[273] Sneha Bheemireddy, Sankaran Sandhya, Narayanaswamy Srinivasan and Ramanathan Sowdhamini (2022) Computational tools to study RNA-protein complexes. Frontiers in Molcular BioSciences (accepted).

[272] Neha V. Kalmankar, Bhuvaneshwari Rajendrakumar Gehi and Ramanathan Sowdhamini (2022) Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations. Frontiers in Molecular BioSciences (in press).

[271] Adwait G. Joshi, Praveen P., Uma Ramakrishnan and Ramanathan Sowdhamini (2022) Draft genome sequence of the invasive plant Lantana camara L. Bioinformation (in press).  

[270] Nagarajan Naveenkumar, Vasam Manjveekar Prabantu, Sneha Vishwanath, Ramanathan Sowdhamini, and Narayanaswamy Srinivasan. Structures of remotely related interacting protein homologues are less divergent than non-interacting homologues. FEBS Open Bio (accepted).

[269] Shailya Verma and R. Sowdhamini (2022). A genome-wide search of Toll/Interleukin-1 receptor (TIR) domain-containing adapter molecule (TICAM) and their evolutionary divergence from other TIR domain containing proteins. Biology Direct https://rdcu.be/cUSg4.

[268] Naika, M., Sathyanarayanan, N., Sajeevan, R. S., Bhattacharyya, T., Ghosh, P., Iyer, M. S., Jarjapu, M., Joshi, A. G., Harini, K., Shafi, K. M., Kalmankar, N., Karpe, S. D., Mam, B., Pasha, S. N., & Sowdhamini, R. (2022). Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.). Scientific reports12(1), 13534. https://doi.org/10.1038/s41598-022-17779-8

[267]  Shafi, K. M., & Sowdhamini, R. (2022). Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. BMC genomics, 23(1), 516. https://doi.org/10.1186/s12864-022-08751-x.

[266] Sarkar, S. R., Dubey, V. K., Jahagirdar, A., Lakshmanan, V., Haroon, M. M., Sowndarya, S., Sowdhamini, R., & Palakodeti, D. (2022). DDX24 is required for muscle fiber organization and the suppression of wound-induced Wnt activity necessary for pole re-establishment during planarian regeneration. Developmental biology, S0012-1606(22)00080-X. https://doi.org/10.1016/j.ydbio.2022.04.011


[265]   Bhattacharyya, T., Nayak, S., Goswami, S., Gadiyaram, V., Mathew, O. K., & Sowdhamini, R. (2022). PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. Database : the journal of biological databases and curation, 2022, baac025. https://doi.org/10.1093/database/baac025


[264]    Mondal, S., Shafi, K. M., Raizada, A., Song, H., Badigannavar, A. M., & Sowdhamini, R. (2022). Development of candidate gene-based markers and map-based cloning of a dominant rust resistance gene in cultivated groundnut (Arachis hypogaea L.). Gene, 827, 146474. https://doi.org/10.1016/j.gene.2022.146474

[263]    Chauhan, P. K., & Sowdhamini, R. (2022). LIM domain-wide comprehensive virtual mutagenesis provides structural rationale for cardiomyopathy mutations in CSRP3. Scientific reports, 12(1), 3562. https://doi.org/10.1038/s41598-022-07553-1

[262]    Kalmankar, N. V., Pavalam, M., Indrakumar, S., Srinivasan, N., & Sowdhamini, R. (2022). DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins. Database : the journal of biological databases and curation, 2022, baac005. https://doi.org/10.1093/database/baac005

[261]    Gromiha, M. M., Orengo, C., Sowdhamini, R., & Thornton, J. (2022). Srinivasan (1962-2021) in Bioinformatics and beyond. Bioinformatics (Oxford, England), btac054. Advance online publication. https://doi.org/10.1093/bioinformatics/btac054 .

[260]    Rebehmed, J., de Brevern, A. G., Sowdhamini, R., & Joseph, A. P. (2022). Editorial: Advances in Molecular Docking and Structure-Based Modelling. Frontiers in molecular biosciences, 9, 839826. https://doi.org/10.3389/fmolb.2022.839826

[259]    Sankaradoss, A., Jagtap, S., Nazir, J., Moula, SE., Modak, A., Fialho, J., Iyer, M., Shastri, JS., Dias, M, Gadepalli, R., Aggarwal, A., Vedpathak, M., Agrawal, S., Pandit, A., Nisheetha, A., Kumar, A., Bordoloi, M., Shafi, M., Shelar, B., Balachandra, SS., Damodar, T., Masika, MM., Mwaura, P., Anzala, O., Muthumani, K., Sowdhamini, R., Medigeshi, GR., Roy, R., Pattabiraman, C., Krishna, S., & Sreekumar, E. (2022). Immune profile and responses of a novel Dengue DNA vaccine encoding EDIII-NS1 consensus design based on Indo-African sequences. Molecular therapy: the journal of the American Society of Gene Therapy, S1525-0016(22)00013-2. Advance online publication. https://doi.org/10.1016/j.ymthe.2022.01.013

[258]    Ambardar, S., Vakhlu, J., & Sowdhamini, R. (2022). Insights from the analysis of draft genome sequence of Crocus sativus L. Bioinformation, 18(1), 1-13.

