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Shameer, Khader ; Shingate, Prashant N. ; Manjunath, S. C. P. ; Karthika, M. ; Pugalenthi, Ganesan ; Sowdhamini, Ramanathan (2011) 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping Database, 2011 . pp. 1-15. ISSN 1758-0463

Shameer, Khader ; Pugalenthi, Ganesan ; Kandaswamy, Krishna Kumar ; Sowdhamini, Ramanathan (2011) 3dswap-pred: prediction of 3D domain swapping from protein sequence using random forest approach Protein and Peptide Letters, 18 (10). pp. 1010-1020. ISSN 0929-8665

Madan, Lalima L. ; Veeranna, S. ; Shameer, Khader ; Reddy, Chilamakuri C. S. ; Sowdhamini, R. ; Gopal, B. (2011) Modulation of catalytic activity in multi-domain protein tyrosine phosphatases PLoS One, 6 (9). e24766. ISSN 1932-6203

Kalaimathy, Singarevelu ; Sowdhamini, Ramanathan ; Kanagarajadurai, Karuppiah (2011) Critical assessment of structure-based sequence alignment methods at distant relationships Briefings in Bioinformatics, 12 (2). pp. 163-175. ISSN 1467-5463

Chilamakuri, Chandra Sekhar Reddy ; Joshi, Adwait ; Rani, Sane Sudha ; Offmann, Bernard ; Sowdhamini, R. (2011) Cross-genome comparisons of newly identified domains in Mycoplasma gallisepticum and domain architectures with other mycoplasma species Comparative and Functional Genomics, 2011 . 878973_1-878973_13. ISSN 1531-6912

Syamaladevi, Divya P. ; Sowdhamini, R. (2011) Evolutionary traces decode molecular mechanism behind fast pace of myosin XI BMC Structural Biology, 26 (11). pp. 1-11. ISSN 1472-6807

Nagarathnam, Balasubramanian ; Kannan, Sankar ; Dharnidharka, Varadhan ; Balakrishnan, Veluchamy ; Archunan, Govindaraju ; Sowdhamini, Ramanathan (2011) Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters Bioinformation, 7 (1). pp. 15-20. ISSN 0973-2063

Kumar, Jitendra ; Choudhary, Bikash C. ; Metpally, Raghu ; Zheng, Qun ; Nonet, Michael L. ; Ramanathan, Sowdhamini ; Klopfenstein, Dieter R. ; Koushika, Sandhya P. (2010) The Caenorhabditis elegans kinesin-3 motor UNC-104/KIF1A is degraded upon loss of specific binding to cargo PLoS Genetics, 6 (11). e1001200_1-e1001200_19. ISSN 1553-7390

Shameer, Khader ; Pugalenthi, Ganesan ; Kandaswamy, Krishna Kumar ; Suganthan, Ponnuthurai N. ; Archunan, Govindaraju ; Sowdhamini, Ramanathan (2010) Insights into protein sequence and structure-derived features mediating 3D domain swapping mechanism using support vector machine based approach Bioinformatics and Biology Insights (4). pp. 33-42. ISSN 1177-9322

Rajkumar, Ramalingam ; Prakash, Subramanya ; Archunan Ramanathan, Govindaraju (2010) Primary structural documentation of the major urinary protein of the Indian commensal rat (Rattus rattus) using a proteomics platform Protein and Peptide Letters, 17 (4). pp. 449-457. ISSN 0929-8665

Kolatkar, Prasanna R. ; Martinetz, Thomas ; Sowdhamini, R. ; Suganthan, P. N. ; Kandaswamy, Krishna Kumar ; Pugalenthi, Ganesan (2010) SMpred: a support vector machine approach to identify structural motifs in protein structure without using evolutionary information Journal of Biomolecular Structure and Dynamics, 28 (3). pp. 405-414. ISSN 0739-1102

Sowdhamini, Ramanathan ; Parthiban, Marimuthu ; Koshy, Caroline (2010) 100 ns molecular dynamics simulations to study intramolecular conformational changes in bax Journal of Biomolecular Structure and Dynamics, 28 (1). pp. 71-83. ISSN 0739-1102

Sundaramurthy, Pandurangan ; Shameer, Khader ; Sreenivasan, Raashi ; Gakkhar, Sunita ; Sowdhamini, Ramanathan (2010) HORI: a web server to compute Higher Order residue interactions in protein structures BMC Bioinformatics, 11 (1). No pp. given. ISSN 1471-2105

