BOOK

  • Rao, V.S.R., Qasba, P.K., Balaji, P.V., and Chandrasekaran, R. (1998) Conformation of Carbohydrates. Harwood Academic Publishers, The Netherlands.

    OBITUARY

  • Sundararajan, P.R., Balaji, P.V. and Yathindra, N. (2013) Professor Vallurupalli Sita Raghavendra Rao. Curr. Sci., 105, 1303-1304.

    ARTICLES IN PEER-REVIEWED JOURNALS

  • Busi, R., Machingal, P., Hemachandra, N. and Balaji, P.V. (2024) How suitable are clustering methods for functional annotation of proteins? bioRxiv. doi: https://doi.org/10.1101/2024.12.26.630370

  • Machingal, P., Busi, R., Hemachandra, N. and Balaji, P.V. (2024) Identifying key amino acid types that distinguish paralogous proteins using Shapley value based feature subset selection. bioRxiv. doi: https://doi.org/10.1101/2024.04.26.591291

  • Srivastava, J. and Balaji, P.V. (2022) Clues to reaction specificity in PLP-dependent fold type I aminotransferases of monosacchride biosynthesis. Proteins: Structure, Function, and Bioinformatics, 90, 1247-1258. doi.org/10.1002/prot.26305

  • Srivastava, J., Sunthar, P. and Balaji, P.V. (2022) Monosacchraide biosynthesis pathways database. Glycobiology, 31, 1636-1644. doi.org/10.1093/glycob/cwab030

  • Srivastava, J., Hembrom, R., Kumawat, A., and Balaji, P.V. (2021) Searching sequence ddatabases for functional homologs using profile HMMs: how to set bit score thresholds? bioRxiv. doi: https://doi.org/10.1101/2021.06.24.449764

  • Anu Prabha and Balaji, P.V. (2021) Characterization of left-handed beta helix-domains, and identification and functional annotation of proteins containing such domains. Proteins: structure, function and bioinformatics, 89, 6-20. PubMed id 32748987 doi.org/10.1002/prot.259990

  • Srivastava, J., Sunthar, P. and Balaji, P.V. (2020) The glycan alphabet is not universal: a hypothesis. Microbial Genomics, 6, mgen000452. PubMed id 33048043. doi.org/10.1099/mgen.0.000452.

  • Mishra, T. and Balaji, P.V. (2019) Highly clade-specific biosynthesis of rhamnose: present in all plants and in only 42% of prokaryotes. Only pseudomonas uses both D- and L-rhamnose. bioRxiv. doi: https://doi.org/10.1101/854612.

  • Kaundinya, C.R., Savithri, H.S., Rao, K.K. and Balaji, P.V. (2018) EpsM from Bacillus subtilis 168 has UDP-2,4,6-trideoxy 2-acetamido 4-amino glucose acetyltransferase activity in vitro. Biochem. Biophys. Res. Comm., 505, 1057-1062. PubMed id 30314705

  • Kaundinya, C.R., Savithri, H.S., Rao, K.K. and Balaji, P.V. (2018) In vitro characterization of N-terminal truncated EpsC from Bacillus subtilis 168, a UDP-N-acetyl 4,6-dehydratase. Arch. Biochem. Biophys., 657, 78-88. PubMed id 30222950

  • Kaundinya, C.R., Savithri, H.S., Rao, K.K. and Balaji, P.V. (2018) EpsN from Bacillus subtilis 168 has UDP 2,6-dideoxy 2-acetamido 4-keto aminotransferase activity in vitro. Glycobiology, 28, 802-812. PubMed id 29982582

  • Pardeshi, P., Rao, K.K. and Balaji, P.V. (2017) Rv3634c from Mycobacterium tuberculosis H37Rv encodes an enzyme with UDP-Gal/Glc and UDP-GalNAc 4-epimerase activities. PLoS ONE, 12, e0175193. PubMed id 28403215

  • Prabhakar, P.K., Srivastava, A., Rao, K.K. and Balaji, P.V. (2016) Monomerization alters the dynamics of the lid region in Campylobacter jejuni CstII: an MD simulation study. J. Biomolec. Struct. Dyn., 34, 778-791. PubMed id 26208676