[257]    Pulipati, S., Somasundaram, S., Rana, N., Kumaresan, K., Shafi, M., Civáň, P., Sellamuthu, G., Jaganathan, D., Ramaravi, P. V., Punitha, S., Raju, K., Mantri, S. S., Sowdhamini, R., Parida, A., & Venkataraman, G. (2022). Diversity of Sodium Transporter HKT1;5 in Genus Oryza. Rice Science, 29(1), 31–46. https://doi.org/10.1016/j.rsci.2021.12.003

[256]    Harini, K., Jayashree, S., Tiwari, V., Vishwanath, S., & Sowdhamini, R. (2021). Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors. Bioinformatics and biology insights, 15, 11779322211037769. https://doi.org/10.1177/11779322211037769

[255]    Juma, M., Sankaradoss, A., Ndombi, R., Mwaura, P., Damodar, T., Nazir, J., Pandit, A., Khurana, R., Masika, M., Chirchir, R., Gachie, J., Krishna, S., Sowdhamini, R., Anzala, O., & Meenakshi, I. S. (2021). Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting. Frontiers in microbiology, 12, 647565. https://doi.org/10.3389/fmicb.2021.647565

[254]    Ahmed, A., Mam, B., & Sowdhamini, R. (2021). DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity. Bioinformatics and biology insights, 15, 11779322211030364. https://doi.org/10.1177/11779322211030364

[253]    Kalmankar, N. V., Hari, H., Sowdhamini, R., & Venkatesan, R. (2021). Disulfide-Rich Cyclic Peptides from Clitoria ternatea Protect against β-Amyloid Toxicity and Oxidative Stress in Transgenic Caenorhabditis elegans. Journal of medicinal chemistry, 64(11), 7422–7433. https://doi.org/10.1021/acs.jmedchem.1c00033

[252]    Bhattacharyya, T., & Sowdhamini, R. (2021). Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes. Cellular signalling, 84, 110009. https://doi.org/10.1016/j.cellsig.2021.110009

[251]    Nishad, S., Chauhan, P. K., Sowdhamini, R., & Ghosh, A. (2021). Chronic exposure of humans to high level natural background radiation leads to robust expression of protective stress response proteins. Scientific reports, 11(1), 1777. https://doi.org/10.1038/s41598-020-80405-y

[250]    Karpe, S. D., Tiwari, V., & Ramanathan, S. (2021). InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. PloS one, 16(1), e0245324. https://doi.org/10.1371/journal.pone.0245324

[249]    Joshi, AG., Harini, K., Meenakshi, I., Shafi, KM., Pasha, SN., Mahita, J., Sajeevan, RS., Karpe, SD., Ghosh, P., Nitish, S., Gandhimathi, A., Mathew, OK., Prasanna, SH., Malini, M., Mutt, E., Naika, M., Ravooru, N., Rao, RM., Shingate, PN., Sukhwal, A., Sunitha, MS., Upadhyay, AK., Vinekar, RS., & Sowdhamini, R. (2020). A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways. MethodsX, 7, 101053. https://doi.org/10.1016/j.mex.2020.101053

[248]    Manikkaraja, C., Bhavika, M., Singh, R., Nagarathnam, B., George, G., Gulyani, A., Archunan, G., & Sowdhamini, R. (2020). Molecular and functional characterization of buffalo nasal epithelial odorant binding proteins and their structural insights by in silico and biochemical approaches. Journal of biomolecular structure & dynamics, 1–24. Advance online publication. https://doi.org/10.1080/07391102.2020.1854117

[247]    Bhavika Mam and Ramanathan Sowdhamini (2020) SoCCer: A pipeline to identify classes of soluble proteins in chemical communication in insect genomes. Protocol Exchange. https://doi.org/10.21203/rs.3.pex-1095/v1

[246]    Manjunath, L., Coombes, D., Davies, J., Dhurandhar, M., Tiwari, V. R., Dobson, R., Sowdhamini, R., Ramaswamy, S., & Bose, S. (2020). Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida. Proteins, 10.1002/prot.25996. Advance online publication. https://doi.org/10.1002/prot.25996

[245]    Kalmankar, N. V., Venkatesan, R., Balaram, P., & Sowdhamini, R. (2020). Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis. Scientific reports, 10(1), 12658. https://doi.org/10.1038/s41598-020-69452-7

[244]    Sharma, A., Tiwari, V., & Sowdhamini, R. (2020). Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. Journal of biosciences, 45(1), 100. https://doi.org/10.1007/s12038-020-00069-8

[243]    Somasundaram, S., Véry, A. A., Vinekar, R. S., Ishikawa, T., Kumari, K., Pulipati, S., Kumaresan, K., Corratgé-Faillie, C., Sowdhamini, R., Parida, A., Shabala, L., Shabala, S., & Venkataraman, G. (2020). Homology Modeling Identifies Crucial Amino-Acid Residues That Confer Higher Na+ Transport Capacity of OcHKT1;5 from Oryza coarctata Roxb. Plant & cell physiology, 61(7), 1321–1334. https://doi.org/10.1093/pcp/pcaa061