Pugalenthi, Ganesan ; Kandaswamy, Krishna Kumar ; Suganthan, P. N. ; Archunan, G. ; Sowdhamini, R. (2010) Identification of functionally diverse lipocalin proteins from sequence information using support vector machine Amino Acids, 39 (3). pp. 777-783. ISSN 1438-2199

Parthiban, Marimuthu ; Shanmughavel, Piramanayagam ; Sowdhamini, Ramanathan (2010) In silico point mutation and evolutionary trace analysis applied to nicotinic acetylcholine receptors in deciphering ligand-binding surfaces Journal of Molecular Modeling, 16 (10). pp. 1651-1670. ISSN 1610-2940

Shameer, Khader ; Madan, Lalima L. ; Veeranna, Shivamurthy ; Gopal, Balasubramanian ; Sowdhamini, Ramanathan (2010) PeptideMine - a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes BMC Bioinformatics, 11 . 473_1-473_14. ISSN 1471-2105

Anbazhagan, Padmanabhan ; Purushottam, Meera ; Kumar, Kiran ; Mukherjee, Odity ; Jain, Sanjeev ; Sowdhamini, Ramanathan (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 and Dynamics, 27 (5). pp. 581-598. ISSN 0739-1102

Reddy, Chilamakuri C. S. ; Rani, Sane Sudha ; Offmann, Bernard ; Sowdhamini, R. (2010) Systematic search for putative new domain families in Mycoplasma gallisepticum genome BMC Research Notes, 3 . 98_1-98_10. ISSN 1756-0500

Bhaduri, Anirban ; Kalaimathy, S. ; Sowdhamini, R. (2009) Conservation and divergence among Salmonella enterica subspecies Infectious Disorders - Drug Targets, 9 (3). pp. 248-259. ISSN 1871-5265

Doodhi, Harinath ; Ghosal, Debnath ; Krishnamurthy, Mahalakshmi ; Jana, Swadhin C. ; Shamala, Divya ; Bhaduri, Anirban ; Sowdhamini, R. ; Ray, Krishanu (2009) KAP, the accessory subunit of kinesin-2, binds the predicted coiled-coil stalk of the motor subunits Biochemistry, 48 (10). pp. 2248-2260. ISSN 0006-2960

Shameer, Khader ; Nagarajan, Paramasivam ; Gaurav, Kumar ; Sowdhamini, Ramanathan (2009) 3PFDB - a database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach BioData Mining, 2 . 8_1-8_10. ISSN 1756-0381

Sundaramurthy, Pandurangan ; Gakkhar, Sunita ; Sowdhamini, Ramanathan (2009) Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each other: a systems approach Bioinformation, 3 (6). pp. 244-249. ISSN 0973-2063

Sundaramurthy, Pandurangan ; Gakkhar, Sunita ; Sowdhamini, Ramanathan (2009) Computational prediction and analysis of impact of the cross‐talks between JNK and P38 kinase cascades Bioinformation, 3 (6). pp. 250-254. ISSN 0973-2063

Sandhya, Sankaran ; Rani, Saane Sudha ; Pankaj, Barah ; Govind, Madabosse Kande ; Offmann, Bernard ; Srinivasan, Narayanaswamy ; Sowdhamini, Ramanathan (2009) Length variations amongst protein domain superfamilies and consequences on structure and function PLoS ONE, 4 (3). No PP. Given.. ISSN 1932-6203

Kanagarajadurai, Karuppiah ; Malini, Manoharan ; Bhattacharya, Aditi ; Panicker, Mitradas M. ; Sowdhamini, Ramanathan (2009) Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT_2A) receptor for the identification of hotspots for ligand binding Molecular BioSystems, 5 (12). pp. 1877-1888. ISSN 1742-206X

Shameer, K. ; Ambika, S. ; Varghese, SusanMary ; Karaba, N. ; Udayakumar, M. ; Sowdhamini, R. (2009) STIFDB—arabidopsis stress responsive transcription factor data base International Journal of Plant Genomics, 2009 . pp. 583429-1. ISSN 1687-5370