  • Srivastava, A. and Balaji, P.V. (2015) Molecular events during the early stages of aggregation of GNNQQNY: an all atom MD simulation study of randomly dispersed peptides. J. Struct. Biol., 192, 376-391. With cover page illustration. PubMed id 26433030

  • Prabhakar, P.K., Rao, K.K. and Balaji, P.V. (2014) The Cys78-Asn88 loop region of the Campylobacter jejuni CstII is essential for a2,3-sialyltransferase activity: analysis of the His85 mutants. J. Biochem., 156, 229-238. PubMed id 24817703

  • Srivastava, A. and Balaji, P.V. (2014) Interplay of sequence, topology, and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS ONE, 9, e96660. PubMed id 24817093

  • Kumar, M. and Balaji, P.V. (2014) CH...pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location and contribution to protein stability. J. Mol. Model., 20, 2136(1-14). PubMed id 24526385

  • Kumari, M., Balaji, P.V. and Sunoj, R.B. (2012) Exploration of CH...pi mediated stacking interactions in saccharide : aromatic residue complexes through conformational sampling. Carbohydr. Res., 361, 133-140. PubMed id 23017780

  • Srivastava, A. and Balaji, P.V. (2012) Size, orientation and organization of oligomers that nucleate amyloid fibrils: clues from MD simulations of pre-formed aggregates. Biochim. Biophys. Acta (Proteins and Proteomics), 1824, 963-973. PubMed id 22609417

  • Kumari, M., Balaji, P.V. and Sunoj, R.B. (2012) Conformational mapping and energetics of saccharide-aromatic residue interactions: implications for the discrimination of anomers and epimers and in protein engineering. Org. Biomol. Chem., 10, 4186-4200. PubMed id 22527756

  • Balaji, P.V. (2011) Contribution of C-H...pi interactions to the affinity and specificity of carbohydrate binding sites. Mini Rev. Org. Chem., 8, 222-228. DOI: 10.2174/157019311796197355

  • Patel, R.Y. and Balaji, P.V. (2011) Structure and dynamics of glycosphingolipids in lipid bilayers: insights from molecular dynamics simulations. Int. J. Carbohydr. Chem., Vol. 2011, Article ID 950256. DOI: 10.1155/2011/950256.

  • Kumar, M. and Balaji, P.V. (2011) Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes. Mol. Biosyst., 7, 1629-1645. Placed in the top 2% of published articles in Biology and Medicine by a member of the Faculty of 1000 (F1000).

  • Kumari, M., Balaji, P.V. and Sunoj, R.B. (2011) Quantification of binding affinities of essential sugars with tryptophan analogue and the ubiquitous role of C-H...pi interactions. Phys. Chem. Chem. Phys., 13, 6517-6530.

  • Jaiswal, R., Patel, .Y., Asthana, J., Jindal, B., Balaji, P.V. and Dulal Panda (2010) E93R substitution of Escherichia coli FtsZ induces bundling of protofilaments, reduces GTPase activity and impairs bacterial cytokinesis. J. Biol. Chem., 285, 31796-31805.

  • Rathinasamy, K., Jindal, B., Asthana, J., Singh, P., Balaji, P.V. and Panda, D. (2010) Griseofulvin stabilizes microtubule dynamics, activates p53 and inhibits the proliferation of MCF-7 cells synergistically with vinblastine. BMC Cancer, 10, 213.

  • Patel, R.Y. and Balaji, P.V. (2008) Characterization of symmetric and asymmetric lipid bilayers composed of varying concentrations of ganglioside GM1 and DPPC. J. Phys. Chem B, 112, 3346-3356.

  • Patel, R.Y. and Balaji, P.V. (2007) Length and composition analysis of the cytoplasmic, transmembrane and stem regions of human Golgi glycosyltransferases. Protein Pept. Lett., 14, 601-609.

  • Patel, R.Y. and Balaji, P.V. (2007) Fold recognition and comparative modeling of human beta3GalT I, II, IV, V and VI and beta3GalNAcT I: prediction of residues conferring acceptor substrate specificity. J. Mol. Graph. Model., 26, 255-268.

