA splicing Factor Prp17p is Critical for Function. RNA 6, 1289-1305.


[41] K. Vijayachandra, M. Guruprasad, R. Bhandari, U.H. Manjunath, B.P. Somesh, N. Srinivasan, K. Suguna and S.S. Visweswariah (2000) Biochemical characterization of the intracellular domain of the human guanylyl cyclase C receptor provides evidence for a catalytically active homotrimer. Biochemistry 36, 16075-16083.


[42] S.Deam, N.Srinivasan, J.Westby, E.H.Horn & G.Dolan (2001) Factor X Nottingham and factor X Taunton: Two novel mutations in factor X resulting in loss of functional activity and an interpretation using molecular modelling. Thrombosis and Haemostasis 85, 265-269.


[43] S. Balaji, S. Sujatha, S. Sai Chetan Kumar & N. Srinivasan (2001) PALI - A database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res. 29, 61-65.


[44] S. Sujatha, S. Balaji & N. Srinivasan (2001) PALI: a database of alignments and phylogeny of homologous protein structures. Bioinformatics, 17, 375-376.


[45] R.J.Newbold, E.C.Raux, C.E.Walker, S.E.Wilkie, N.Srinivasan, D.M.Hunt, S.S.Bhattacharya & M.J.Warren (2001)The destabilization of human GCAP1 by a proline to leucine mutation might cause cone-rod dystrophy. Human Mol. Gen. 10, 47-54.


[46] S. Balaji & N. Srinivasan (2001) Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins. Prot. Engng., 14, 219-226.


[47] R.Bhandari, N. Srinivasan, Mahaboobi, K. Suguna & S.S.Visweswariah (2001) Functional inactivation of the human guanylys cyclase C receptor: Modelling and mutation of the protein kinase -like domain. Biochemistry, 40, 9196-9206.


[48] S.B. Pandit, D. Gosar, S. Abhiman, S. Sujatha, S.S. Dixit, N.S. Mhatre, R. Sowdhamini & N. Srinivasan (2002) SUPFAM - A database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: Implications for structural genomics and function annotation in genomes. Nucleic Acids Res. 30, 289-293.


[49] S. Balaji, S. Sujatha, S. Aruna, N.S. Mhatre & N. Srinivasan (2002) PALI (Release 1.3) Nucleic Acids Res. Link -on-line publication.


[50] A. Krupa & N. Srinivasan (2002) Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram-negative bacteria are related to the eukaryotic protein kinases. Prot. Sci. 11, 1580-1584.


[51] S.Gupta, S.B. Pandit, N. Srinivasan & D. Chatterji (2002) Proteomics analysis of carbon starved Mycobacterium smegmatis: Induction of Dps like protein. Prot. Engng..15, 503-511.


[52] A.R. Shenoy, N. Srinivasan & S. S. Visweswariah (2002) The ascent of nucleotide cyclases: conservation and evolution of a theme. J. Biosci. 27, 85-91.


[53] N.Eswar, H.A.Nagarajaram, C.Ramakrishnan & N.Srinivasan (2002) Influence of solvent molecules on the stereochemical code of glycyl residues in proteins. Proteins Str. Fn. Gen., 49, 326-334.


[54] S. Sehrawat, N. Srinivasan & K.P.Gopinathan (2002) Functional characterization and structural modeling of late gene expression factor 4 from Bombyx mori nucleopolyhedrovirus. Biochem. J. 368, 159-169.>


[55] A. Krupa & N. Srinivasan (2002) The repertoire of protein kinases encoded in the draft version of the human genome: Atypical variations and uncommon domain combinations. Genome Biology 3, 66.1-66.14.
See Nature News India (March 2003 issue, pp.12) for a news item on this work.


[56] V.S. Gowri, S.B. Pandit, P.S. Karthik, N. Srinivasan & S. Balaji (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res. 31, 486-488.


[57] S.B. Pandit, S. Balaji, V.S. Gowri, K.R. Abhinandan, R. Vaishnavi & N. Srinivasan (2003) SUPFAM - Release 1.2. Nucleic Acids Res. Link -On-line publication.


[58] A. Krupa, K. Sandhya, N. Srinivasan & S. Jonnalagadda (2003) A conserved domain in the prokaryotic bifunctional FAD synthetases can potentially catalyze nucleotide transfer Trends. Biochem. Sci. 28, 10-13.


[59] A. Rahaman, N. Srinivasan, N. Shamala & M.S. Shaila (2003) Fusion Core Complex of Peste des Petits Ruminants Virus is a Six-Helix Bundle Assembly. Biochemistry, 42, 922-931.


[60] R. Pudi, S. Abhiman, N. Srinivasan & S. Das (2003) Hepatitis C virus Internal Ribosome Entry Site-mediated translation is stimulated by specific interaction of independent regions of human La autoantigen. J. Biol. Chem. 278, 12231-12240.


[61] S.B. Pandit & N. Srinivasan (2003) Survey for G-proteins in the prokaryotic genomes: Prediction of functional roles based on classification. Proteins Str. Fn. Gen. 52, 585-597.


The paper mentioned above is listed in Faculty of 1000

[62] S. Sopory, S. Balaji, N. Srinivasan & S.S. Visweswariah (2003) Modeling and mutational analysis of the GAF domain of the cGMP-binding, cGMP-specific phosphodiesterase PDE5. FEBS Letters. 539, 161-166.


[63] N. Eswar, C. Ramakrishnan & N. Srinivasan (2003) Stranded in isolation: Structural role of isolated extended-strands in proteins. Prot. Engng. 16, 331-339.


[64] N. Rekha & N. Srinivasan (2003) Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions. BMC Strl. Biol. 3, 4.1-4.13.


[65] A.R. Shenoy, N. Srinivasan, M. Subramaniam & S.S. Visweswariah (2003) Mutational analysis of Mycobacterium tubercolosis Rv1625c adenylyl cyclase: Residues that confer nucleotide specificity contribute to dimerization. FEBS Letters 545, 253-259.


[66] S. Balaji, S. Aruna & N. Srinivasan (2003) Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures. Proteins Str. Fn. Gen. 53, 783-791.


[67] S. Sandhya, S. Kishore, R. Sowdhamini & N. Srinivasan (2003) Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. FEBS Letters, 552, 225-230.


[68] V. Sampath, N. Rekha, N. Srinivasan & P.P. Sadhale (2003) The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae. J. Biol. Chem. 278, 51566-51576.


[69] M. Praseeda, K.K. Pradeep, A. Krupa, S. Sri Krishna, S. Leena, R. Rajeev Kumar, J. Cheriyan, M. Mayadevi, N. Srinivasan & R.V. Omkumar (2003) Influence of a mutation in the ATP-binding region of Calcium/Calmodulin dependent protein kinase II on its interaction with peptide substrates. Biochem. J. 378, 391-397.