Vyas, Neha ; Goswami, Debanjan ; Manonmani, A. ; Sharma, Pranav ; Ranganath, Hassan Annegowda ; VijayRaghavan, Krishnaswamy ; Shashidhara, L. S. ; Sowdhamini, Ramanathan ; Mayor, Satyajit (2008) Nanoscale organization of hedgehog is essential for long-range signaling Cell, 133 (7). pp. 1214-1227. ISSN 0092-8674

Sandhya, Sankaran ; Pankaj, Barah ; Govind, Madabosse Kande ; Offmann, Bernard ; Srinivasan, Narayanaswamy ; Sowdhamini, Ramanathan (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 Structural Biology, 8 (28). No PP. Given.. ISSN 1472-6807

Shah, Parantu K. ; Tripathi, Lokesh P. ; Jensen, Lars Juhl ; Gahnim, Murad ; Masone, Christopher ; Furlong, Eileen E. ; Rodrigues, Veronica ; White, Kevin P. ; Bork, Peer ; Sowdhamini, R. (2008) Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families Gene, 407 (1-2). pp. 199-215. ISSN 0378-1119

Sowdhamini, R. ; Alva, V. ; Syamala Devi, D. P. (2008) COILCHECK: an interactive server for the analysis of interface regions in coiled coils Protein and Peptide Letters, 15 (1). pp. 33-38. ISSN 0929-8665

Thangudu, Ratna R. ; Manoharan, Malini ; Srinivasan, N. ; Frédéric, Cadet ; Sowdhamini, R. ; Offmann, Bernard (2008) Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families BMC Structural Biology, 8 . 55_1-55_22. ISSN 1472-6807

Anbazhagan, Padmanabhan ; Purushottam, Meera ; Kiran Kumar, H. B. ; Kubendran, Shobana ; Mukherjee, Odity ; Brahmachari, Samir Kumar ; Jain, Sanjeev ; Sowdhamini, Ramanathan (2008) Evolutionary analysis of PHLPP1 gene in humans and non-human primates Bioinformation, 2 (10). pp. 471-474. ISSN 0973-2063

Tripathi, Lokesh P. ; Sowdhamini, R. (2008) Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes BMC Genomics, 9 . 49_1-49_28. ISSN 1471-2164

Reddy, Chilamakuri C. S. ; Shameer, Khader ; Offmann, Bernard O. ; Sowdhamini, Ramanathan (2008) PURE: a webserver for the prediction of domains in unassigned regions in proteins BMC Bioinformatic, 9 . 281_1-281_8. ISSN 1471-2105

Sundar, Ambika Shyam ; Varghese, Susan Mary ; Shameer, Khader ; Karaba, Nataraja ; Udayakumar, Makarla ; Sowdhamini, Ramanathan (2008) STIF: identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana Bioinformation, 2 (10). pp. 431-437. ISSN 0973-2063

Kanagarajadurai, Karuppiah ; Sowdhamini, Ramanathan (2008) Sequence and structural analyses of interleukin-8-like chemokine superfamily In Silico Biology, 8 (3-4). pp. 307-330. ISSN 1386-6338

Pugalenthi, Ganesan ; Tang, Ke ; Suganthan, P. N. ; Archunan, G. ; Sowdhamini, R. (2007) A machine learning approach for the identification of odorant binding proteins from sequence-derived properties BMC Bioinformatics, 8 . 351_1-351_7. ISSN 1471-2105

Gadkari, Rupali A. ; Sandhya, S. ; Sowdhamini, R. ; Dighe, Rajan R. (2007) The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor Molecular and Cellular Endocrinology, 260-262 . pp. 23-32. ISSN 0303-7207

Metpally, Raghu Prasad Rao ; Vigneshwar, Ramakrishnan ; Sowdhamini, Ramanathan (2007) Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis Journal of Biosciences, 32 (1). pp. 43-50. ISSN 0250-5991

Shameer, Khader ; Sowdhamini, Ramanathan (2007) IWS: integrated web server for protein sequence and structure analysis Bioinformation, 2 (3). pp. 86-90. ISSN 0973-2063

Pugalenthi, Ganesan ; Suganthan, P. N. ; Sowdhamini, R. ; Chakrabarti, Saikat (2007) MegaMotifBase: a database of structural motifs in protein families and superfamilies Nucleic Acids Research, 36 (S-1). D218-D221. ISSN 0305-1048

