[108] Ganesan Pugalenthi, Krishna Kumar Kandaswamy, PN. Suganthan, G.Archunan and R.Sowdhamini (2010). Identification of functionally diverse lipocalin proteins from sequence information using support vector machine.  Amino Acids (in press) [107] Caroline Koshy, Marimuthu Parthiban, and Ramanathan Sowdhamini (2010). 100ns Molecular Dynamics Simulations to study intramolecular conformational changes in Bax.  Journal of Biomolecular Structure and Dynamics (in press). [106] Ramalingam Rajkumar, Subramanya Prakash, Govindaraju Archunan and Ramanathan Sowdhamini (2010). Primary Structural Documentation of the Major Urinary Protein of the Indian Commensal Rat (Rattus rattus) Using a Proteomics Platform. Protein and Peptide Letters (in press). [105]  Padmanabhan Anbazhagan, Meera Purushottam, H. B. Kiran Kumar, Odity Mukherjee, Sanjeev Jain and Ramanathan Sowdhamini (2010) Phylogenetic Analysis and Selection Pressures of 5-HT Receptors in Human and Non-human Primates: Receptor of an Ancient Neurotransmitter. Journal of Biomolecular Structure & Dynamics 27:5 [104]  Parthiban.M, P.Shanmughavel and R.Sowdhamini (2009) In silico Point Mutations and Evolutionary Trace Analysis of Nicotinic Acetylcholine Receptors in deciphering ligand-binding surfaces. J Mol Model.(Accepted) [103] Khader Shameer, P. Nagarajan, K. Gaurav and R. Sowdhamini (2009)  3PFDB – A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach BioDataMining 2:8 [102] P. Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar, and R. Sowdhamini (2009) HORI:  A web server to compute Higher Order Residue Interactions in protein structures ( Accepted to APBC 2010 , to be published in BMC Bioinformatics ) [101] K. Kanagarajadurai, S. Kalaimathy, P. Nagarajan and R. Sowdhamini (2009) A bioinformatics protocol for rigorous structure-based sequence alignment of distantly related proteins. Nature Protocols Network [ Link ] [100] Karuppiah Kanagarajadurai, Manoharan Malini, Aditi Bhattacharya, Mitradas M. Panicker and Ramanathan Sowdhamini (2009) Molecular Modeling and docking studies of human 5-hydroxytryptamine A (5-HT2A) receptor for the identification of hotspots for ligand binding. Molecular Bio Systems 5, 1877 - 1888 [99] K. Shameer, S Ambika, Susan Mary Varghese, N. Karaba, M. Udayakumar, and R. Sowdhamini  (2009) STIFDB – Arabidopsis Stress responsive TranscrIption Factor DataBase. Int J Plant Genomics 2009:583429 [98] Harinath Doodhi, Debnath Ghosal, Mahalakshmi Krishnamurthy, Swadhin C. Jana, Divya Shamala, Anirban Bhaduri, R. Sowdhamini, and Krishanu Ray (2009) KAP, the Accessory Subunit of Kinesin-2, Binds the Predicted Coiled-Coil Stalk of the Motor Subunits . Biochemistry 48(10) 2248-2260 [97] Sankaran Sandhya, Saane Sudha Rani, Barah Pankaj, Madabosse Kande Govind, Bernard Offman, Narayanaswamy Srinivasan and Ramanathan Sowdhamini (2009) Length variations amongst protein domain superfamilies and consequences on structure and function . PLoS One   4(3): e4981 [96] Bhaduri, A., Kalaimathy, S. and Sowdhamini, R. (2009)Conservation and Divergence among Salmonella enterica subspecies . Infectious Disorders-Drug Targets special in silico issue 9(3): 248-256 [95] P.Sundaramurthy, Sunita Gakkhar and R. Sowdhamini (2008) Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each ther: A systems approach . Bioinformation 3(6): 244-249 [94] P.Sundaramurthy, Sunita Gakkhar and R. Sowdhamini (2008) Computational prediction and analysis of impact of the cross-talks between JNK and P38 kinase cascades . Bioinformation 3(6): 250-254 [93] Rajesh R Thangudu, Malini Manoharan, N Srinivasan, Fraderic Cadet, R Sowdhamini and Bernard Offmann (2008) Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families . BMC Structural Biology 8:55. [92] Lokesh P. Tripathi and R. Sowdhamin (2008) Genome wide survey of prokaryotic serine proteases : Analysis of distribution and architecture of five serine protease families in prokaryotes . BMC Genomics 9:549 [91] Pugalenthi G, Tang K, Suganthan PN, Archunan G, Sowdhamini R.  (2007) A machine learning approach for the identification of odorant binding proteins from sequence-derived properties . BMC Bioinformatics 8:351.  [90] Ambika Shyam Sundar, Susan Mary Varghese, Khader Shameer, Nataraja Karaba,Makarla Udayakumar and Ramanathan Sowdhamini (2008) STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana . Bioinformation 2, 431-437. [89] Padmanabhan Anbazhagan, Meera Purushottam, H. B. Kiran Kumar,Shobana Kubendran, Odity Mukherjee, Samir Kumar Brahmachari,Sanjeev Jain and Ramanathan Sowdhamini (2008)Evolutionary analysis of PHLPP1 gene in humans and non-human primates . Bioinformation 2, 471-474. [88] Chilamakuri CS Reddy, Khader Shameer, Bernard Offmann and Ramanthan Sowdhamini (2008) PURE: A webserver for the Prediction of domains in Unassigned Regions in proteins . BMC Bioinformatics 9:281 [87]Neha Vyas, Debanjan Goswami, Manonmani A, Pranav Sharma, H.A. Ranganath, K. VijayRaghavan, L.S. Shashidhara, R. Sowdhamini and Satyajit Mayor (2008) Nanoscale organization of Hh is essential for long range signaling . Cell 133(7):1214-27 [86] Kanagarajadurai K. and Ramanathan Sowdhamini (2008) Sequence and structural analyses of interleukin-8-like chemokine superfamily . Insilico Biology 8, 0025. [85] Sandhya S, Pankaj B, Govind MK, Offmann B, Srinivasan N, Sowdhamini R. (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 Struct Biol. 8:28. [84] Vikram Alva, Divya P. Syamala Devi and R. Sowdhamini (2008) COILCHECK: an interactive server for the analysis of interface regions in coiled coils Protein and Pept Lett .  15:33-38 [83] Ganesan Pugalenthi, P. N. Suganthan, R. Sowdhamini and Saikat Chakrabarti (2008) MegaMotifBase: a database of structural motifs in protein families and superfamilies . Nucl. Acids Res. 36:D218-21. [82] Parantu K. Shah, Lokesh P. Tripathi, Lars Juhl Jensen, Murad Gahnim, Christopher Mason, Eileen E Furlong, Veronica Rodrigues, Kevin P. White, Peer Bork and R. Sowdhamini (2007) Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families .Gene  407(1-2):199-215 [81] Chilamakuri C Sekhar Reddy, Khader Shameer, Offmann Bernard and Ramanathan Sowdhamini (2007) PURE: A web server for querying the relationship between Pre-existing domains and Unassigned Regions in proteins Nature Protocols [Link] [80] Khader Shameer & Ramanathan Sowdhamini (2007) IWS: Integrated Web Server for protein sequence and structure analysis Bioinformation 2(3): 86-90 [79] Lokesh P. Tripathi and Ramanathan Sowdhamini (2007) Genome-wide survey of protein families and superfamilies Biobytes [Link] [78] M. Vijayalakshmi, G.V.Shivashankar and R. Sowdhamini, (2007) Simulations of SIN mutations and histone variants in human nucleosomes reveal altered protein-DNA and core histone interactions . J. Bio. Struc. Dyn. 25(3):207-18 [77] Parikh N, Koshy C, Dhayabharan V, Perumalsamy LR, Sowdhamini R, Sarin A (2007) The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL BMC Cell Biology 8:16 (23 May) [76] Bhaduri A, and Sowdhamini R (2007) O-protein phosphatases in Signal Transduction Pathways in “New Trends in Bioinformatics” .(Book Chapter) P. Shanmugavel (ed):40-58 [75] Pugalenthi G, Suganthan PN, Sowdhamini R, Chakrabarti S.(2007)SMotif: A server for structural motifs in proteins. Bioinformatics. 