[70] A. Shenoy, K. Sivakumar, A. Krupa, N. Srinivasan & S.S. Visweswariah. (2003) A survey of nucleotide cyclases in Actinobacteria: unique domain organization and expansion of the class III cyclase family in Mycobacterium tuberculosis. Comp. Fnl. Genomics 5, 17-38.


[71] A. Krupa, K.R. Abhinandan & N. Srinivasan (2004) KinG: A database of protein Kinases IN Genomes. Nucl. Acids Res. 32, 153-155.


[72] V.S. Gowri, S.B. Pandit., B. Anand., N. Srinivasan & S. Balaji (2004) PALI. Nucl. Acids Res. Link (on-line publication).


[73] S.B. Pandit, R. Bhadra, V.S. Gowri, S. Balaji, B. Anand & N.Srinivasan (2004) SUPFAM. Nucl. Acids Res., Link (on-line publication).


[74] S. Singh, N. Rekha, B. Pillai, V. Singh, A. Naorem, V. Sampath, N. Srinivasan & P.P. Sadhale (2004) Domainal Organization Of The Lower Eukaryotic Homologs Of The Yeast RNA Polymerase II Core Subunit Rpb7 Reflects Functional Conservation. Nucl. Acids Res. 32, 201-210.


[75] A. Rahaman, N. Srinivasan, N. Shamala & M.S. Shaila (2004) Phosphoprotein of Rinderpest virus forms a tetramer through coiled-coil region important for biological function: A structural insight. J. Biol. Chem., 279, 23606-23614.


[76] B. Anand, S. Namboori, S. Sandhya & N. Srinivasan (2004) Influence of protein structural similarities in adding value to genome data. Ind. J. Biotech. 3, 473-485.


[77] S.B. Pandit, R. Bhadra, V.S. Gowri, S. Balaji, B. Anand & N. Srinivasan (2004) SUPFAM: A database of sequence superfamilies of protein domains. BMC Bioinformatics, 5, 28.1-28.5.


[78] A. Krupa, G. Preethi & N. Srinivasan (2004) Structural modes of stabilization of permissive phosphorylation sites in protein kinases: Distinct strategies in Ser/Thr and Tyr kinases. J. Mol. Biol., 339, 1025-1039.


[79] A. Mahajan, A. Sharma, S. Chavali, M. Kabra, M.R. Chowdhury, N. Srinivasan & D. Bharadwaj (2004) Novel missense mutation in the coagulation factor IX catalytic domain associated with severe hemophilia B factor IXDelhi. Haemophilia, 10, 550-552.


[80] S. Namboori, N. Mhatre, S. Sujatha, N. Srinivasan & S.B. Pandit (2004) Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv. J. Biosci., 29, 245-259.


[81] S. Namboori, N. Srinivasan & S.B. Pandit (2004) Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures. In Silico Biol., 4, 445-460.


[82] S.B. Pandit, S. Balaji & N. Srinivasan (2004) Structural and functional characterization of gene products encoded in the human genome by homology detection. IUBMB Life, 56, 317-331.


[83] S.B. Pandit & N. Srinivasan (2004) Identification and analysis of a new family of bacterial serine proteinases. In Silico Biol., 4, 563-572.


[84] V.S. Gowri, S. Balaji, O. Krishnadev, S.B. Pandit. & N. Srinivasan (2005) PALI. Nucl. Acids Res. link (on-line publication).


[85] O. Krishnadev, V.S. Gowri, S. Balaji, N.Srinivasan & S.B. Pandit (2005) SUPFAM. Nucl. Acids Res., link (on-line publication).


[86] A. Krupa, K.R. Abhinandan, Anamika & N.Srinivasan (2005) KinG. Nucl. Acids Res., link (on-line publication).


[87] Anamika, N. Srinivasan & A. Krupa (2005) A genomic perspective of protein kinases in Plasmodium falciparum. Proteins Str. Fn. Bioinf., 58, 180-189.


[88] N. Rekha, S.M. Machado, C. Narayanan, A. Krupa & N. Srinivasan (2005) Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signalling pathways. Proteins Str. Fn. Bioinf., 58, 339-353.


[89] R. Gadkari, S. Roy, G.S. Murthy, N. Rekha, N. Srinivasan & R.R. Dighe (2005) Identification Of A Heterodimer-Specific Epitope Present In Human Chorionic Gonadotropin (hCG) Using A Monoclonal Antibody That Can Distinguish Between hCG and Human Luteinizing Hormone. J. Mol. Endocrin. 34, 879-884.


[90] B. Anand, V.S. Gowri & N. Srinivasan (2005) Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues. Bioinformatics 21, 2821-2826.


[91] O. Krishnadev, N. Rekha, S.B. Pandit, S. Abhiman, S. Mohanty, L.S. Swapna, S. Gore & N. Srinivasan (2005) PRODOC resource for comparison of tethered protein domain architectures with in-built information on distantly related domain families. Nucl. Acids Res. 33, W126-129.


[92] R. Bhadra, N. Srinivasan & S.B. Pandit (2005) A new domain family in the superfamily of alkaline phosphatases. In Silico Biol. 5, 0034.


[93] S. Sandhya, C. Jayadev, S. Chakrabarti, K.R. Abhinandan, R. Sowdhamini & N. Srinivasan (2005) Relating protein families in sequence space through multiple intermediates. In Mathematical Biology edited by P.Chandra & B.V.R.Kumar, Anamaya Publishers, New Delhi pp. 173-180.


[94] S. Sandhya, S. Chakrabarti, K.R. Abhinandan, R. Sowdhamini & N. Srinivasan (2005) Assessment of a rigorous transitive profile based search method to detect remotely similar proteins. J. Biomol. Str. Dyn. 23, 283-298.


[95] S. De, O. Krishnadev, N. Srinivasan & N. Rekha (2005) Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. BMC Strl. Biol. 5, 15.


[96] A. Krupa & N. Srinivasan (2005) Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes. BMC Genomics . 6, 129.


[97] P.K. Padmanabhan, A. Mukherjee, S. Singh, S. Chattopadhyaya, V.S. Gowri, P.J Myler, N. Srinivasan & M. Rentala (2005) Glyoxalase I from Leishmania donovani: A potential target for anti-parasite drug. Biochem. Biophys. Res. Commn. 337, 1237-1248.


[98] H.G. Mahesha, S.A., Singh, N. Srinivasan & A.G.A. Rao (2006) A spectroscopic study of the interactions of isoflavones with human serum albumin. FEBS Journal 273, 451-467.


[99] V.S. Gowri, O. Krishnadev, C.S. Swamy & N. Srinivasan (2006) MulPSSM: A database of multiple position specific scoring matrices of protein domain families. Nucl. Acids Res. 34, D243-246.