[242]    Dhingra, S., Sowdhamini, R., Cadet, F., & Offmann, B. (2020). A glance into the evolution of template-free protein structure prediction methodologies. Biochimie, 175, 85–92. https://doi.org/10.1016/j.biochi.2020.04.026

[241]    Shafi, KM., Joshi, AG., Meenakshi, I., Pasha, SN., Harini, K., Mahita, J., Sajeevan, RS., Karpe, SD., Ghosh, P., Nitish, S., Gandhimathi, A., Mathew, OK., Prasanna, SH., Malini, M., Mutt, E., Naika, M., Ravooru, N., Rao, RM., Shingate, PN., Sukhwal, A., Sunitha, MS., Upadhyay, AK., Vinekar, RS., & Sowdhamini, R. (2020). Dataset for the combined transcriptome assembly of M. oleifera and functional annotation. Data in brief, 30, 105416. https://doi.org/10.1016/j.dib.2020.105416

[240]    Sellamuthu, G., Jegadeeson, V., Sajeevan, R. S., Rajakani, R., Parthasarathy, P., Raju, K., Shabala, L., Chen, Z. H., Zhou, M., Sowdhamini, R., Shabala, S., & Venkataraman, G. (2020). Distinct Evolutionary Origins of Intron Retention Splicing Events in NHX1 Antiporter Transcripts Relate to Sequence Specific Distinctions in Oryza Species. Frontiers in plant science, 11, 267. https://doi.org/10.3389/fpls.2020.00267

[239]    Gurung, P. D., Upadhyay, A. K., Bhardwaj, P. K., Sowdhamini, R., & Ramakrishnan, U. (2019). Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species. BMC genomics, 20(1), 989. https://doi.org/10.1186/s12864-019-6354-1

[238]    Naveenkumar, N., Sowdhamini, R., & Srinivasan, N. (2019). Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family. FEBS open bio, 9(11), 1848–1859. https://doi.org/10.1002/2211-5463.12725

[237]    Sathyanarayanan, N., Cannone, G., Gakhar, L., Katagihallimath, N., Sowdhamini, R., Ramaswamy, S., & Vinothkumar, K. R. (2019). Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nature communications, 10(1), 4127. https://doi.org/10.1038/s41467-019-11931-1

[236]    Iyer, M. S., Bhargava, K., Pavalam, M., & Sowdhamini, R. (2019). GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies. Database : the journal of biological databases and curation, 2019, baz042. https://doi.org/10.1093/database/baz042

[235]    Tiwari, V., Karpe, S. D., & Sowdhamini, R. (2019). Topology prediction of insect olfactory receptors. Current opinion in structural biology, 55, 194–203. https://doi.org/10.1016/j.sbi.2019.05.014

[234]    Naveenkumar, N., Kumar, G., Sowdhamini, R., Srinivasan, N., & Vishwanath, S. (2019). Fold combinations in multi-domain proteins. Bioinformation, 15(5), 342–350. https://doi.org/10.6026/97320630015342

[233]    Ghosh, P., Joshi, A., Guita, N., Offmann, B., & Sowdhamini, R. (2019). EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins. BMC genomics, 20(1), 403. https://doi.org/10.1186/s12864-019-5755-5

[232]    Pasha, SN., Shafi, KM., Joshi, AG., Meenakshi, I., Harini, K., Mahita, J., Sajeevan, RS., Karpe, SD., Ghosh, P., Nitish, S., Gandhimathi, A., Mathew, OK., Prasanna, SH., Malini, M., Mutt, E., Naika, M., Ravooru, N., Rao, RM., Shingate, PN., Sukhwal, A., Sunitha, MS., Upadhyay, AK., Vinekar, RS., & Sowdhamini, R. (2020). The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera). Genomics, 112(1), 621–628. https://doi.org/10.1016/j.ygeno.2019.04.014

[231]    Batra, S., Corcoran, J., Zhang, D. D., Pal, P., K P, U., Kulkarni, R., Löfstedt, C., Sowdhamini, R., & Olsson, S. B. (2019). A Functional Agonist of Insect Olfactory Receptors: Behavior, Physiology and Structure. Frontiers in cellular neuroscience, 13, 134. https://doi.org/10.3389/fncel.2019.00134

[230]    Bhattacharyya, T., & Sowdhamini, R. (2019). Genome-Wide Search for Tyrosine Phosphatases in the Human Genome Through Computational Approaches Leads to the Discovery of Few New Domain Architectures. Evolutionary bioinformatics online, 15, 1176934319840289. https://doi.org/10.1177/1176934319840289

[229]    Ghosh, P., Bhattacharyya, T., Mathew, O. K., & Sowdhamini, R. (2019). PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. Database : the journal of biological databases and curation, 2019, baz028. https://doi.org/10.1093/database/baz028

[228]    Jayashree, S., Murugavel, P., Sowdhamini, R., & Srinivasan, N. (2019). Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions. Biology direct, 14(1), 1. https://doi.org/10.1186/s13062-019-0232-2

[227]    Shameer, K., Naika, M., Shafi, K. M., & Sowdhamini, R. (2019). Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. Progress in biophysics and molecular biology, 145, 19–39. https://doi.org/10.1016/j.pbiomolbio.2018.12.002

[226]    Upadhyay, A. K., & Sowdhamini, R. (2019). Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: Ocimum tenuiflorum. Bioinformatics and biology insights, 13, 1177932218821362. https://doi.org/10.1177/1177932218821362

[225]    Pandey, R. K., Dahiya, S., Mahita, J., Sowdhamini, R., & Prajapati, V. K. (2019). Vaccination and immunization strategies to design Aedes aegypti salivary protein based subunit vaccine tackling Flavivirus infection. International journal of biological macromolecules, 122, 1203–1211.