Parikh, Neha ; Koshy, Caroline ; Dhayabaran, Vaigundan ; Perumalsamy, Lakshmi R. ; Sowdhamini, R. ; Sarin, Apurva (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-x_L BMC Cell Biology, 8 (1). 16_1-16_16. ISSN 1471-2121

Reddy, Sekhar Chilamakuri C. ; Bernard, Offmann ; Sowdhamini, Ramanathan ; Shameer, Khader (2007) PURE: a web server for querying the relationship between pre-existing domains and unassigned regions in proteins Nature . pp. 1-15. ISSN 0028-0836

Pugalenthi, Ganesan ; Suganthan, P. N. ; Sowdhamini, R. ; Chakrabarti, Saikat (2007) SMotif: a server for structural motifs in proteins Bioinformatics, 23 (5). pp. 637-638. ISSN 1367-4803

Vijayalakshmi, M. ; Shivashankar, G. V. ; Sowdhamini, R. (2007) Simulations of SIN mutations and histone variants in human nucleosomes reveal altered protein-DNA and core histone interactions Journal of Biomolecular Structure & Dynamics, 25 (2). pp. 207-218. ISSN 0739-1102

Khajamohiddin, Syed ; Babu, Pakala Suresh ; Chakka, Deviprasanna ; Merrick, Mike ; Bhaduri, Anirban ; Sowdhamini, Ramanathan ; Siddavattam, Dayananda (2006) A novel meta-cleavage product hydrolase from Flavobacterium sp. ATCC27551 Biochemical and Biophysical Research Communications, 351 (3). pp. 675-681. ISSN 0006-291X

Bhaduri, Anirban ; Sowdhamini, R. (2006) Domain architectural census of eukaryotic gene products containing O-protein phosphatases Gene, 366 (2). pp. 246-255. ISSN 0378-1119

Bhadra, R. ; Sandhya, S. ; Abhinandan, K. R. ; Chakrabarti, S. ; Sowdhamini, R. ; Srinivasan, N. (2006) Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains Nucleic Acids Research, 34 (S-2). W143-W146. ISSN 0305-1048

Tripathi, Lokesh P. ; Sowdhamini, R. (2006) Cross genome comparisons of serine proteases in Arabidopsis and rice BMC Genomics, 7 . 200_1-200_31. ISSN 1471-2164

Reddy, Chandrashekar ; Manonmani, Arunachalam ; Babu, Meenakshi ; Sowdhamini, Ramanathan (2006) Enhanced structure prediction of gene products containing class III adenylyl cyclase domains In Silico Biology, 6 (5). pp. 351-362. ISSN 1386-6338

Pugalenthi, G. ; Shameer, K. ; Srinivasan, N. ; Sowdhamini, R. (2006) HARMONY: a server for the assessment of protein structures Nucleic Acids Research, 34 (S-2). W231-W234. ISSN 0305-1048

Chakrabarti, Saikat ; Manohari, Gowri ; Pugalenthi, Ganesan ; Sowdhamini, Ramanathan (2006) SSToSS - sequence-structural templates of single-member superfamilies In Silico Biology, 6 (4). pp. 311-319. ISSN 1386-6338

Pugalenthi, Ganesan ; Bhaduri, Anirban ; Sowdhamini, R. (2006) iMOTdb-a comprehensive collection of spatially interacting motifs in proteins Nucleic Acids Research, 34 (S-1). D285-D286. ISSN 0305-1048

Bhaduri, Anirban ; Sowdhamini, R. (2005) Genome-wide survey of prokaryotic O-protein phosphatases Journal of Molecular Biology, 352 (3). pp. 736-752. ISSN 0022-2836

Thangudu, Ratna Rajesh ; Vinayagam, A. ; Pugalenthi, G. ; Manonmani, A. ; Offmann, B. ; Sowdhamini, R. (2005) Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides Proteins: Structure, Function, and Bioinformatics, 58 (4). pp. 866-879. ISSN 0887-3585

Chakrabarti, S. ; Abhinandan, K. R. ; Sowdhamini, R. ; Srinivasan, N. ; Sandhya, S. (2005) Assessment of a rigorous transitive profile based search method to detect remotely similar proteins Journal of Biomolecular Structure and Dynamics, 23 (3). pp. 283-298. ISSN 0739-1102