[100] N. Srinivasan (2006) Computational Biology and Bioinformatics: A tinge of Indian spice. Bioinformation, 1, 105-109. Reproduced with permission in Biobytes by the editors of Biobytes.


[101] O. Krishnadev, V.S. Gowri, C.S. Swamy & N.Srinivasan (2006) SUPFAM - Grouping of sequence families into superfamilies. Nucl. Acids Res., link (on-line publication).


[102] C.S. Swamy, O. Krishnadev, N. Srinivasan & V.S. Gowri (2006) PALI – Phylogeny and alignment of homologous protein structures. Nucl. Acids Res. link (on-line publication).


[103] Anamika, A. Krupa & N. Srinivasan (2006) KinG –Kinases IN Genomes. Nucl. Acids Res. link (on-line publication).


[104] L.S.Swapna, B. Offmann & N. Srinivasan (2006) Evolutionary dynamics of protein-protein interactions: A case study using the DJ-1/PfpI family of enzymes. In Knowledge Discovery in Bioinformatics: Techniques, Methods and Application edited by Yi Pan and Tony Hu. Wiley publishers. Pp.209-231.


[105] R. Bhadra, S. Sandhya, K.R. Abhinandan, S. Chakrabarti, R. Sowdhamini & N. Srinivasan (2006) Cascade PSI-BLAST Web server: A remote homology search tool for relating protein domains. Nucl. Acids Res. 34, W143-146.


[106] M. Tyagi, P. Sharma, S. Swamy, F. Cadet, N. Srinivasan, A. de Brevern & B. Offmann (2006) Protein Block Expert (PBE): A web-based protein structure analysis server using a structural alphabet. Nucl. Acids Res. 34, W119-223.


[107] G. Pugalenthi, , K. Shameer., N. Srinivasan & R. Sowdhamini.(2006) HARMONY: a web-server for the assessment of protein structures. Nucl. Acids Res. 34, W231-234.


[108] A. Krupa, Anamika & N. Srinivasan (2006) Genome wide comparative analyses of domain organisation of repertoires of protein kinases of Arabidopsis thaliana and Oryza sativa. Gene 318, 1-13.


[109] M. Tyagi, V.S. Gowri, N. Srinivasan, A.G. de Brevern & B. Offmann (2006) A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications. Proteins Str. Fn. Bioinf., 65, 32-39.


[110] K. Sharma, M. Gupta, A. Krupa, N. Srinivasan & Y. Singh (2006) EmbR, a regulatory protein with ATPase activity, is a substrate of multiple serine/threonine kinases and phosphatase in Mycobacterium tuberculosis. FEBS J. 273, 2711-2721.


[111] V.S. Gowri, Tina K. Graceline, O. Krishnadev and N. Srinivasan (2007) Strategies for the effective identification of remotely related sequences in multiple PSSM search approach. Proteins Str. Fn. Bioinf., 67, 789-794.


[112] R.R. Thangudu, P. Sharma, N. Srinivasan & B. Offmann (2006) Analycys: a database for conservation and conformation of disulphide bonds in homologous proteins. Proteins Str. Fn. Bioinf., 67, 255-261.


[113] V. Talla, C. Narayanan, N. Srinivasan & D. Balasubramanian (2006) Mutations causing self-aggregation in human gamma-C crystalline leads to congenital cataract. Investigative Ophthalmology & Visual Science. 47, 5212-5217.


[114] N.Srinivasan as one of the members of the NMITLI BioSuite team. (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration). Curr. Sci., 92, 29-38.


[115] O. Krishnadev, L.S., Swapna, V.S. Gowri, G. Agarwal, S.B. Pandit & N.Srinivasan (2007) SUPFAM - Grouping of sequence families into superfamilies. Nucl. Acids Res., (on-line publication).


[116] G. Agarwal, O. Krishnadev, A. Sebastian, N. Srinivasan, S. Balaji & V.S. Gowri (2007) PALI – Phylogeny and alignment of homologous protein structures. Nucl. Acids Res. (on-line publication).


[117] Anamika, A. Krupa, K.R. Abhinandan & N. Srinivasan (2007) KinG –Kinases IN Genomes. Nucl. Acids Res. (on-line publication).


[118] S. Mohanty, L.S. Swapna, V.S., Gowri, G. Agarwal, N. Srinivasan & O. Krishnadev (2007) MulPSSM – A database of multiple profiles of protein domain families. Nucl. Acids Res. (on-line publication).


[119] N. Srinivasan, R. Sowdhamini & A. Bhattacharya (2007) Computational Biology: More than just a set of techniques. J. Biosci., 32, 1-2.


[120] S. Balaji & N. Srinivasan (2007) Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution. J. Biosci. 32, 83-96.


[121] K.G. Tina, R. Bhadra & N. Srinivasan (2007) PIC: Protein Interactions Calculator. Nucl. Acids Res. 35, W473-476.


[122] K. Anamika & N. Srinivasan (2007) Comparative kinomics of Plasmodium organisms: Unity in diversity. Pept. Prot. Letts. 14, 509-517.


[123] V.S. Gowri, K. Anamika, S. Gore & N. Srinivasan (2007) Analysis of sliding helices and strands in protein structural comparisons: A case study with protein kinases. J. Biosci., 32, 921-928.


[124] M. Tyagi, N. Srinivasan, A.G. de Brevern & B. Offmann (2007) Protein structure mining using a structural alphabet. Proteins 71, 720-737.


[125] C. Ramakrishnan, B. Lakshmi, A. Kurien, D. Devipriya & N. Srinivasan (2007) Structural compromise of disallowed conformations in peptide and protein structures. Pept. Prot. Letts. 14, 672-682.


[126] K. Anamika, A. Bhattacharya & N. Srinivasan (2007) Analysis of the kinome of Entamoeba histolytica. Proteins 71, 995-1006.


[127] G. Agarwal, O. Krishnadev O., V.S. Gowri N. Srinivasan & S. Balaji S. (2008) PALI- Phylogeny and alignment of homologous protein structures. Nucl Acids Res. (online publication)


[128] O. Krishnadev, L.S. Swapna, V.S. Gowri, G. Agarwal, N. Srinivasan & S.B. Pandit (2008) SUPFAM- Grouping of sequence families into superfamilies. Nucl Acids Res. (online publication)


[129] S. Mohanty, L.S. Swapna, V.S. Gowri, G. Agarwal, N. Srinivasan & O. Krishnadev (2008) MulPSSM- A database of multiple profiles of protein domain families. Nucl Acids Res. (online publication)


[130] Anamika, K., Martin, J., Krupa, A, Abhinandan, K.R., Srinivasan, N. (2008) KinG –Kinases IN Genomes. Nucl. Acids Res. (on-line publication).


[131] A. Jhingran, P.K. Padmanabhan, S. Singh, K. Anamika, A. A. Bakre, S. Bhattacharya, A. Bhattacharya, N. Srinivasan and R. Madhubala (2008) Characterization of the Entamoeba histolytica Ornithine decarboxylase-like enzyme. PLoS NTD 2, e115.


