Publications of Dr. H.A. Nagarajaram

Achary, M.S. and Nagarajaram, H.A. (2008) Comparative docking studies of CYP1b1 and its PCG associated mutant forms. J. Biosci. (Accepted)

Md. Tabrez Anwar Shamim, Mohammad Anwaruddin and H. A. Nagarajaram (2007) Support Vector Machine based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs. Bioinformatics 23:3320-3327

Suresh B. M. and Nagarajaram, H.A. (2007) IMEx: Imperfect Microsatellite Extractor. Bioinformatics 15 May 2007; 23: 1181 - 1187

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

Sreenu,V.B., Kumar, P., Nagaraju, J. and Nagarajaram, H.A. (2007) Simple sequence repeats in mycobacterial genomes J.Biosci. (A peer-reviewed special issue on Computational Biology) 32: 1-15

M.S. Achary, A. B.M. Reddy, S. Chakrabarti, S.G. Panicker, A.K.Mandal, N.Ahmed, D. Balasubramanian, S.E. Hasnain, and H.A.Nagarajaram (2006) Disease Causing Mutations in Proteins: Structural Analysis of the CYP1b1 Mutations Causing Primary Congenital Glaucoma in Humans Biophysical J. 91: 4329-4339

Sreenu,V.B., Kumar, P., Nagaraju, J. and Nagarajaram, H.A. (2006) Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity. BMC Genomics 7:78-88 (Highly accessed article)

Cheeran, A., Suganthan, R.B., Swapna, G., Bandey, I., Acharya, S., Nagarajaram, H.A. and Sen. R. (2005) E. coli RNA polymerase mutations located near the upstream edge of RNA:DNA hybrid and the beginning of the RNA exit channel are defective for transcription antitermination by N protein from lambdoid phage H-19B J.Mol. Biol 352: 28-43

Prasad,M.D., Muthulakshmi,M., Arunkumar,K.P., Madhu,M., Sreenu,V.B., Pavithra,V., Bose,B., Nagarajaram, H.A., Mita,K., Shimada, T. and Nagaraju, J.(2005) SilkSatDb: A microsatellite database of the silkworm, Bombyx mori. Nucleic Acids Research. 33: D403-D406.

R.K.Gundu, B.Bose, S.Swamynathan, V.B.Sreenu, N.Pavan, S.Acharya and H.A.Nagarajaram (2005) Frontiers in Bioinformatics Research: The Biodiversity Issues "Biodiversity : Status and Prospects" Editors: Pramod Tandon, Manju Sharma and Renu Swarup, Narosa Publishing House, New Delhi.

Ahmed Kamal, G. Ramesh, O. Srinivas, P. Ramulu, N. Laxman ,Tasneem Rehana, M.Deepak, M.S. Achary and H. A. Nagarajaram (2004). Design, Synthesis, and Evaluation of Mixed Imine-Amine Pyrrolobenzodiazepine Dimers with Efficient DNA-Binding Affinity and Potent CytotoxicityBio-organic & Medicinal Chemistry 12:5427-5436.

Buddhaditta Bose, Gyan Rajkumar, M. Narendar Pavan, A RadhaRama Devi, H.A. Nagarajaram. (2004) NBSdb: New Born Screening Database Indian Journal of Medical Informatics online.

Sreenu, V.B., Ranjitkumar, G., Swaminathan, S., Priya, S., Bose, B., Narendra Pavan, M., Nagaraju, J., Nagarajaram, H.A. (2004) MICdb - Database of Prokaryotic Microsatellites. Nucleic Acids Research Published in online database issue.

Majeed, A.A., Ahmed, N., Rao, K.R., Ghousunnissa, S., Kausar, F., Bose, B., Nagarajaram, H.A., Katoch, V.M., Cousins, D.V., Sechi, L.A., Gilman, R.H. and Hasnain, S.E. (2004) AmpliBASE MTTM: A Mycobacterium tuberculosis diversity knowledgebase. Bioinformatics 20:989-92.

V.B.Sreenu, G.Ranjitkumar, S.Swaminathan, S.Priya, B.Bose, M.N.Pavan, Geetha Thanu, J.Nagaraju and H.A.Nagarajaram (2003) MICAS: A fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. Applied Bioinformatics 2(3) 165-168.

G Ranjit Kumar, M Narendar Pavan, B. Bose, S Swaminathan, Geetha Thanu, P Prashanthi, B Phani Prasad, V B Sreenu, M Sridhar Achary and H A Nagarajaram (2003) EMBnet India Node (EIN) at the Centre for DNA Fingerprinting and Diagnostics: Serving the Indian sub-continent in Bioinformatics Bioinformatics India 1 2:67-77.

V.B.Sreenu, Vishwanath Alevoor, J.Nagaraju and H.A.Nagarajaram (2003) MICdb: Database of Prokaryotic Microsatellites Nucleic Acids Research 31 106-108.