  • Sujatha, M.S., Sasidhar, Y.U. and Balaji, P.V. (2007) MP2/6-311++G(d,p) study on galactose-aromatic residue analog complexes in different position-orientations of the saccharide relative to aromatic residues. J. Mol. Struct. (Theochem), 814, 11-24.

  • Patel, R.Y. and Balaji, P.V. (2007) Characterization of the conformational and orientational dynamics of ganglioside GM1 in a dipalmitoylphosphatidylcholine bilayer by molecular dynamics simulations. Biochim. Biophys. Acta (Biomembranes), 1768, 1628-1640.

  • Patel, S., Balaji, P.V., Sasidhar, Y.U. (2007) The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between alpha-helical and beta-hairpin conformations mediated by collapsed conformational states. J. Pept. Sci., 13, 314-326.

  • Idicula-Thomas, S. and Balaji, P.V. (2007) Correlation between the structural stability and aggregation propensity of proteins. In Silico Biol., 7, 0023. Article

  • Idicula-Thomas, S. and Balaji, P.V. (2007) Protein aggregation: a perspective from amyloid and inclusion body formation. Curr. Sci., 92, 758-767. PDF

  • The NMITLI-BioSuite Team (2007) BioSuite: a comprehensive bioinformatics software package (a unique industry-academia collaboration). Curr. Sci., 92, 29-38. PDF

  • Sujatha, M. S., and Balaji, P.V. (2006) Fold recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni. BMC Struct. Biol., 6, 9. PDF Coordinates of top models

  • Patel, S., Sista, P., Balaji, P.V., Sasidhar, Y.U. (2006) Beta-hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease. J. Mol. Graph. Model., 25, 103-115.

  • Idicula-Thomas, S., Kulkarni, A.J., Kulkarni, B.D., Jayaraman, V.K. and Balaji, P.V. (2006) A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on over-expression in Escherichia coli. Bioinformatics, 22, 278-284.

  • Patel, R.Y. and Balaji, P.V. (2006) Identification of linkage-specific sequence motifs in sialyltransferases. Glycobiology, 16, 108-116.

  • Patel, R.Y. and Balaji, P.V. (2005) Effect of the choice of pressure coupling method on the spontaneous aggregation of DPPC molecules. J. Phys. Chem. B, 109, 14667-14674.

  • Sujatha, M.S., Sasidhar, Y.U. and Balaji, P.V. (2005) Insights into the role of aromatic residue in galactose-binding sites: MP2/6-311G++** study on galactose- and glucose-aromatic residue analog complexes.   Biochemistry, 44, 8554-8562.

  • Idicula-Thomas, S. and Balaji, P.V. (2005) Understanding the relationhip between the primary structure of proteins and their amyloidogenic propensity: clues from inclusion body formation. Prot. Eng. Des. Sel., 18, 175-180.

  • Idicula-Thomas, S. and Balaji, P.V. (2005) Understanding the relationship between the primary structure of proteins and their propensity to be soluble on overexpression in Escherichia coli.   Prot. Sci., 14, 582-592.

  • Sujatha, M.S., Sasidhar,Y.U. and Balaji, P.V. (2004) Energetics of galactose- and glucose-aromatic amino acid interactions: implications for binding in galactose-specific proteins. Prot. Sci., 13, 2502-2514.   

  • Sujatha, M.S. and Balaji, P.V. (2004) Identification of common structural features of binding sites in galactose-specific proteins. Proteins. Struct. Funct. Bioinformatics., 55, 44-65.

  • Vasudevan, S.V. and Balaji, P.V. (2002) Comparative analysis of ganglioside conformations by MD simulations: implications for specific recognition by proteins. J. Mol. Struct. (Theochem), 583, 215-232.

  • Vasudevan, S.V. and Balaji, P.V. (2002) Conformation, orientation and dynamics of dodecylphosphocholine in micellar aggregate: a 3.2 ns molecular dynamics simulation study. Ind. J. Biochem. Biophys., 39, 87-92.

  • Vasudevan, S.V. and Balaji, P.V. (2002) Molecular dynamics simulation of alpha2-8-linked disialoside: conformational flexibility and implications for binding to proteins. Biopolymers, 63, 168-180.