[132] V.S. Gowri, D. Venkatasubramanian, K.S. Raghavendran, C.S. Swamy & N. Srinivasan (2008) Stretching the limits of comparative modeling of proteins: Modeling on the basis of remote relationships. In Recent Advances in Structural Bioinformatics , Research Signpost. pp. 299-312.


[133] A. Krupa & N. Srinivasan (2008) Evolution of FAD synthatases and associated functional domains. In Recent Advances in Structural Bioinformatics , Research Signpost. pp. 313-329.


[134] D.V. Pantakani, L.S. Swapna, N. Srinivasan & A.U. Mannan (2008) Spastin oligomerizes into a hexamer and the mutant spastin (E442Q) redistribute the wild-type spastin into filamentous microtubule. J. Neurochem., 106, 613-624.


[135] V. Talla, N. Srinivasan & D. Balasubramanian (2008) Visualization of in situ intracellular aggregation of two cataract-associated human gamma-Crystallin mutants: Lose a tail, lose transparency.Invest Ophthalmol Vis Sci. 49, 3483-3490.


[136] S. Sandhya, B. Pankaj, M.K. Govind, B. Offmann, N. Srinivasan & R. Sowdhamini (2008) CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. BMC Strl. Biol., 8, 28.


[137] O. Krishnadev & N. Srinivasan (2008) A data integration approach to predict host - pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite. In Silico Biol., 8, 20.


[138] D. Varughese & N. Srinivasan (2008) New resources for remote homology detection of proteins. BioBytes, 2, 14-16.


[139] A. Roy, N. Srinivasan & V.S. Gowri (2008) Molecular and structural basis of drift in the functions of closely-related homologous enzyme domains: Implications for function annotation based on homology searches and structural genomics. In Silico Biol.,9,S41-55.


[140] Thangudu RR, Manoharan M, Srinivasan N, Cadet F, Sowdhamini R, Offmann B. (2008)Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families. BMC Struct Biol.


[141] G. Agarwal, O. Krishnadev O., V.S. Gowri N. Srinivasan & S. Balaji S.(2009) PALI- Phylogeny and alignment of homologous protein structures. Nucl Acids Res. (online publication)


[142] O. Krishnadev, R.M. Bhaskara, G. Agarwal, & N. Srinivasan (2009) SUPFAM- Grouping of sequence families into superfamilies. Nucl Acids Res. (online publication)


[143] O. Krishnadev, R.M. Bhaskara, G. Agarwal & N. Srinivasan (2009) MulPSSM- Multiple PSSMs of protein domain families. Nucl Acids Res. (online publication)


[144] K. Anamika, N. Tyagi, J. Martin, A. Krupa, K.R. Abhinandan, Srinivasan, N. (2008) KinG –Ser/Thr/Tyr-specific protein kinases encoded in complete genomes. Nucl. Acids Res. (on-line publication).


[145] K. Anamika, J. Martin & N. Srinivasan (2008) Comparative kinomics of human and chimpanzee reveals unique kinship and functional diversity generated by new domain combinations.BMC Genomics, 9, 625.


[146] J. Rath, V.S. Gowri, S. Chattapadhyay, P.K. Padmanabhan, N. Srinivasan & M. Rentala (2009) A glutathione-specific aldose reductase of Leishmania donovani and its potential implications for methylglyoxal detoxification pathway. Gene, 429, 1-9.


[147] A. Kumar, S. Reddy, N. Srinivasan & D. Nandi (2009)Interaction between two residues in the inter-domain interface of Escherichia coli peptidase N modulates catalytic activity. Prot. Pept. Lett., 16, 415-422.


[148] S. Mohanty & N. Srinivasan (2009) Identification of “missing” metabolic proteins of Plasmodium falciparum: A bioinformatics approach. Prot. Pept. Lett. 16, 961-968.


[149] S. Mohanty, S.B. Pandit & N. Srinivasan (2009)Dynamics of protein-protein interaction network in Plasmodium falciparum in “Biological Data Mining in Protein Interaction Networks” (Editors: Xiao-Li Li & See-Kiong Ng). IGI Global Press. pp. 257-285.


[150] R. Gadkari, D. Varughese & N. Srinivasan (2009) Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of Ca atoms. PLoS ONE, 4, e4476.i


[151] A.J. Kandathil, A.P. Joseph, R. Kannangai, N. Srinivasan, O.C. Abraham, S.A. Pulimood & G. Sridharam (2009) Structural basis of drug resistance by genetic variants of HIV-1 clade C protease from India. AIDS Res. Human Reteroviruses, 25, 511-519.


[152] S. Sandhya, S.S. Rani, B. Pankaj, M.K. Govind, B. Offmann, N. Srinivasan & R. Sowdhamini (2009) Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS ONE, 4, e4981.


[153] T. Nidhi , L.S. Swapna, S. Mohanty, G. Agarwal, V.S. Gowri, K. Anamika, M.L. Priya, O. Krishnadev & N. Srinivasan (2009) Evolutionary divergence of Plasmodium falciparum: Sequences, protein-protein interactions, pathways and processes.Infectious Disorders-Drug Targets 9, 257-271.


[154] G. Agarwal, M. Rajavel, B. Gopal & N. Srinivasan (2009) Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PLoS ONE, 4, e5736.


[155] A. Kumar, M. Bhosale, S. Reddy, N. Srinivasan & D. Nandi (2009) Importance of non-conserved distal carboxyl terminal amino acids in two peptidases belonging to the M1 family: Thermoplasma acidophilum Tricorn interacting factor F2 and Escherichia coli Peptidase N. Biochimie, 91, 1145-1155.


[156] N. Tyagi, O. Krishnadev & N. Srinivasan (2009) Prediction of Protein-Protein Interactions between Helicobacter Pylori and human. Mol. Bio. Sys. 5, 1630-1635.


[157] A.J. Kandathil, A.P. Joseph, R. Kannangai, N. Srinivasan, O.C. Abraham, S.A. Pulimood & G. Sridharan (2009) HIV reverse transcriptase: Structural interpretation of drug resistant genetic variants from India. Bioinformation, 4, 36-45.


[158] S. Mohanty & N. Srinivasan (2009) How effective is the data on co-occurrence of domains in multi-domain proteins in prediction of protein-protein interactions? In IEEE proceedings on Genomic Signal Processing and Statistics, 2009. (GENSIPS 2009.). 1-4.


[159] K. Anamika, K.R. Abhinandan, K. Deshmukh & N. Srinivasan (2009) Classification of Non-enzymatic Homologues of Protein Kinases . Comp. Fnl. Genomics , e365637.