H.A.Nagarajaram and S.E.Hasnain.(2003) Current Status of Post-Genomics Computational Biology "Computing and Information Sciences : Recent Trends" Editor: J.C.Misra, Narosa Publishing House, New Delhi.

A.Kamal, N. Laxman, G. Ramesh, P. Ramulu, O. Srinivas, K. Neelima, A. K. Kondapi, V. B. Sreenu and H.A.Nagarajaram 2002 Design, synthesis, and evaluation of new non-cross linking pyrrolobenzodiazepine dimers with efficient DNA-binding ability and potent antitumour activity J. Med. Chem 45 4679-4688.

E.Narayanan, H.A.Nagarajaram, C. Ramakrishnan and N.Srinivasan 2002 Influence of solvent molecules on the stereochemical code of glycine residue PROTEINS 49 326-334.

S.G.Panicker, A.B.M.Reddy, A.K.Mandal,N.Ahmed, H.A.Nagarajaram, S.E.Hasnain and D.B. Balasubramanian 2002 Identification of novel mutations causing familial primary congenital glaucoma in indian pedigrees Investigative Ophthalmology & Visual Science 43 1358-1366 2002.

J. Mendes, H.A. Nagarajaram, Cláudio M. Soares, Tom L. Blundell, Maria Arménia Carrondo 2001. Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure Biopolymers 59:2 72-86.

N. Campillo, H.A. Nagarajaram & I. Ghosh 2001. Phosphoribosyltransferase superfamily: A comparative structural analysis J.Mol.Model. 7 80-89.

D.F.Burke@, C.Dean@, H.A.Nagarajaram@, ... , Tom L.Blundell and K.Mizuguchi 1999. An iterative structure-assisted approach to sequence alignment and comparative modeling PROTEINS 3 55-60. @joint first authors.

H.A.Nagarajaram, B.V.B.Reddy and Tom L. Blundell 1999. Analysis and prediction of inter-strand packing distances between beta-sheets of globular proteins. Protein Eng. 12 1055-1062.

B.V.B.Reddy, H.A.Nagarajaram and Tom L. Blundell 1999. Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins Protein Sci. 8 573-586.

R.Sowdhamini, D.F.Burke, Jing-Fei Huang, K.Mizuguchi, H.A.Nagarajaram, N.Srinivasan, R.E.Stewart and Tom L. Blundell 1998. CAMPASS: A database of structurally aligned protein superfamilies Structure 61087-1094.

R.Sowdhamini, D. F. Burke, C. Deane, Jing-Fei Huang, K.Mizuguchi, H.A.Nagarajaram, J.P.Overington, N.Srinivasan, R.E.Steward and Tom L.Blundell 1998. Protein 3D structural databases: Domains, structurally aligned homologues and superfamilies Acta Crystallogr. D54 1168-1177.

K.Gunasekaran, H.A.Nagarajaram, C. Ramakrishnan and P. Balaram 1998. Stereochemical punctuation marks in protein structures: Glycine and Proline containing helix stop signals J.Mol.Biol. 275 917-932.

H.A.Nagarajaram, B.V.B.Reddy and T.L.Blundell 1997. Packing of secondary structural elements in proteins - An analysis Prot.Sci. 6 pp87.

R.Sowdhamini, N.Srinivasan, S.Rufino, H.A.Nagarajaram, K.Mizuguchi, D.F.Burke, K.Guruprasad, R.Stewart and T.L.Blundell 1997. Protein domains, superfamilies and functions Prot. Sci. 6 pp75.

R.Sowdhamini, N.Srinivasan, S.Rufino, H.A.Nagarajaram, K.Mizuguchi, D.F.Burke, K.Guruprasad, R.Stewart and T.L.Blundell 1996. Protein domains, superfamilies and functions Fold. Des., 1(supplement) pp. S59.

R.Varadarajan, H.A.Nagarajaram and C. Ramakrishnan 1996. A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence Proc. Natl. Acad. Sci. (USA) 93 13908-13913.

H.A.Nagarajaram and C. Ramakrishnan 1995. Stereochemical studies on cyclic peptides - Detailed energy minimisation studies on hydrogen bonded all-trans cyclic pentapeptide backbones J.Biosci. 20 591-611.

H.A.Nagarajaram, R.Sowdhamini, C.Ramakrishnan and P.Balaram 1993. Termination of right handed helices in proteins by the residues in left handed helical conformation FEBS letters 321 79-83.

H.A.Nagarajaram, P.K.Paul, K. Ramanarayanan, K.V.Soman and C. Ramakrishnan 1992. Conformational studies on beta-bends containing a cis peptide unit Int. J. Peptides Proteins Res. 40 383-394.

H.A.Nagarajaram and C. Ramakrishnan 1991. Energy minimisation studies on cyclic pentapeptides Indian J. Phys. 65B 449-454.