[224]    Gandhimathi A., Nitish Sathyanarayanan, Meenakshi Iyer, Rachit Gupta & R. Sowdhamini (2018) Evolutionary Analysis of a Few Protein Superfamilies in Ocimum tenuiflorum. In Compendium Plant Genomes, Chittaranjan Kole and Ajit Kumar Shasany (Eds): THE OCIMUM GENOME

[223]    Iyer, M. S., Joshi, A. G., & Sowdhamini, R. (2018). Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes. Molecular omics, 14(4), 266–280. https://doi.org/10.1039/c8mo00008e

[222]    Bendigiri, C., Harini, K., Yenkar, S., Zinjarde, S., Sowdhamini, R., & RaviKumar, A. (2018). Evaluating Ylehd, a recombinant epoxide hydrolase from Yarrowia lipolytica as a potential biocatalyst for the resolution of benzyl glycidyl ether. RSC Advances, 8(23), 12918–12926. https://doi.org/10.1039/C8RA00628H

[221]    Mahita, J., & Sowdhamini, R. (2018). Probing subtle conformational changes induced by phosphorylation and point mutations in the TIR domains of TLR2 and TLR3. Proteins, 86(5), 524–535. https://doi.org/10.1002/prot.25471

[220]    Mahita, J., & Sowdhamini, R. (2018). Investigating the effect of key mutations on the conformational dynamics of toll-like receptor dimers through molecular dynamics simulations and protein structure networks. Proteins, 86(4), 475–490. https://doi.org/10.1002/prot.25467

[219]    Gangadharan, B., Sunitha, M. S., Mukherjee, S., Chowdhury, R. R., Haque, F., Sekar, N., Sowdhamini, R., Spudich, J. A., & Mercer, J. A. (2017). Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region. Proceedings of the National Academy of Sciences of the United States of America, 114(42), 11115–11120. https://doi.org/10.1073/pnas.1710354114

[218]    Karpe, S. D., Dhingra, S., Brockmann, A., & Sowdhamini, R. (2017). Computational genome-wide survey of odorant receptors from two solitary bees Dufourea novaeangliae (Hymenoptera: Halictidae) and Habropoda laboriosa (Hymenoptera: Apidae). Scientific reports, 7(1), 10823. https://doi.org/10.1038/s41598-017-11098-z

[217]    Ghosh, P., & Sowdhamini, R. (2017). Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. BMC genomics, 18(1), 658. https://doi.org/10.1186/s12864-017-4045-3

[216]    Mahita, J., & Sowdhamini, R. (2017). Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-β (TRIF) provides insights into its autoinhibited state. Biology direct, 12(1), 9. https://doi.org/10.1186/s13062-017-0179-0

[215]    Vishwanath, S., Sukhwal, A., Sowdhamini, R., & Srinivasan, N. (2017). Specificity and stability of transient protein-protein interactions. Current opinion in structural biology, 44, 77–86. https://doi.org/10.1016/j.sbi.2016.12.010

[214]    Vinekar, R. S., & Sowdhamini, R. (2017). Three-dimensional Modelling of the Voltage-gated Sodium Ion Channel from Anopheles gambiae Reveals Spatial Clustering of Evolutionarily Conserved Acidic Residues at the Extracellular Sites. Current neuropharmacology, 15(8), 1062–1072. https://doi.org/10.2174/1567201814666161205131213

[213]    Ghosh, P., Mathew, O. K., & Sowdhamini, R. (2016). RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. BMC bioinformatics, 17(1), 411. https://doi.org/10.1186/s12859-016-1289-x

[212]    Karpe, S. D., Jain, R., Brockmann, A., & Sowdhamini, R. (2016). Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera. Genome biology and evolution, 8(9), 2879–2895. https://doi.org/10.1093/gbe/evw202

[211]    Pasha, S. N., Meenakshi, I., & Sowdhamini, R. (2016). Revisiting Myosin Families Through Large-scale Sequence Searches Leads to the Discovery of New Myosins. Evolutionary bioinformatics online, 12, 201–211. https://doi.org/10.4137/EBO.S39880

[210]    Rao, R. M., Pasha, S. N., & Sowdhamini, R. (2016). Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes. BMC genomics, 17(1), 742. https://doi.org/10.1186/s12864-016-3002-x

[209]    Upadhyay, A. K., & Sowdhamini, R. (2016). Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information. PloS one, 11(7), e0159627. https://doi.org/10.1371/journal.pone.0159627

[208]    Mutt, E., & Sowdhamini, R. (2016). Molecular Dynamics Simulations and Structural Analysis to Decipher Functional Impact of a Twenty Residue Insert in the Ternary Complex of Mus musculus TdT Isoform. PloS one, 11(6), e0157286. https://doi.org/10.1371/journal.pone.0157286