[160] B. Chawla, A. Jhingran, S. Singh, N. Tyagi, M.H. Park, N Srinivasan, S.C. Roberts & R. Madhubala (2009) Identification and characterization of a novel Deoxyhypusine synthase in Leishmania donovani. J. Biol. Chem. 285, 453-463.


[161] K. Anamika, N. Garnier & N. Srinivasan (2009) Functional diversity of human protein kinase splice variants marks significant expansion of human kinome. BMC Genomics, 10, 622.


[162] G. Agarwal, D.C. Dinesh, N. Srinivasan & A.G. de Brevern (2009) Characterization of conformational patterns in active and inactive forms of kinases using protein blocks approach. In"Computational Intelligence and Pattern Analysis in Biological Informatics" edited by U. Maulik, S. Bandyopadhyay & J. T. L. Wang. John Wiley Press, pp. 169-188.


[163] K. Deshmukh, K. Anamika & N. Srinivasan (2009) Evolution of domain combinations in protein kinases and its implications for functional diversity. Prog. Biophys. Mol. Biol. Mol. Biol. 102, 1-15.


[164] Bhaskara R.M., Mohanty, S., Krishnadev O., Srinivasan, N., Balaji S., Gowri V.S., and Agarwal, G.(2010) PALI- Phylogeny and alignment of homologous protein structures. Nucl Acids Res. (online publication)


[165] Krishnadev, O., and Srinivasan, N.(2010) SUPFAM- Grouping of sequence families into superfamilies. Nucl Acids Res. (online publication)


[166] Mohanty, S., Mudgal, R., Krishnadev, O., and Srinivasan, N. (2010) MulPSSM- A database of multiple profiles of protein domain families. Nucl Acids Res. (online publication)


[167] Garnier, N., Tyagi, N., Rakshambikai R., Dinesh, D.C., Anamika, K., Martin, J., Krupa, A., Abhinandan, K.R., and Srinivasan, N. (2010) KinG –Kinases in Genomes. Nucl. Acids Res. (online publication)


[168] (2010) Novel insertion and deletion mutants of RpoB which render Mycobacterium smegmatis RNA polymerase recalcitrant to rifampicin mediated inhibition of transcription. Microbiology.Link(online publication)


[169] O. Krishnadev, S. Bisht & N. Srinivasan (2010) Prediction of protein-protein interactions between human host and two mycobacterial organisms. Int. J. Knowledge Discovery Bioinf.Link(online publication)


[170] P. Aggarwal, M.D. Gupta, A.P. Joseph, N. Chatterjee, N. Srinivasan & U. Nath (2010) Identification of specific DNA-binding residues in the TCP family of transcription factors. Plant Cell.Link(online publication)


[171] R. Gadkari & N. Srinivasan (2010) Prediction of Protein-protein Interactions in Dengue Virus Coat Proteins Guided by Low Resolution cryoEM Structures. BMC Strl. Biol.,Link(online publication)


[172] N. Tyagi, K. Anamika & N. Srinivasan (2010) A Framework for Classification of Prokaryotic Protein Kinases. PLoS ONE.Link(online publication)


[173] A.P.Joseph, G.Agarwal, S.Mahajan, J.-C.Gelly, L.S.Swapna, B.Offmann, F.Cadet, A.Bornot, M.Tyagi, H.Valadié, B.Schneider, C.Etchebest, N.Srinivasan, A.G. de Brevern (2010) A short survey on protein blocks. Biophys. Rev.Link(online publication)


[174] L.S. Swapna, B. Offmann & N. Srinivasan (2010) Evolutionary dynamics at protein-protein interfaces of legume lectins. In Protein-protein interactions. Book Chapter Nova publishers, New York. pp 293-310.


[175] J. Martin, K. Anamika & N. Srinivasan (2010) Classification of protein kinases on the basis of both kinase and non-kinase regions. PLoS ONE.Link(online publication)


[176] O. Krishnadev & N. Srinivasan (2011) Prediction of protein - protein interactions between human host and a pathogen and its application to three pathogenic bacteria. Int. J. Biol. Macromol.Link(online publication)


[177] G. Agarwal, S. Mahajan, N. Srinivasan & A.G. de Brevern (2011) Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.PLoS ONE.Link(online publication)


[178] N. Srinivasan, G. Agarwal, R.M. Bhaskara, R. Gadkari, O. Krishnadev, B. Lakshmi, S. Mahajan, S. Mohanty, R. Mudgal, R. Rakshambikai, S. Sankaran, G. Sudha, L.S. Swapna & N. Tyagi (2011) Influence of genomic and other biological data sets in the understanding of protein structures, functions and interactions. Int. J. Knowledge Discovery Bioinf.Link(online publication)


[179] A.P. Joseph, N. Srinivasan & A.G. de Brevern (2011) Improvement of protein structure comparison using a structural alphabet. Biochimie.Link(online publication)


[180] J.C. Gelly, A.P. Joseph, N. Srinivasan & A.G. de Brevern (2011) iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucl. Acids Res.Link(online publication)


[181] O. Krishnadev & N. Srinivasan (2011) AlignHUSH : Alignment of HMMs Using Structure and Hydrophobicity information. BMC Bioinformatics.Link(online publication)


[182] R.M. Bhaskara & N. Srinivasan (2011) Stability of domain structures in multi-domain proteins Nature Sci. Rep.Link(online publication)


[183] R.M. Bhaskara, S. Mohanty, S. Mahajan, G. Agarwal, S. Balaji, V.S. Gowri & N. Srinivasan (2012) PALI- Phylogeny and alignment of homologous protein structures. Nucl Acids Res.(online publication)


[184] R. Mudgal, O. Krishnadev, S. Mukherjee & N. Srinivasan (2012) SUPFAM- Grouping of sequence families into superfamilies. Nucl Acids Res.(online publication)


[185] R. Rakshambikai, N. Tyagi, N. Garnier, D.C. Dinesh, K. Anamika, J. Martin, A. Krupa, K.R. Abhinandan & N. Srinivasan (2012) KinG –Ser/Thr/Tyr-specific protein kinases encoded in complete genomes. Nucl Acids Res.(online publication)


[186] R. Gayatri, S. Mohanty, R. Mudgal, O. Krishnadev & N. Srinivasan (2012) MulPSSM- Multiple PSSMs of protein domain families. Nucl Acids Res.>(online publication)


[187] L.S. Swapna, N. Rekha & N. Srinivasan (2012) Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly. Bioinformation.


[188] A.P. Joseph, N. Srinivasan & A.G. de Brevern (2012) Cis - trans peptide inter-conversions in structurally similar proteins. Amino Acids.