Blaise, Mathias-Costa ; Sowdhamini, Ramanathan ; Pradhan, Nithyananda (2005) Comparative analysis of different competitive antagonists interaction with NR2A and NR2B subunits of N-methyl-D-aspartate (NMDA) ionotropic glutamate receptor Journal of Molecular Modeling, 11 (6). pp. 489-502. ISSN 1610-2940

Metpally, Raghu Prasad Rao ; Sowdhamini, Ramanathan (2005) Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors BMC Genomics, 6 . 106_1-106_20. ISSN 1471-2164

Pugalenthi, Ganesan ; Archunan, Govindaraju ; Sowdhamini, Ramanathan (2005) DIAL: a web-based server for the automatic identification of structural domains in proteins Nucleic Acids Research, 33 (S-2). W130-W132. ISSN 0305-1048

Gaurav, Kumar ; Gupta, Nitin ; Sowdhamini, Ramanathan (2005) FASSM: enhanced function association in whole genome analysis using sequence and structural motifs In Silico Biology, 5 (5-6). pp. 425-438. ISSN 1386-6338

Pugalenthi, Ganesan ; Bhaduri, Anirban ; Sowdhamini, Ramanathan (2005) GenDiS: Genomic Distribution of protein structural domain Superfamilies Nucleic Acids Research, 33 (S-1). D252-D255. ISSN 0305-1048

Metpally, Raghu Prasad Rao ; Sowdhamini, Ramanathan (2005) Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis BMC Evolutionary Biology, 5 . 41_1-41_10. ISSN 1471-2148

Chakrabarti, Saikat ; Prem Anand, A. ; Bhardwaj, Nitin ; Pugalenthi, Ganesan ; Sowdhamini, R. (2005) SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs Nucleic Acids Research, 33 (S-2). W274-W276. ISSN 0305-1048

Blaise, Mathias-Costa ; Bhattacharyya, Dananjay ; Sowdhamini, Ramanathan ; Pradhan, Nityananda (2005) Structural consequences of D481N/K483Q mutation at glycine binding site of NMDA ionotropic glutamate receptors: a molecular dynamics study Journal of Biomolecular Structure and Dynamics, 22 (4). pp. 399-410. ISSN 0739-1102

Blaise, Mathias-Costa ; Sowdhamini, Ramanathan ; Rao, Metpally Raghu Prasad ; Pradhan, Nithyananda (2004) Evolutionary trace analysis of ionotropic glutamate receptor sequences and modeling the interactions of agonists with different NMDA receptor subunits Journal of Molecular Modeling, 10 (5-6). pp. 305-316. ISSN 1610-2940

Chakrabarti, Saikat ; 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 (1-3). pp. 31-36. ISSN 0014-5793

Axel Innis, C. ; Prem Anand, A. ; Sowdhamini, R. (2004) Prediction of functional sites in proteins using conserved functional group analysis Journal of Molecular Biology, 337 (4). pp. 1053-1068. ISSN 0022-2836

Bhaduri, Anirban ; 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, and Bioinformatics, 54 (4). pp. 657-670. ISSN 0887-3585

Vinayagam, A. ; Pugalenthi, G. ; Rajesh, R. ; Sowdhamini, R. (2004) DSDBASE: a consortium of native and modelled disulphide bonds in proteins Nucleic Acids Research, 32 (S-1). D200-D202. ISSN 0305-1048

Chakrabarti, Saikat ; Bhardwaj, Nitin ; Anand, Prem A. ; Sowdhamini, Ramanathan (2004) Improvement of alignment accuracy utilizing sequentially conserved motifs BMC Bioinformatics, 5 . 167_1-167_12. ISSN 1471-2105

Chakrabarti, Saikat ; John, Jaisurya ; Sowdhamini, Ramanathan (2004) Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints Journal of Molecular Modeling, 10 (1). pp. 69-75. ISSN 1610-2940

Bhaduri, Anirban ; Pugalenthi, Ganesan ; Sowdhamini, Ramanathan (2004) PASS2: an automated database of protein alignments organised as structural superfamilies BMC Bioinformatics, 5 . 35_1-35_7. ISSN 1471-2105

Bhaduri, A. ; Pugalenthi, G. ; Gupta, N. ; Sowdhamini, R. (2004) iMOT: an interactive package for the selection of spatially interacting MOTifs Nucleic Acids Research, 32 (S-2). W602-W605. ISSN 0305-1048