[207]    Mathew, O. K., & Sowdhamini, R. (2016). PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies. Bioinformatics and biology insights, 10, 105–109. https://doi.org/10.4137/BBI.S38416

[206]    Dhanyalakshmi, K. H., Naika, M. B., Sajeevan, R. S., Mathew, O. K., Shafi, K. M., Sowdhamini, R., & N Nataraja, K. (2016). An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. PloS one, 11(3), e0151323. https://doi.org/10.1371/journal.pone.0151323

[205]    Gandhimathi A, Margaret Sunitha S, Pritha Ghosh, Harini K, Subramanian Hariprasanna P, Iyer Meenakshi S, Joshi G, Karpe Snehal D, Jarjapu Mahita, Manoharan Malini, Oommen Mathew K, Eshita Mutt, Mahantesha Naika, Nithin Ravooru, Sathyanarayanan Nitish, Shaik Naseer Pasha, Upadhyayula Raghavender S, Rajas Rao M, Mohamed Shafi K, Prashant Shingate N, Anshul Sukhwal, Atul Upadhyay K, Rithvik Vinekar S & Ramanathan Sowdhamini. (2016). Draft Genome of Cissus quadrangularis to elucidate the Medicinal Values. Herbal Medicine, 2, 1-7, https://dx.doi.org/10.21767/2472-0151.10007

[204]    Kaleeckal Mathew, O., & Sowdhamini, R. (2016). PIMA: Protein-Protein interactions in Macromolecular Assembly - a web server for its Analysis and Visualization. Bioinformation, 12(1), 9–11. https://doi.org/10.6026/97320630012009

[203]    Sandhya, S., Mudgal, R., Kumar, G., Sowdhamini, R., & Srinivasan, N. (2016). Protein sequence design and its applications. Current opinion in structural biology, 37, 71–80. https://doi.org/10.1016/j.sbi.2015.12.004

[202]    Ghosh, P., & Sowdhamini, R. (2016). Genome-wide survey of putative RNA-binding proteins encoded in the human proteome. Molecular bioSystems, 12(2), 532–540. https://doi.org/10.1039/c5mb00638d

[201]    Barah, P., B N, M. N., Jayavelu, N. D., Sowdhamini, R., Shameer, K., & Bones, A. M. (2016). Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses. Nucleic acids research, 44(7), 3147–3164. https://doi.org/10.1093/nar/gkv1463

[200]    Gandhimathi, A., Ghosh, P., Hariharaputran, S., Mathew, O. K., & Sowdhamini, R. (2016). PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. Nucleic acids research, 44(D1), D410–D414. https://doi.org/10.1093/nar/gkv1205

[199]    Ghosh, P., Grellscheid, S. N., & Sowdhamini, R. (2016). A tale of two paralogs: human Transformer2 proteins with differential RNA-binding affinities. Journal of biomolecular structure & dynamics, 34(9), 1979–1986. https://doi.org/10.1080/07391102.2015.1100551

[198]    Kaushik, S., Nair, A. G., Mutt, E., Subramanian, H. P., & Sowdhamini, R. (2016). Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space. Bioinformatics (Oxford, England), 32(3), 338–344. https://doi.org/10.1093/bioinformatics/btv538

[197]    Shameer, K., Tripathi, L. P., Kalari, K. R., Dudley, J. T., & Sowdhamini, R. (2016). Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. Briefings in bioinformatics, 17(5), 841–862. https://doi.org/10.1093/bib/bbv084

[196]    Mahita, J., Harini, K., Rao Pichika, M., & Sowdhamini, R. (2016). An in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway. Journal of biomolecular structure & dynamics, 34(6), 1345–1362. https://doi.org/10.1080/07391102.2015.1079243

[195]    Gandhimathi, A., & Sowdhamini, R. (2016). Molecular modelling of human 5-hydroxytryptamine receptor (5-HT2A) and virtual screening studies towards the identification of agonist and antagonist molecules. Journal of biomolecular structure & dynamics, 34(5), 952–970. https://doi.org/10.1080/07391102.2015.1062802

[194]    Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, Gowda M, & Sowdhamini R. (2015). Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC plant biology, 15, 212. https://doi.org/10.1186/s12870-015-0562-x

[193]    Harini, K., & Sowdhamini, R. (2015). Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening. PloS one, 10(7), e0131077. https://doi.org/10.1371/journal.pone.0131077

[192]    Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. (2015). Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database: the journal of biological databases and curation, 2015, bav063. https://doi.org/10.1093/database/bav063

[191]    Metri, R., Hariharaputran, S., Ramakrishnan, G., Anand, P., Raghavender, U. S., Ochoa-Montaño, B., Higueruelo, A. P., Sowdhamini, R., Chandra, N. R., Blundell, T. L., & Srinivasan, N. (2015). SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. Database: the journal of biological databases and curation, 2015, bav060. https://doi.org/10.1093/database/bav060

[190]    Manoharan, M., Muhammad, S. A., & Sowdhamini, R. (2015). Sequence Analysis and Evolutionary Studies of Reelin Proteins. Bioinformatics and biology insights, 9, 187–193. https://doi.org/10.4137/BBI.S26530