[189] S. Amarnath, T. Kawli, S. Mohanty, N. Srinivasan & V. Nanjundiah (2012) Pleiotropic Roles of a Ribosomal Protein in Dictyostelium discoideum. PLoS ONE


[190] R.A. Gadkari & N. Srinivasan (2012) Protein-protein interactions in clathrin vesicular assembly: Radial distribution of evolutionary constraints in interfaces.PLoS ONE


[191] B. Chawla, R.R. Kumar, N. Tyagi, G. Subramanian, N. Srinivasan, M.H. Park & R. Madhubala (2012) Unique Modification of the Eukaryotic Initiation Factor 5A shows the Presence of the Complete Hypusine Pathway in Leishmania donovani. PLoS ONE, 7, e33138.


[192] R. Rakshambikai, S. Yamunadevi, K. Anamika, N. Tyagi & N. Srinivasan (2012) Repertoire of protein kinases encoded in the genome of Takifugu rubripes. Comp. Fnl. Genomics, 2012, 258284.


[193] L.S. Swapna, S. Mahajan, A. G. de Brevern & N. Srinivasan (2012) Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. BMC Strl. Biol., 12, 6.


[194] L.S. Swapna, K. Srikeerthana & N. Srinivasan (2012) Extent of structural asymmetry in homodimeric proteins: prevalence and relevance. PLoS ONE, 7, e36688.


[195] S. Sandhya, R. Mudgal, C. Jayadev, K.R. Abhinandan, R. Sowdhamini & N. Srinivasan (2012) Cascaded walks in protein sequence space: Use of artificial sequences in remote homology detection between natural proteins. Mol. Biosyst., 8, 2076-2084.


[196] A.P. Joseph, H. Valadie, N. Srinivasan & A.G. de Brevern (2012) Local structural differences in homologous proteins: Specificities in different SCOP classes. PLoS ONE, 7, e38805.


[197] G. Sudha, S. Yamunadevi, N. Tyagi, S. Das & N. Srinivasan (2012) Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR. BMC Strl. Biol. 12, 28.


[198] A.P. Joseph, N. Srinivasan & A.G. de Brevern (2012) Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies. Biochimie, 94, 2025-2034.


[199] L.S. Swapna, R.M. Bhaskara, J. Sharma & N. Srinivasan (2012) Roles of residues in the interface of transient protein-protein complexes in their unbound forms. Nature Sci. Rep. 2, 334.


[200] L.S. Swapna, N. Srinivasan, D.L. Robertson & S.C. Lovell (2012) The origins of evolutionary signals used to predict protein-protein interactions. BMC Evol. Biol., 12, 238.Link


[201] R. Rakesh, R. Mudgal, R.M. Bhaskara & N. Srinivasan (2013) PALI- Phylogeny and alignment of homologous protein structures. Nucl Acids Res. http://www3.oup.co.uk/nar/database/summary/274 (online publication)Link


[202] R. Mudgal, O. Krishnadev & N. Srinivasan (2013) SUPFAM- Grouping of sequence families into superfamilies. Nucl Acids Res. http://www3.oup.co.uk/nar/database/summary/219 (online publication)


[203] M. Gnanavel, R. Rakshambikai & N. Srinivasan (2013) KinG –Ser/Thr/Tyr-specific protein kinases encoded in complete genomes. Nucl. Acids Res. http://www3.oup.co.uk/nar/database/summary/518 (on-line publication).Link


[204] G. Ramakrishnan, R. Mudgal, S. Mohanty, O. Krishnadev & N. Srinivasan (2013) MulPSSM- Multiple PSSMs of protein domain families. Nucl Acids Res. http://www3.oup.co.uk/nar/database/summary/844 (online publication)


[206] B. Lakshmi, G. Archunan & N. Srinivasan (2013) Propensities of amino acid residues in proteins for different regions of the Ramachandran map. In Biomolecular Forms and Functions (Eds. Manju Bansal & N. Srinivasan), World Scientific Press. pp.128-135.


[207] U. Ray, C. L. Roy, A. Kumar, P. Mani, A.P. Joseph, G.Sudha, D. P. Sarkar, N. Srinivasan & S. Das (2013) Inhibition of the interaction between NS3 protease and HCV IRES with a small peptide: A novel therapeutic strategy. Nature Mol. Therapy 21, 57-67.


[208] N. Tyagi & N. Srinivasan (2013) Recognition of Nontrivial Remote Homology Relationships Involving Proteins of Helicobacter pylori: Implications for Function Recognition. Methods Mol. Biol., 993, 155-175.


[209] S. Gabriel, S. Hareendran, D. Sen, R.A. Gadkari, G. Sudha, R. Selot, M. Hussain, R. Daksnamoorthy, R. Samuel, N. Srinivasan, A. Srivastava & G.R. Jayandharan (2013) Bio-engineering of AAV-2 capsid at specific serine, threonine or lysine residues improves its transduction efficiency in vitro and in vivo. Hum. Mol. Therapy Methods, 24, 80-93.


[210] S. Kaushik, E. Mutt, A. Chellappan, S. Sankaran, N. Srinivasan & R. Sowdhamini (2013) Improved detection of remote homologues using Cascade PSI_BLAST: Influence of neighboring protein families on sequence coverage. PLoS ONE 8, e56449.


[211] D. Sen,R. A Gadkari, G. Sudha, N. Gabriel,Y. Kumar, R. Selot, R. Samuel, N. Srinivasan, A. Srivastava, G.R Jayandharan (2013) Targeted modifications in adeno-associated virus serotype (AAV)-8 capsid improves its hepatic gene transfer efficiency in vivo. Hum. Mol. Therapy Methods, 24, 104-116.


[212] G. Ramakrishnan, V.S. Gowri, R. Mudgal, N.R. Chandra & N. Srinivasan (2013) Mining the sequence databases for homology detection: Application to recognition of functions of Trypanosoma brucei brucei proteins and drug targets. In Biological Data Mining and its Applications in Healthcare (Editors: X.-L. Li, S.-K. Ng & J.T.L. Wang), World Scientific, Singapore. pp. 3-31.


[213] S. Mohanty, M. Purwar, N. Srinivasan & N. Rekha (2013) Tethering preferences of domain families co-occurring in multi-domain proteins. Mol. BioSyst. 9, 1708-1725.


[214] A.-M.Hansen, R.Chaerkady, J.Sharma, J.J. Díaz-Mejía, N.Tyagi, S.Renuse, H.K.C. Jacob, S.M. Pinto, N.A Sahasrabuddhe, M.-K.Kim, B.Delanghe, N. Srinivasan, A.Emili, J.B.Kaper & A. Pandey (2013) The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathogens 9, e1003403.


[215] S.Mahajan, G.Agarwal, M.Iftekhar, B.Offmann, A.G.de Brevern & N.Srinivasan (2013) DoSA: Database of Structural Alignments. Database bat048, doi:10.1093/database/bat04.