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 (2-3). pp. 225-230. ISSN 0014-5793

Vinayagam, A. ; Shi, J. ; Pugalenthi, G. ; Meenakshi, B. ; Blundell, T. L. ; Sowdhamini, R. (2003) DDBASE2.0: updated domain database with improved identification of structural domains Bioinformatics, 19 (14). pp. 1760-1764. ISSN 1367-4803

Bhaduri, Anirban ; Krishnaswamy, Lakshminarasimhan ; Ullal, Gautam R. ; Panicker, Mitradas M. ; Sowdhamini, Ramanathan (2003) Fold prediction and comparative modeling of Bdm1: a probable α/β hydrolase associated with hot water epilepsy Journal of Molecular Modeling, 9 (1). pp. 3-8. ISSN 1610-2940

Chakrabarti, Saikat ; Sowdhamini, R. (2003) Functional sites and evolutionary connections of acylhomoserine lactone synthases Protein Engineering Design and Selection, 16 (4). pp. 271-278. ISSN 1741-0126

Chakrabarti, Saikat ; Venkatramanan, K. ; Sowdhamini, R. (2003) SMoS: a database of structural motifs of protein superfamilies Protein Engineering Design and Selection, 16 (11). pp. 791-793. ISSN 1741-0126

Bhaduri, Anirban ; Sowdhamini, R. (2003) A genome-wide survey of human tyrosine phosphatases Protein Engineering Design and Selection, 16 (12). pp. 881-888. ISSN 1741-0126

Mallika, V. ; Bhaduri, Anirban ; Sowdhamini, R. (2002) PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies Nucleic Acids Research, 30 (1). pp. 284-288. ISSN 0305-1048

Pandit, Shashi B. ; Gosar, Dilip ; Abhiman, S. ; Sujatha, S. ; Dixit, Sayali S. ; Mhatre, Natasha S. ; Sowdhamini, R. ; Srinivasan, N. (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 Research, 30 (1). pp. 289-293. ISSN 0305-1048

Shah, Parantu K. ; Buslje, Cristina Marino ; Sowdhamini, R. (2001) Structural determinants of binding and specificity in transforming growth factor-receptor interactions Proteins: Structure, Function, and Bioinformatics, 45 (4). pp. 408-420. ISSN 0887-3585

Pullinger, Gillian D. ; Sowdhamini, R. ; Lax, Alistair J. (2001) Localization of functional domains of the mitogenic toxin of Pasteurella multocida Infection and Immunity, 69 (12). pp. 7839-7850. ISSN 0019-9567

Shah, Parantu K. ; Sowdhamini, R. (2001) Structural understanding of the transmembrane domains of inositol triphosphate receptors and ryanodine receptors towards calcium channeling Protein Engineering Design and Selection, 14 (11). pp. 867-874. ISSN 1741-0126

Sowdhamini, R. ; Burke, D. F. ; Deane, C. ; Huang, J. ; Mizuguchi, K. ; Nagarajaram, H. A. ; Overington, J. P. ; Srinivasan, N. ; Steward, R. E. ; Blundell, T. L. (1998) Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies Acta Crystallographica Section D, D54 (6). pp. 1168-1177. ISSN 0907-4449

Sowdhamini, R. ; Burke, David F. ; Huang, Jing-fei ; Mizuguchi, Kenji ; Nagarajaram, Hampapathalu A. ; Srinivasan, N. ; Steward, Robert E. ; Blundell, Tom L. (1998) CAMPASS: a database of structurally aligned protein superfamilies Structure, 6 (9). pp. 1087-1094. ISSN 0969-2126

Chirgadze, Dimitri Y. ; Hepple, Jonathan ; Andrew Byrd, R. ; Sowdhamini, R. ; Blundell, Tom L. ; Gherardi, Ermanno (1998) Insights into the structure of hepatocyte growth factor/scatter factor (HGF/SF) and implications for receptor activation FEBS Letters, 430 (1-2). pp. 126-129. ISSN 0014-5793

Sowdhamini, R. ; Mitchell, T. J. ; Andrew, P. W. ; Morgan, P. J. (1997) Structural and functional analogy between pneumolysin and proaerolysin Protein Engineering Design and Selection, 10 (3). pp. 207-215. ISSN 1741-0126