[189]    Raghavender, U. S., & Sowdhamini, R. (2015). Mechanistic Basis Of Peptide-Protein Interaction In AtPep1-PEPR1 Complex In Arabidopsis thaliana. Protein and peptide letters, 22(7), 618–627. https://doi.org/10.2174/0929866522666150506154201

[188]    Sukhwal, A., & Sowdhamini, R. (2015). PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots. Bioinformatics and biology insights, 9, 141–151. https://doi.org/10.4137/BBI.S25928

[187]    Shingate, P., Warwicker, J., & Sowdhamini, R. (2015). Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins. PloS one, 10(6), e0127716. https://doi.org/10.1371/journal.pone.0127716

[186]    Malhotra, S., Mathew, O. K., & Sowdhamini, R. (2015). DOCKSCORE: a webserver for ranking protein-protein docked poses. BMC bioinformatics, 16(1), 127. https://doi.org/10.1186/s12859-015-0572-6

[185]    Holliday, G. L., Bairoch, A., Bagos, P. G., Chatonnet, A., Craik, D. J., Finn, R. D., Henrissat, B., Landsman, D., Manning, G., Nagano, N., O'Donovan, C., Pruitt, K. D., Rawlings, N. D., Saier, M., Sowdhamini, R., Spedding, M., Srinivasan, N., Vriend, G., Babbitt, P. C., & Bateman, A. (2015). Key challenges for the creation and maintenance of specialist protein resources. Proteins, 83(6), 1005–1013. https://doi.org/10.1002/prot.24803

[184]    Gupte, T. M., Haque, F., Gangadharan, B., Sunitha, M. S., Mukherjee, S., Anandhan, S., Rani, D. S., Mukundan, N., Jambekar, A., Thangaraj, K., Sowdhamini, R., Sommese, R. F., Nag, S., Spudich, J. A., & Mercer, J. A. (2015). Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies. The Journal of biological chemistry, 290(11), 7003–7015. https://doi.org/10.1074/jbc.M114.596676

[183]    Malhotra, S., & Sowdhamini, R. (2015). Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. Molecular bioSystems, 11(4), 1110–1118. https://doi.org/10.1039/c4mb00629a

[182]    Ramakrishnan, G., Ochoa-Montaño, B., Raghavender, U. S., Mudgal, R., Joshi, A. G., Chandra, N. R., Sowdhamini, R., Blundell, T. L., & Srinivasan, N. (2015). Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function. Tuberculosis (Edinburgh, Scotland), 95(1), 14–25. https://doi.org/10.1016/j.tube.2014.10.009

[181]    Mudgal, R., Sandhya, S., Kumar, G., Sowdhamini, R., Chandra, N. R., & Srinivasan, N. (2015). NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. Nucleic acids research, 43(Database issue), D300–D305. https://doi.org/10.1093/nar/gku888

[180]    Lakshmi, B., Ramakrishnan, C., Archunan, G., Sowdhamini, R., & Srinivasan, N. (2014). Investigations of Ramachandran disallowed conformations in protein domain families. International journal of biological macromolecules, 63, 119–125. https://doi.org/10.1016/j.ijbiomac.2013.10.032

[179]    Malhotra, S., & Sowdhamini, R. (2014). Sequence search and analysis of gene products containing RNA recognition motifs in the human genome. BMC genomics, 15(1), 1159. https://doi.org/10.1186/1471-2164-15-1159

[178]    Shameer, K., Naika, M. B., Mathew, O. K., & Sowdhamini, R. (2014). POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. Bioinformatics and biology insights, 8, 209–214. https://doi.org/10.4137/BBI.S19057

[177]    Kaushik, S., & Sowdhamini, R. (2014). Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages. BMC genomics, 15(1), 985. https://doi.org/10.1186/1471-2164-15-985

[176]    Shingate, P., Manoharan, M., Sukhwal, A., & Sowdhamini, R. (2014). ECMIS: computational approach for the identification of hotspots at protein-protein interfaces. BMC bioinformatics, 15(1), 303. https://doi.org/10.1186/1471-2105-15-303

[175]    Malhotra, S., & Sowdhamini, R. (2014). Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes. Bioinformatics and biology insights, 8, 193–198. https://doi.org/10.4137/BBI.S16313

[174]    Gupta, G. D., Dey, G., Swetha, M. G., Ramalingam, B., Shameer, K., Thottacherry, J. J., Kalappurakkal, J. M., Howes, M. T., Chandran, R., Das, A., Menon, S., Parton, R. G., Sowdhamini, R., Thattai, M., & Mayor, S. (2014). Population distribution analyses reveal a hierarchy of molecular players underlying parallel endocytic pathways. PloS one, 9(6), e100554. https://doi.org/10.1371/journal.pone.0100554

[173]    Dharmaprakash, A., Mutt, E., Jaleel, A., Ramanathan, S., & Thomas, S. (2014). Proteome profile of a pandemic Vibrio parahaemolyticus SC192 strain in the planktonic and biofilm condition. Biofouling, 30(6), 729–739. https://doi.org/10.1080/08927014.2014.916696

[172]    Joseph, A. P., Shingate, P., Upadhyay, A. K., & Sowdhamini, R. (2014). 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. Database : the journal of biological databases and curation, 2014, bau026. https://doi.org/10.1093/database/bau026