[216] V.P.R. Vendra, G. Agarwal, V. Talla, N. Srinivasan & D. Balasubramanian (2013) Structural integrity of the Greek Key motif in βγ-crystallins is Vital for Central Eye Lens Transparency. PLoS ONE 8, e70336


[217] S. Mohanty, G. Ramakrishnan, P. Dave & N. Srinivasan (2013) Analysis of Sequence Divergence in Metabolic Proteins of Plasmodium falciparum: Implications for Remote Homology Detection. In "Frontiers in Protein and Peptide Sciences" (Ed. B. Dunn), Bentham Science Publishers. pp. 226-272.


[218] R. Rakshambikai, N. Srinivasan & K.T. Nishant (2013) Structural insights into Saccharomyces cerevisiae MSH4-MSH5 complex function using homology modeling. PLoS ONE 8, e78753.


[219] R.M. Bhaskara, A. Padhi & N. Srinivasan (2013) Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: Implications for 3-D modelling. Proteins 82, 1219-1234.


[220] L.S. Swapna, G. Sudha, R. Rakesh & N. Srinivasan (2014) Current trends in structural bioinformatics of protein-protein interactions. Proc. AP Acad. Sci., 15, 69-79.


[221] R. Rakesh, R.M. Bhaskara & N. Srinivasan (2014) PALI- Phylogeny and alignment of homologous protein structures. Nucl Acids Res. Link (online publication)


[222] R. Mudgal, O. Krishnadev & N. Srinivasan (2014) SUPFAM- Grouping of sequence families into superfamilies. Nucl Acids Res.Link (online publication)


[223] M. Gnanavel, R. Rakshambikai & N. Srinivasan (2014) KinG –Ser/Thr/Tyr-specific protein kinases encoded in complete genomes. Nucl. Acids Res. Link (on-line publication).


[224] G. Ramakrishnan, S. Mohanty, O. Krishnadev & N. Srinivasan (2014) MulPSSM- Multiple PSSMs of protein domain families. Nucl Acids Res. Link (online publication)


[225] S. Léonard, A.P. Joseph, N. Srinivasan, J.-C. Gelly & A.G. de Brevern (2013) mulPBA : an efficient multiple protein structure alignment method based on a structural alphabet. J. Biomol. Str. Dyn., 32, 661-668


[226] R. Rakshambikai, N. Srinivasan & R.A. Gadkari (2013) Repertoire of protein kinases encoded in the genome of zebrafish shows remarkably large population of PIM kinases. J. Bioinf. Comp. Biol., 12, 1350014.


[227] B. Lakshmi, C. Ramakrishnan, G. Archunan, R. Sowdhamini & N. Srinivasan (2013) Investigations of Ramachandran disallowed conformations in protein domain families. Int. J. Biol. Macromol, 63, 119-125.


[228] S. Mahajan, A.G. de Brevern, B. Offmann & N. Srinivasan (2013) Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. J. Biomol. Str. Dyn. 32, 751-758.


[229] R. Mudgal, R. Sowdhamini, N. Chandra, N. Srinivasan & S. Sandhya (2014) Filling in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability. J. Mol. Biol. 426, 962-979.


[230] R.M. Bhaskara, P. Mehrotra, R. Rakshambikai, M. Gnanavel, J. Martin & N. Srinivasan (2014) The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: A case study with immunoglobulins. Mol. Biosyst., 10, 1082-1093


[231] B. Lakshmi, C. Sinduja, G. Archunan & N. Srinivasan (2014) Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure. Prot. Sci. 23, 843-850.


[232] A.P. Joseph, P. Bhat, S. Das & N. Srinivasan (2014) Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA.. RNA Biol. RNA Biol. 11, 891-905.


[233] U.B. Reddy, R. Mullick, A. Kumar, G. Sudha, N. Srinivasan & S. Das (2014) Small molecule inhibitors of HCV replication from Pomegranate. Sci. Rep. 4, 5411.


[234] G. Sudha, R. Nussinov & N. Srinivasan (2014) An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. Prog. Biophys. Mol. Biol., 116, 141-150.


[235] S. Vishwanath & N. Srinivasan (2014) Chemical specificity and conformational flexibility in proteinase - inhibitor interaction: Scaffolds for promiscuous binding. Prog. Biophys. Mol. Biol. 116, 151-157.


[236] R. Rakshambikai, M. Gnanavel &. N. Srinivasan (2014) Hybrid and rogue kinases encoded in the genomes of model eukaryotes. PLoS ONE, 9, e107956.


[237] M. Gnanavel, P. Mehrotra, R. Rakshambikai, J. Martin, N. Srinivasan & R.M. Bhaskara, (2014) CLAP: A web server for automatic classification of proteins with special reference to multi-domain proteins. BMC Bioinformatics 15, 343.


[238] S. Mahajan, A. G. de Brevern, Y. -H. Sanejouand, N. Srinivasan & B. Offmann (2014) Use of a structural alphabet to find compatible folds for amino acid sequences. Prot. Sci., 24, 145-153.


[239] G. Ramakrishnan, B. Ochoa-Montano, U.S. Raghavender, R. Mudgal, A.G. Joshi, N.R. Chandra, R. Sowdhamini, T.L. Blundell & N. Srinivasan (2014) Enriching the annotation of Mycobacterium tuberculosis proteome using remote homology detection approaches: Insights into structure and function. Tuberculosis, 95, 14-25.


[240] G. Ramakrishnan, N.R. Chandra & N. Srinivasan (2014) From workstations to workbenches: Towards predicting physicochemically viable protein-protein interactions across a host and a pathogen. IUBMB Life, 66, 759-774.


[241] M. Manoharan, P. Sharma, Ch. Janaki, S. Shekhar, N. Srinivasan & R. Rakshambikai (2015) KinG – Kinases in genomes. Nucl. Acids Res. http://www.oxfordjournals.org/our_journals/nar/database/summary/518 (online publication)


[242] R. Mudgal, S. Sandhya, G. Kumar, R. Sowdhamini, N. R. Chandra & N. Srinivasan (2015) NrichD Database: Sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. Nucl. Acids Res., 43, 300-305.


[243] R. Kalaivani & N. Srinivasan (2015) A Gaussian network model study suggests that structural fluctuations are higher for inactive than active states of protein kinases. Mol. Biosyst., 11, 1079-1095.


[244] P. Bhat, S. Shwetha, D. Sharma, A.P. Joseph, N. Srinivasan & S. Das (2015) The beta hairpin structure within ribosomal protein S5 mediates interplay between domain II and IV and regulates HCV-IRES function. Nucl. Acids Res. 43, 2888-2901.


[245] R. Rakshambikai, M.Manoharan, M. Gnanavel &. N. Srinivasan (2015) Typical and atypical domain combinations of human protein kinases: Functions, disease causing mutations and conservation in other primates. RSC Advances, 5, 25132-25148.