Sowdhamini, R. ; Rufino, Stephen D. ; Blundell, Tom L. (1996) A database of globular protein structural domains: clustering of representative family members into similar folds Folding & Design, 1 (3). pp. 209-220. ISSN 1359-0278

Nataraj, D. V. ; Srinivasan, N. ; Sowdhamini, R. ; Ramakrishnan, C. (1995) α-Turns in protein structure Current Science, 69 (5). pp. 434-447. ISSN 0011-3891

Sowdhamini, R. ; Srinivasan, N. ; Guruprasad, K. ; Rufino, S. ; Dhanaraj, V. ; Wood, S. P. ; Emsley, J. ; White, H. E. ; Blundell, Tom (1995) Protein three-dimensional structure and molecular recognition: a story of soft locks and keys Pharmaceutica Acta Helvetiae, 69 (4). pp. 185-192. ISSN 0031-6865

Sowdhamini, R. ; Blundell, Tom L. (1995) An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins Protein Science, 4 (3). pp. 506-520. ISSN 0961-8368

Donate, Luis Enrique ; Srinivasan, N. ; Sowdhamini, R. ; Gherardi, Ermanno ; Blundell, Tom L. ; Aparicio, Samuel (1994) Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP) Protein Science, 3 (12). pp. 2378-2394. ISSN 0961-8368

May, Alex C. W. ; Johnson, Mark S. ; Rufino, Stephen D. ; Wako, Hiroshi ; Zhu, Zhan-Yang ; Sowdhamini, Ramanathan ; Srinivasan, Narayanaswamy ; Rodionov, Michael A. ; Blundell, Tom L. ; Dover, G. A. (1994) The recognition of protein structure and function from sequence: adding value to genome data [and discussion] Philosophical Transactions: Biological Sciences, 344 (1310). pp. 373-381. ISSN 0962-8436

Johnson, Mark S. ; Srinivasan, Narayanaswamy ; Sowdhamini, Ramanathan ; Blundell, Tom L. (1994) Knowledge-based protein modeling Critical Reviews in Biochemistry and Molecular Biology, 29 (1). pp. 1-68. ISSN 1040-9238

Srinivasan, N. ; Anuradha, V. S. ; Ramakrishnan, C. ; Sowdhamini, R. ; Balaram, P. (1993) Conformational characteristics of asparaginyl residues in proteins International Journal of Peptide and Protein Research, 44 (2). pp. 112-122. ISSN 0367-8377

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 (1). pp. 79-83. ISSN 0014-5793

Sowdhamini, R. ; Ramakrishnan, C. ; Balaram, P. (1993) Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I Protein Engineering Design & Selection, 6 (8). pp. 873-882. ISSN 1741-0126

Overington, John P. ; Zhu, Zhan‑Yang ; Šali, Andrej ; Johnson, Mark S. ; Sowdhamini, Ramanathan ; Louie, Gordon V. ; Blundell, Tom L. (1993) Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins Biochemical Society Transactions, 21 (3). pp. 597-604. ISSN 0300-5127

Sowdhamini, R. ; Srinivasan, N. ; Ramakrishnan, C. ; Balaram, P. (1992) Orthogonal ββ motifs in proteins Journal of Molecular Biology, 223 (4). pp. 845-851. ISSN 0022-2836

Srinivasan, N. ; Sowdhamini, Ramanathan ; Ramakrishnan, Chandrashekharan ; Balaram, Padmanabhan (1991) Analysis of short loops connecting secondary structural elements in proteins Molecular Conformation and Biological Interactions . pp. 59-73.

Srinivasan, N. ; Sowdhamini, R. ; Ramakrishnan, C. ; Balaram, P. (1990) Conformations of disulfide bridges in proteins International Journal of Peptide and Protein Research, 36 (2). pp. 147-155. ISSN 0367-8377

Sowdhamini, R. ; Srinivasan, N. ; Shoichet, Brian ; Santi, Daniel V. ; Ramakrishnan, C. ; Balaram, P. (1989) Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis Protein Engineering Design & Selection, 3 (2). pp. 95-103. ISSN 1741-0126

Ramakrishnan, Chandrashekharan ; Sowdhamini, Ramanathan ; Balaram, Padmanabhan (1988) Analysis of short interproton distances in proline peptides as a guide in the interpretation of nuclear overhauser effects Collection of Czechoslovak Chemical Communications, 53 (11). pp. 2801-2809. ISSN 0010-0765