23(5):637-638 [74] Raghu Prasad Rao Metpally, Ramakrishnan Vigneshwar and Ramanathan Sowdhamini Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis (2007) J. Biosci. 32(1):43-50 [73] Gadkari RA, Sandhya S, Sowdhamini R, Dighe RR.(2007) The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor .Mol Cell Endocrinol.,260-262:23-32 [72] Khajamohiddin S, Babu PS, Chakka D, Merrick M, Bhaduri A, Sowdhamini R, Siddavattam D (2006) A novel meta-cleavage product hydrolase from Flavobacterium sp. ATCC27551 .Biochem Biophys Res Commun.,351(3):675-81 [71] Lokesh P Tripathi and R Sowdhamini (2006) Cross genome comparisons of serine proteases in Arabidopsis and rice . BMC Genomics,7:200 [70] Chakrabarti, S., Manohari, G. and R. Sowdhamini (2006) SSToSS -Sequence-Structural Templates of Single-member Superfamilies. Nucl.Acids Res, . http://www3.oup.co.uk/nar/database/summary/530 (web publication) [69] Pugalenthi G., Bhaduri A. and Sowdhamini R. (2006) iMOTdb- Spatially interacting motifs in proteins. Nucl. Acids Res.,http://www3.oup.co.uk/nar/database/summary/829 (web publication) [68] Chandrashekar, C., Manonmani, A., Babu, M. and Sowdhamini, R.(2006) Enhanced structure prediction of gene products containing adenylyl cyclase . In Silico Biol. 6 0033: http://www.bioinfo.de/isb/2006/06/0033/main.html [67] Chakrabarti, S., Manohari, G., Pugalenthi, G. and Sowdhamini, R. (2006) SSToSS: Sequence Structural Templates of Single-member superfamilies . In Silico Biol6 0029: http://www.bioinfo.de/isb/2006/06/0029/main.html [66] ** Rhana, R., Sandhya, S., Abhinandan, K.R., Chakrabarthi S, Sowdhamini, R. and Srinivasan, N.(2006) Cascade PSI-BLAST Web server: A remote homology search tool for relating protein domains. Nucl. Acids Res.,34: W143-W146. [65] ** Pugalenthi, G., Shameer, K. Srinivasan, N. and Sowdhamini, R.(2006) HARMONY: a web-server for the assessment of protein structures Nucl. Acids Res., 34: W143-W146 . [64] Pugalenthi.G., Bhaduri, A. and R. Sowdhamini (2006) iMOTdb - a comprehensive collection of spatially interacting motifs in proteins . Nucl. Acids Res., 34 (Database issue): D285-6. [63] Kumar Gaurav, Nitin Gupta and Ramanathan Sowdhamini (2005) FASSM: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs In Silico Biol. 5, 425-38. [62] Anirban Bhaduri and R. Sowdhamini (2006) Domain architectural census of eukaryotic gene products containing O-protein phosphatases Gene,366, 246-255. [61] Metpally, R.R. and Sowdhamini, R. (2005) Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors . BMC Genomics, 6,106. [60] ** Bhaduri, A. & Sowdhamini, R. (2005) Genome-wide survey of prokaryotic O-protein phosphatases. J. Mol. Biol352736-52. [59] Bhaduri, A. & Sowdhamini, R. Diversity of phosphatases: study in bacterial and archael genomes in 'Mathematical Biology : Recent trends' Peeyush Chandra and B.V. Rathish Kumar (Eds) Copyright © 2006 Anamaya Publishers, New Delhi, India. [58] Sandhya, S., Chakrabarti, S., Abhinandan, K.R., Sowdhamini, R. & Srinivasan, N. (2005) Assessment of a rigorous transitive profile based search method to detect remotely similar proteins. J. Bio. Strc. Dyn. 23, 283-98. [57] ** Metpally, R.R. & Sowdhamini, R. Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis . BMC Evolutionary Biology [56] ** Chakrabarti, S., Anand, P., Bharadwaj, N., Pugalenthi, G. & Sowdhamini, R. (2005) SCANMOT: Searching for similar sequences using simultaneous scan of multiple sequence motifs. Nucleic Acid Research, 33, 274-276. [55] Pugalenthi, G., Archunan, G. & Sowdhamini, R. (2005) DIAL: a web-based server for the automatic identification of structural domains in proteins. Nucleic Acid Research, 33, 130-132. [54] Blaise, M. C., Sowdhamini, R. & Pradhan, N.