[171]    Nagarathnam, B., Karpe, S. D., Harini, K., Sankar, K., Iftekhar, M., Rajesh, D., Giji, S., Archunan, G., Balakrishnan, V., Gromiha, M. M., Nemoto, W., Fukui, K., & Sowdhamini, R. (2014). DOR - a Database of Olfactory Receptors - Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes. Bioinformatics and biology insights, 8, 147–158. https://doi.org/10.4137/BBI.S14858

[170]    Chacko, A. R., Mathew, O. K., Joshi, A., Raghavender, U. S., & Sowdhamini, R. (2014). SMoS. 2: update of database of structural motifs in superfamilies. Nucleic Acids Res. doi, 10

[169]    Kaushik, S., Etchebest, C., & Sowdhamini, R. (2014). Decoding the structural events in substrate-gating mechanism of eukaryotic prolyl oligopeptidase using normal mode analysis and molecular dynamics simulations. Proteins, 82(7), 1428–1443. https://doi.org/10.1002/prot.24511

[168]    Mudgal, R., Sowdhamini, R., Chandra, N., Srinivasan, N., & Sandhya, S. (2014). Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability. Journal of molecular biology, 426(4), 962–979. https://doi.org/10.1016/j.jmb.2013.11.026

[167]    Mutt, E., Mathew, O. K., & Sowdhamini, R. (2014). LenVarDB: database of length-variant protein domains. Nucleic acids research, 42(Database issue), D246–D250. https://doi.org/10.1093/nar/gkt1014

[166]    Malhotra, S., Sankar, K., & Sowdhamini, R. (2014). Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions. PloS one, 9(2), e80255. https://doi.org/10.1371/journal.pone.0080255

[165]    Manoharan, M., Fuchs, P. F., Sowdhamini, R., & Offmann, B. (2014). Insights on pH-dependent conformational changes of mosquito odorant binding proteins by molecular dynamics simulations. Journal of biomolecular structure & dynamics, 32(11), 1742–1751. https://doi.org/10.1080/07391102.2013.834118

[164]    Chacko, A., Patil, S., Upadhayay, A., Arya, D., Nagrajan, A., Khatri, R., Krishna, S., Sowdhamini, R., Ross, C., & Behl, R. (2013). A High Throughput Exome Sequencing Approach To Analyse Events Within a Good Responder CML Patient Under Imatinib At Diagnosis and Under Remission. Blood, 122(21), 5161. https://doi.org/10.1182/blood.V122.21.5161.5161

[163]    Mutt, E., Rani, S. S., & Sowdhamini, R. (2013). Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies. BioData mining, 6(1), 20. https://doi.org/10.1186/1756-0381-6-20

[162]    Arumugam, G., Nair, A. G., Hariharaputran, S., & Ramanathan, S. (2013). Rebelling for a reason: protein structural "outliers". PloS one, 8(9), e74416. https://doi.org/10.1371/journal.pone.0074416

[161]    Naika, M., Shameer, K., & Sowdhamini, R. (2013). Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics. Molecular bioSystems, 9(7), 1888–1908. https://doi.org/10.1039/c3mb70072k

[160]    Malhotra, S., & Sowdhamini, R. (2013). Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana: analysis of distribution and functions. Nucleic acids research, 41(15), 7212–7219. https://doi.org/10.1093/nar/gkt505

[159]    Joshi, A. G., Raghavender, U. S., & Sowdhamini, R. (2013). Improved performance of sequence search approaches in remote homology detection. F1000Research, 2, 93. https://doi.org/10.12688/f1000research.2-93.v2

[158]    Sukhwal, A., & Sowdhamini, R. (2013). Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies. Molecular bioSystems, 9(7), 1652–1661. https://doi.org/10.1039/c3mb25484d

[157]    Kaushik, S., Mutt, E., Chellappan, A., Sankaran, S., Srinivasan, N., & Sowdhamini, R. (2013). Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage. PloS one, 8(2), e56449. https://doi.org/10.1371/journal.pone.0056449

[156]    Manoharan, M., Sankar, K., Offmann, B., & Ramanathan, S. (2013). Association of putative members to family of mosquito odorant binding proteins: scoring scheme using fuzzy functional templates and cys residue positions. Bioinformatics and biology insights, 7, 231–251. https://doi.org/10.4137/BBI.S11096

[155]    Syamaladevi, D. P., Joshi, A., & Sowdhamini, R. (2013). An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins. Bioinformation, 9(10), 491–499. https://doi.org/10.6026/97320630009491

[154]    Mahantesha Naika, Khader Shameer, Ramanjini Gowda and Ramanathan Sowdhamini in the book entitled "Molecular Approaches for Abiotic Stress" edited by R. K. Gaur and P. Sharma (Centre for Agricultural Bioscience International Press, U.K.).

[153]    Manoharan, M., Ng Fuk Chong, M., Vaïtinadapoulé, A., Frumence, E., Sowdhamini, R., & Offmann, B. (2013). Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. Genome biology and evolution, 5(1), 163–180. https://doi.org/10.1093/gbe/evs131

[152]    Naika, M., Shameer, K., Mathew, O. K., Gowda, R., & Sowdhamini, R. (2013). STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant & cell physiology, 54(2), e8. https://doi.org/10.1093/pcp/pcs185

[151]    Prashant Shingate, Atul K. Upadhyay, U.S. Raghavender and R. Sowdhamini. (2012) Identification and Conformational Analysis of hinge regions in proteins that undergo domain swapping. To appear as a Chapter in a book entitled “Biomolecular Forms and Functions” (Eds. M. Bansal and N. Srinivasan).