[246] G.L. Holliday, A. Bairoch, P.G. Bagos, A. Chatonnet, D.J. Craik, R.D. Flinn, B. Henrissat, D. Landsman, G. Manning, N. Nagano, C.O’Donovan, K.D. Pruitt, N.D. Rawlings, M. Saier, R. Sowdhamini, M. Spedding, N. Srinivasan, G. Vriend, P.C. Babbitt & A. Bateman (2015) Key challenges for the creation and maintenance of specialist protein resources. Proteins 83, 1005-1013.


[247] P. Craveur, A.P Joseph, J. Esque, T.J. Narwani, F. Noel, N. Shinada, M. Goguet, L. Sylvain, P. Poulain, O. Bertrand, G. Faure, J. Rebehmed, A. Ghozlane, L.S. Swapna, R.M. Bhaskara, J. Barnoud, S. Téletchéa, V. Jallu, J. Cerny, B. Schneider, C. Etchebest, N. Srinivasan, J.-C. Gelly & A.G. de Brevern (2015) Protein flexibility in the light of structural alphabets. Frontiers in Mol. Biosci. 2, 20.


[248] P.C. Babbitt, P. G. Bagos, A. Bairoch, A. Bateman, A. Chatonnet, M. J. Chen, D. Craik, R. Finn, D. Gloriam, D. Haft, B. Henrissat, G. L. Holliday, V. Isberg, Q. Kaas, D. Landsman, N. Lenfant, G. Manning, N. Nagano, N. Srinivasan, C. O’Donovan, K. D. Pruitt, R. Sowdhamini, N. D. Rawlings, M. Saier. Jr, J. L. Sharman, M. Spedding, K. D. Tsirigos, A. Vastermark & G. Vriend (2015) Creating a Specialist Protein Resource Network: A meeting report for the Protein Bioinformatics and Community Resources Retreat. DATABASE :bav063.


[249] ­R. Metri, S. Hariharaputran, G. Ramakrishnan, P. Anand, U. S. Raghavender, B. Ochoa-Montaño, A. P. Higueruelo, R. Sowdhamini, N. R. Chandra, T. L. Blundell & N. Srinivasan (2015) SInCRe - Structural Interactome Computational Resource for Mycobacterium tuberculosis. DATABASE :bav060.


[250] G. Sudha, N. Naveenkumar & N. Srinivasan (2015) Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold. Proteins 83, 1766-1786.


[251] R. Mudgal, S. Sandhya, N. Chandra & N. Srinivasan (2015) De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive remote homology detection methods. Biology Direct 10, 38


[252] B. Lakshmi, M. Mishra, N. Srinivasan & G. Archunan (2015) Structure-based phylogenetic analysis on superfamily of lipocalins. PLoS ONE 10, e0135507


[253] G. Sudha, P. Singh, L.S. Swapna & N. Srinivasan (2015) Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes. Prot. Sci. 24, 1856-1873.


[254] G. Ramakrishnan, N. Chandra & N. Srinivasan (2015) Recognizing drug targets using evolutionary information: Implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv. Mol. Biosyst., 11, 3316-3331.


[255] G. Ramakrishnan, N. Srinivasan, P. Padmapriya & V. Natarajan (2015) Structure-influenced prediction of potential protein-protein interactions between human erythrocytes and Plasmodium falciparum. Bioinf. Biol. Insights 9, 195-206.


[256] S. Sandhya, R. Mudgal, G. Kumar, R. Sowdhamini & N. Srinivasan (2016) Protein sequence design and its applications. Curr. Opin. Strl. Biol. 37, 71-80.


[257] R. Rakesh & N. Srinivasan (2016) Improving the accuracy of fitted atomic models in cryo-EM density maps of protein assemblies using evolutionary information from aligned homologous proteins. Methods Mol. Biol. 1415, 193-209.


[258] Ch. Janaki, N. Srinivasan & M. Manoharan (2016) Classification of protein kinases influenced by conservation of substrate binding residues. Methods Mol. Biol. 1415, 301-313.


[259] K. Balamurugan, L. Bjorkhaug, S. Mahajan, S. Kanthimathi, P.R. Njolstad, N. Srinivasan, V. Mohan & V. Radha (2016) Structure - Function studies of HNF1A (MODY3) gene mutations in South Indian patients with monogenic diabetes. Clinical Genetics (in press).


[260] M. Das, M. Bhosale, N. Wadhwa, S.M. Ahmed, C. Bhaskarla, A. Kumar, N. Srinivasan & D. Nandi (2016) Importance of Amino Acids, Gln-119 and Tyr-376, in the S1 Pocket of Escherichia coli Peptidase N in Determining Substrate Specificity. Prot. Pept. Lett. (in press)


]261] R. Kalaivani, A.G. de Brevern & N. Srinivasan (2016) Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites. Proteins Str. Fn. Bioinf. (in press).


[262] M. Orozco & N. Srinivasan (2016) Theory and Simulation. Curr. Opin. Strl. Biol. (in press).


[263] G. Sudha & N. Srinivasan (2016) Comparative analyses of quaternary arrangements of homo-oligomeric proteins in superfamilies: Functional implications. Proteins: Str. Fn. Bioinf.. (in press).


[264] A.P. Joseph, L.S. Swapna, R. Rakesh & N. Srinivasan (2016) Use of evolutionary information in the fitting of atomic level protein models in low resolution cryoEM map of a protein assembly improves the accuracy of the fitting. (Submitted revised version).


[265] G. Ramakrishnan, A. Jain, N. Chandra & N. Srinivasan (2016) Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. (in revision).


[266] R. Rakesh, A.P. Joseph, R.M. Bhaskara & N. Srinivasan (2016) Structural and mechanistic insights into SF3b complex derived using an integrated approach guided by the cryo-EM density maps. (in revision).


Other Publications

[01] O. Krishnadev, K.V. Brinda, and Saraswathi Vishveshwara(2005) A Graph Spectral Analysis of the Structural Similarity Network of Protein Chains. PROTEINS: Structure, Function, and Bioinformatics 61:152–163.


[02] V.S. Gowri & Sankaran Sandhya (2006) Recent trends in Remote homology detection: an Indian Medley. Bioinformation 1(3), 94-96.


[03] Garima Agarwal (February 2007) Towards Logical Designs In Biology. Resonance, 29- 38.


[04]Ramachandra M.Bhaskara, C. M.Brijesh, Saveer Ahmed, Renee M.Borges. (2009) Perception of ultraviolet light by crab spiders and its role in selection of hunting sites. Journal of Comparative Physiology A 195:4, 409-417.


[05]S Indu, Senthil T Kumar, Sudhir Thakurela, Mansi Gupta,Ramachandra M Bhaskara, C Ramakrishnan, Raghavan Varadarajan(2010). Disulfide conformation and design at helix N-termini. Proteins:Structure, function and bioinformatics:78, 1228-1242.


[06]M. Bansal & N. Srinivasan (2013) Biomolecular forms and functions. World Scientific Press. & IISc Press.












 


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