(2005) Comparative analysis of different competitive antagonists interaction with NR2A and NR2B subunits of N-methyl-D-aspartate (NMDA) ionotropic glutamate receptor. J Mol Model (Online). [53] Pugalenthi, G. Bhaduri, A. & Sowdhamini, R. (2005) GenDiS: Genomic Distribution of Protein Structural Superfamilies . Nucleic Acid Research, 33, D252-D255. [52] Thangudu, R. R., Vinayagam, A., Pugalenthi, G.,Manonmani, A., Offmann, B. & Sowdhamini, R. (2005) Native and modelled disulphide bonds in proteins: Knowledge-based approaches towards structure prediction of disulphide-rich polypeptides . Proteins: Structure Function and Bioinformatics, 58, 866-79. [51] Blaise, M., Bhattacharyya, D., Sowdhamini, R. &Pradhan, N. (2005) Structural Consequences of D481N/K483Q Mutation at Glycine Binding Site of NMDA Ionotropic Glutamate Receptors: A Molecular Dynamics Study . J Biomol Struct Dyn., 22, 399-410. [50] Chakrabarti, S., Bhardwaj, N., Anand, P. &Sowdhamini, R. (2004) Improvement of alignment accuracy utilizing sequentially conserved motifs . BMC Bioinformatics, 5,167-188. [49] Blaise M., Sowdhamini R., Raghu Prasad Rao M. &Pradhan N. (2004): Evolutionary Trace Analysis of Ionotropic Glutamate Receptors and Modeling the Interactions of Agonists with Different NMDA Receptor Subunits . Journal of Molecular Modeling, 10, 305-16. [48]** Chakrabarti, S. & Sowdhamini, R. (2004) Regions of minimal structural variation among members of protein domain superfamilies : Application to remote homology detection and modelling using distant relationships . FEBS Letters, 569, 31-36. [47] Bhaduri, A., Pugalenthi, G., Gupta, N. &Sowdhamini, R. (2004) iMOT: an interactive package for the selection of spatially interacting motifs. Nucleic Acids Research, W602-W605. [46] Bhaduri, A., Pugalenthi, G. & Sowdhamini, R.(2004) PASS2: an automated database of protein alignments organised as structural superfamilies . BMC Bioinformatics, 5, 35. [45]**  Innis, C.A., Anand, P.A. & Sowdhamini, R.(2004) Prediction of Functional Sites in Proteins using Conserved Functional Group Analysis . J Mol Biol., 337, 1053-1068. [44] Bhaduri, A., Pugalenthi, G. & Sowdhamini, R.(2004) PASS2 Nucleic Acids Research , (http://www3.oup.co.uk/nar/database/summary/275(Web publication). [43] Vinayagam, A., Pugalenthi, G., Rajesh R. &Sowdhamini, R. (2004). DSDBASE - Disulfide Database Nucleic Acids Research ,http://www3.oup.co.uk/nar/database/summary/264(Web publication). [42] Chakrabarti, S., John, J. & Sowdhamini, R. (2004) Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints . Journal of Molecular Modeling, 10, 69-75. [41] Bhaduri, A. & Sowdhamini, R. (2003) A Genome-wide survey of human tyrosine phosphatases. Protein Engng., 16, 881-8. [40] Chakrabarti, S., Venkataramanan, K. & Sowdhamini,R. (2003) SMoS: A database of Structural Motifs of Superfamilies . Prot. Engng.,16,791-793. [39] ** Bhaduri, A., Ravishankar, R. & Sowdhamini, R.(2004) Conserved spatially interacting motifs of protein superfamilies : Application to fold recognition and function annotation of genome data .Proteins: Structure Function Genetics, 54, 657-70. [38] ** Vinayagam.A., Pugalenthi.G., Rajesh.T &Sowdhamini, R. (2004) DSDBASE: A consortium of native and modelled disulphide bonds in proteins. Nucleic Acids Research,  32, D200-202. [37] ** Sandhya, S., Kishore, S., Sowdhamini, R. &Srinivasan, N. (2003) Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. FEBS Letters, 552,225-30. [36] ** Vinayagam, A., Shi, J., Pugalenthi, G.,Meenakshi, B., Blundell, T.L. & Sowdhamini, R.  (2003) DDBASE2.0: Updated Domain Database with Improved Methods for the Identification of Structural Domains. Bioinformatics, 19, 1760-1764. [35] Chakrabarti, S. & Sowdhamini, R. (2003) Potentials of fold recognition methods in structure prediction of homoserine lactone synthases in a book on 'Recent Trends in Bioinformatics<92> (Ed. P. Shanmughavel, MKU, Madurai). [34] Chakrabarti, S. & Sowdhamini, R.(2003) Functional sites and evolutionary connections of acyl homoserine lactone synthases. Prot. Engng., 16, 271-278. [33] Chakrabarti, S., Venkataramanan, K.& Sowdhamini, R. (2003) PASS2: Structural motifs of protein superfamilies. Nucleic Acids Research,http://www3.oup.co.uk/nar/database/summary/275 (web publication). [32] Bhaduri, A.,Krishnaswamy, L., Ullal, G.R., Panicker, M.M. & Sowdhamini, R. (2003) Fold prediction and comparative modeling of Bdm1: a probable a/b hydrolase associated with hot water epilepsy. J. Mol. Model., DOI 10.1007/s00894-002-0102-0 URL: http://dx.doi.org/10.1007/s00894-002-0102-0. [31] **Mallika, V., Bhaduri, A. &Sowdhamini, R. (2002) PASS2: A semi-automated database of protein alignments organised as structural superfamilies. Nucleic Acids Research, 30,284-280. [30] Vinayagam, A. & Sowdhamini, R.(2002) DSDBASE: Native and modelled disulphide bonds in proteins. Nucleic Acids Research,http://www3.oup.co.uk/nar/database/summary/26(Web publication). [29] Mallika, V., Bhaduri, A. &Sowdhamini, R.  (2002) PASS2: Protein structural superfamilies. Nucleic Acids Research,http://www3.oup.co.uk/nar/database/summary/275(Web publication). [28] **Pandit, S.B., Gosar, D., Abhiman, S., Sujatha, S., Dixit, S.B., Mhatre, N.S., Sowdhamini, R. & Srinivasan, N. (2002) SUPFAM - 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 Research, 30, 289-293. [27] Chakrabarti, S., Bhavana, S., Mallika, V. & Sowdhamini, R. (2002) Protein structural similarities and prediction of protein function. in a book 'Trends in Chemistry' (ed. Srivastava, M.M.)., India. [26] ** Shah, P.K., Buslje, C.M. & Sowdhamini, R. (2001) Structural determinants of binding and specificity in transforming growth factor-receptor interactions. Proteins, 454, 408-420. [25] Shah, P.K. & Sowdhamini, R. (2001) Structural Understanding of the Transmembrane domains of Inositol triphosphate receptors and ryanodine receptors towards calcium channeling. Prot. Engng., 14, 867-874. [24] Pullinger, G.D., Sowdhamini, R. & Lax, A.J. (2001) Localization of the Functional Domains of the Mitogenic Toxin of Pasteurella multocida. Infection & Immunity, 69, 7839-7850. [23] ** Sowdhamini, R., Burke, D.F., Huang, J., Mizuguchi, K., Nagarajaram, H.A., Steward, R.E. & Blundell, T.L. (1998) CAMPASS: A database of structurally aligned protein superfamilies. Structure, 6, 1087-1094. [22] Sowdhamini, R., Burke, D.F., Deane, C.M., Huang, J., Mizuguchi, K., Nagarajaram, H.A., Overington, J.P., Rufino, S.D., Srinivasan, N., Steward, R.E. & Blundell, T.L. (1998) Protein 3D structural databases: domains, structurally aligned homologues and superfamilies. Acta Cryst. D, 54, pp.1168-1177. [21] Chirgadze, D.Y., Hepple, J., Byrd, R.A., Sowdhamini, R. & Blundell, T.L. (1998) Insights into the structure of hepatocyte growth factor scatter factor (HGF/SF) and implications for receptor activation. FEBS Letts., 430, 126-129. [20] ** Sowdhamini, R., Mitchell, T., Andrew, P. & Morgan, P. (1997) Structural and functional analogy between pneumolysin and aerolysin. Prot. Engng., 10, 207-215. [19] ** Sowdhamini, R., Rufino, S.D. & Blundell, T.L. (1996) A database of globular protein structural domains: clustering of representative family members into similar folds. Folding and Design, 1, 