  • Vasudevan, S.V. and Balaji, P.V. (2001) Dynamics of ganglioside headgroup in lipid environment: molecular dynamics simulations of GM1 embedded in dodecylphosphocholine micelle. J. Phys. Chem. B, 105, 7033-7041.

  • Ramakrishnan, B., Balaji, P.V. and Qasba, P.K. (2002) Crystal structure of beta1,4-galactosyltransferase complex with UDP-Gal reveals an oligosaccharide acceptor binding site. J. Mol. Biol., 318, 491-502.

  • Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1997) Conformational analysis of Asn-linked oligosaccharides: implications in biological processes. J. Mol. Struct. (Theochem)., 395-396, 333-360. PDF

  • Balaji, P.V., Rao, V.S.R. and Qasba, P.K. (1996) Molecular dynamics simulations of hybrid and complex type oligosaccharides. Int. J. Biol. Macromol., 18, 101-114. PDF

  • Boeggeman, E.E., Balaji, P.V. and Qasba, P.K. (1995) Functional domains of bovine beta1->4-galactosyltransferase. Glycoconj. J., 12, 865-878. PDF

  • Rao, V.S.R., Balaji, P.V. and Qasba, P.K. (1995) Controversial iduronate ring conformation. Glycobiology, 5, 273-276. PDF

  • Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1994) Molecular dynamics simulations of oligosaccharides and their conformation in the crystal structure of lectin-carbohydrate complex: importance of the torsion angle psi for the orientation of alpha1->6-arm. Glycobiology, 4, 805-815. [PMID: 7734844; Medline]

  • Balaji, P.V., Qasba, P.K. and Rao, V.S.R. (1994) Molecular dynamics simulations of high mannose oligosaccharides. Glycobiology, 4, 497-515. [PMID: 7827412; Medline]

  • Balaji, P.V., Qasba, P.K. and Rao, V.S.R. (1993) Molecular dynamics study of asialoglycoprotein receptor ligands. Biochemistry, 32, 12599-12611. [PMID: 8251478; Medline]

  • Boeggeman, E.E., Balaji, P.V., Sethi, N., Masibay, A.S. and Qasba, P.K. (1993) Expression of deletion constructs of bovine beta1->4-galactosyltransferase in Escherichia coli: importance of Cys134 for its activity. Prot. Eng., 6, 779-785. [PMID: 8248102; Medline]

  • Masibay, A.S., Balaji, P.V., Boeggeman, E.E. and Qasba, P.K. (1993) Mutational analysis of the Golgi retention signal of bovine beta1->4 galactosyltransferase. J. Biol. Chem., 268, 9908-9916. PDF

  • Seshadri, K., Balaji, P.V., Rao, V.S.R. and Vishveshwara, S. (1993) Computer modeling studies of ribonuclease A - pyrimidine nucleotide complexes. J. Biomol. Struct. Dyn., 11, 395-415. [PMID: 8286064; Medline]

  • Balaji, P.V., Saenger, W. and Rao, V.S.R. (1993) Computer modelling studies on the binding of 2',5'-linked dinucleotides to RNase T1 - Influence of subsite interactions on substrate binding. J. Biomol. Struct. Dyn., 10, 891-903. [PMID: 8391269; Medline]

  • Balaji, P.V. and Rao, V.S.R. (1992) Computer modeling studies on the subsite interactions of ribonuclease T1. J. Biomol. Struct. Dyn., 9, 971-989. [PMID: 1326282; Medline]

  • Balaji, P.V., Saenger, W. and Rao, V.S.R. (1992) Modes of binding of 2'-AMP to RNase T1 - A computer modeling study. J. Biomol. Struct. Dyn., 9, 959-969. [PMID: 1524709; Medline]

  • Balaji, P.V. and Rao, V.S.R. (1991) Computer modelling studies of ribonuclease T1-2'-deoxy-2'-fluoroguanylyl-(3',5')-cytidine complex. Ind. J. Biochem. Biophys., 28, 358-362. [PMID: 1812067; Medline]

  • Balaji, P.V., Saenger, W. and Rao, V.S.R. (1991) Modes of binding of guanosine monophosphates to ribonuclease T1 - A computer-modelling study. Curr. Sci., 60, 363-373. PDF