209-220. [18] Rufino, S.D., Srinivasan, N., Sowdhamini, R., Murray-Rust, J., Donate, L.E., May, A.C.W., Guruprasad, K., Dhanaraj, V., Sibanda, B.L. & Blundell, T.L. (1995) Structure-based design of proteins: Learning from evolution by comparative analysis of protein families. Proc. Ann. Symp. Prot. Engng., September 1994, Oxford, U.K. pp. 1-8. [17] Sowdhamini, R., Rufino, S.D. & Blundell, T.L. (1994) Recognition of a common fold: The construction and use of databases of protein domain topologies and templates. Chemtracts Biochem. Mol. Biol., 5, 291-306. [16] Nataraj, D.V., Srinivasan, N., Sowdhamini, R. & Ramakrishnan, C. (1995) β - turns in protein structures. Curr. Sci., 69, 434-447. [15] Sowdhamini, R., Srinivasan, N.,Guruprasad, K., Rufino, S., Dhanaraj, V., Wood, S.P., Emsley, J., White, H.E. & Blundell, T.L. (1995) Protein three-dimensional structure and molecular recognition: a story of soft locks and keys. Pharm. Acta Helv., 69, 185-192. [14] Sowdhamini, R. & Blundell, T.L. (1995) Automatic identification and analysis of domains in proteins of known crystal structure. Prot. Sci., 4, 506-520. [13] ** Donate, L.E., Gherardi, E., Srinivasan, N., Sowdhamini, R., Aparicio, S. & Blundell, T.L. (1994) Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGFl/MSP). Prot. Sci., 3, 2378-2394. [12] Srinivasan, N., Anuradha, V.S., Ramakrishnan, C., Sowdhamini, R. & Balaram, P. (1994) Conformational characteristics of asparaginyl residues in proteins. Int. J. Pept. Prot. Res., 44, 112-122. [11] May, A.C.W., Johnson, M.S., Rufino, S.D., Wako, H., Zhu, Z.Y., Sowdhamini, R., Srinivasan, N.,  Rodionov, M.A. & Blundell, T.L. (1994) The recognition of protein structure and function from sequence: adding value to genome data. Phil. Trans. Roy. Soc. (London), 344, 373-381. [10] ** Johnson, M.S., Srinivasan, N., Sowdhamini, R. & Blundell, T.L. (1994) Knowledge-based protein modelling. CRC Crit. Rev. Biochem. Mol. Biol., 29, 1-68. [9] Overington, J.P., Zhu, Z.Y., Sali,  A., Johnson, M.S., Sowdhamini, R., Louie, G.V. & Blundell, T.L. (1993) Molecular recognition in protein families: A database of aligned three-dimensional structures of related proteins. Biochem. Soc. Trans., 21, 597-604. [8] Sowdhamini, R., Ramakrishnan, C. & Balaram, P. (1993) Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of conotoxin GI and endothelin I. Prot. Engng., 6, 873-882. [7] Nagarajaram, H.A., Sowdhamini, R., Ramakrishnan, C. & Balaram, P. (1993) Termination of right handed helices in proteins by residues in left handed helical conformations. FEBS Letters, 321, 79-83. [6] Sowdhamini, R. & Balaram, P. (1993) Protein structure and stability. in Thermostability of Enzymes (Ed. Gupta, M.N.) Narosa Publishing House, Delhi. pp. 2-23. [5] **Sowdhamini, R., Srinivasan, N., Ramakrishnan, C. & Balaram, P. (1992) Orthogonal bb motifs in proteins. J. Mol. Biol., 223, 845-851. [4] Srinivasan, N., Sowdhamini, R., Ramakrishnan, C. & Balaram, P. (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. 59-73. [3] Srinivasan, N., Sowdhamini, R., Ramakrishnan, C. & Balaram, P. (1990) Conformations of disulfide bridges in proteins and peptides. Int. J. Pept. Prot. Res., 36, 147-155. [2] ** Sowdhamini, R., Srinivasan, N., Shoichet, B., Santi, D.V., Ramakrishnan, C. & Balaram, P. (1989) Stereochemical modelling of disulfide bridges: Criteria for introduction into proteins by site-directed mutagenesis. Prot. Engng., 3, 95-103. [1] Ramakrishnan, C., Sowdhamini, R. & Balaram, P. (1988) Analysis of short interproton distances in proline peptides as a guide in the interpretation of nuclear overhauser effects. Coll. Czec. Chem. Commun., 53, 2801-2809. ** Papers that are considered to be particularly important to the field