  • Balaji, P.V., Saenger, W. and Rao, V.S.R. (1991) Computer modeling studies on the mechanism of action of ribonuclease T1. J. Biomol. Struct. Dyn., 9, 215-231. [PMID: 1741959; Medline]

  • Balaji, P.V., Saenger, W. and Rao, V.S.R. (1990) Computer modeling studies of ribonuclease T1-guanosine monophosphate complexes. Biopolymers, 30, 257-272. [PMID: 2177661; Medline]

  • Rao, V.S.R., Biswas, M., Mukhopadhyay, C. and Balaji, P.V. (1989) Computer simulation of protein-carbohydrate complexes: application to arabinose-binding protein and pea lectin. J. Mol. Struct., 194, 203-214. PDF

    ARTICLES IN CONFERENCE PROCEEDINGS

  • Patel, R.Y. and Balaji, P.V. (2006) Molecular dynamics simulations of spontaneous aggregation of dipalmitoyl-phosphatidylcholine into cylindrical micelle and bilayer from the same starting conformation. In Mathematical Biology: Recent Trends. Proceedings of the International Conference on Mathematical Biology ICMB-2004 (Chandra, P. and Kumar, B.V.R., eds.), pp 199-205, Anamaya Publishers, New Delhi.

  • Sujatha, M.S. and Balaji, P.V. (2006) Binding site features of galactose-specific proteins are fuzzy. In Mathematical Biology: Recent Trends. Proceedings of the International Conference on Mathematical Biology ICMB-2004 (Chandra, P. and Kumar, B.V.R., eds.), pp 181-186, Anamaya Publishers, New Delhi.

  • Seshu Kumar, K.V., Nagaraja, G. and Balaji, P.V. (2002) Locally aligned terminal distinguishable languages and identification of proteins. In Artificial Intelligence: Theory and Practice. Proceedings of the International Conference KBCS-2002 (Sasikumar et al., eds.), pp 311-321, Vikas Publishing House Pvt. Ltd., New Delhi. PS file

    SYMPOSIUM ABSTRACTS PUBLISHED IN JOURNALS

  • Qasba, P.K., Ramakrishnan, B. and Balaji, P.V. (2002) Oligosaccharide binding site of b1,4-galactosyltransferases (Gal-Ts) defined by docking various glycan substrates in the binding site. 223rd Am. Chem. Soc. National Meeting on Carbohydrates and Therapeutics Glycoproteins (Code: CARB). Abstract

  • Vasudevan, S.V. and Balaji, P.V. (1999) Headgroup dynamics of GM1 anchored in dodecylphosphocholine micelle. J. Biosci. 24, Suppl. 1, 497.

  • Boeggeman, E.E., Balaji, P.V. and Qasba, P.K. (1995) Functional domains of bovine beta1->4-galactosyltransferase. Glycoconj. J., 12, 451-452.

  • Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1995) Conformations of oligosaccharides accessed by molecular dynamics simulations and selected in the lectin-carbohydrate complexes. Glycoconj. J., 12, 430.

  • Qasba, P.K., Balaji, P.V. and Rao, V.S.R. (1995) Molecular dynamics simulations of oligosaccharides and their conformation in lectin- carbohydrate complexes. Abs. Am. Chem. Soc., 209, 101.

  • Balaji, P.V., Qasba, P.K. and Rao, V.S.R. (1994) Molecular dynamics simulations of high mannose oligosaccharides: possible pathways for processing of Man9GlcNAc2 to Man5GlcNAc2. J. Cell. Biochem., 18D, s269.

  • Qasba, P.K., Masibay, A.S., Boeggeman, E.E. and Balaji, P.V. (1993) Study of the functional domains of beta1->4-galactosyltransferase through the expression of the deletion constructs of cDNA in E. coli and mammalian cells: disulphide bond between Cys134 and Cys247 is required for folding and enzyme activity while the transmembrane domain is essential for stable expression in mammalian cells. Prot. Engng., 6, s99.

    Return to
    P.V.Balaji       Department of Biosciences & Bioengineering       IIT Bombay