[150]    Syamaladevi, D. P., Sunitha, M. S., Kalaimathy, S., Reddy, C. C., Iftekhar, M., Pasha, S. N., & Sowdhamini, R. (2012). Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence-structure-function relationships. Bioinformatics and biology insights, 6, 247–254. https://doi.org/10.4137/BBI.S9902

[149]    Sunitha, M. S., Nair, A. G., Charya, A., Jadhav, K., Mukhopadhyay, S., & Sowdhamini, R. (2012). Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins. BMC research notes, 5, 530. https://doi.org/10.1186/1756-0500-5-530

[148]    Harini Krishnan, Sankar Kannan, Waturu Nemoto, Kazuhiko Fukui and Sowdhamini, R. (2012) Residue conservation and dimer-interface analysis of olfactory receptor molecular models :100 OR models for the molecular biochemists. Journal of Molecular Biochemistry (2012)1,161-170

[147]    Margaret Sunitha, S., Mercer, J. A., Spudich, J. A., & Sowdhamini, R. (2012). Integrative structural modelling of the cardiac thin filament: energetics at the interface and conservation patterns reveal a spotlight on period 2 of tropomyosin. Bioinformatics and biology insights, 6, 203–223. https://doi.org/10.4137/BBI.S9798

[146]    Shingate, P., & Sowdhamini, R. (2012). Analysis of domain-swapped oligomers reveals local sequence preferences and structural imprints at the linker regions and swapped interfaces. PloS one, 7(7), e39305. https://doi.org/10.1371/journal.pone.0039305

[145]    Sandhya, S., Mudgal, R., Jayadev, C., Abhinandan, K. R., Sowdhamini, R., & Srinivasan, N. (2012). Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. Molecular bioSystems, 8(8), 2076–2084. https://doi.org/10.1039/c2mb25113b

[144]    Gromiha, M. M., Harini, K., Sowdhamini, R., & Fukui, K. (2012). Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity. BMC bioinformatics, 13 Suppl 7(Suppl 7), S1. https://doi.org/10.1186/1471-2105-13-S7-S1

[143]    Gandhimathi, A., Nair, A.G., & Sowdhamini, R. (2012). Comparison of Structure Based Sequence Alignment Programs for Protein Domain Superfamilies with Multiple Members. Advances in Computers, 2, 23-28.

[142]    Nagarathnam, B., Kalaimathy, S., Balakrishnan, V., & Sowdhamini, R. (2012). Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors. Evolutionary bioinformatics online, 8, 229–259. https://doi.org/10.4137/EBO.S9405

[141]    Malhotra, S., & Sowdhamini, R. (2012). Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. BMC bioinformatics, 13, 165. https://doi.org/10.1186/1471-2105-13-165

[140]    Shameer, K., & Sowdhamini, R. (2012). Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. Journal of clinical bioinformatics, 2(1), 8. https://doi.org/10.1186/2043-9113-2-8

[139]    Harini, K., & Sowdhamini, R. (2012). Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. Melanogaster. Bioinformatics and biology insights, 6, 33–47. https://doi.org/10.4137/BBI.S8990

[138]    Harbi, D., Parthiban, M., Gendoo, D. M., Ehsani, S., Kumar, M., Schmitt-Ulms, G., Sowdhamini, R., & Harrison, P. M. (2012). PrionHome: a database of prions and other sequences relevant to prion phenomena. PloS one, 7(2), e31785. https://doi.org/10.1371/journal.pone.0031785

[137]    Harbi, D., Parthiban, M., Gendoo, D. M., Ehsani, S., Kumar, M., Schmitt-Ulms, G., Sowdhamini, R., & Harrison, P. M. (2012). PrionHome: a database of prions and other sequences relevant to prion phenomena. PloS one, 7(2), e31785. https://doi.org/10.1371/journal.pone.0031785

[136]    Syamaladevi, D. P., Spudich, J. A., & Sowdhamini, R. (2012). Structural and functional insights on the Myosin superfamily. Bioinformatics and biology insights, 6, 11–21. https://doi.org/10.4137/BBI.S8451

[135]    Gandhimathi, A., Nair, A. G., & Sowdhamini, R. (2012). PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. Nucleic acids research, 40(Database issue), D531–D534. https://doi.org/10.1093/nar/gkr1096

[134]    Sundaramurthy, P., Sreenivasan, R., Shameer, K., Gakkhar, S., & Sowdhamini, R. (2011). HORIBALFRE program: Higher Order Residue Interactions Based ALgorithm for Fold REcognition. Bioinformation, 7(7), 352–359. https://doi.org/10.6026/97320630007352

[133]    Sowdhamini, R., Harrison, P., Harbi, D., Parthiban, M., Gendoo, D., Ehsani, S., Kumar, M., & Schmitt-Ulms, G. (2011). PrionOme: A database of prions and other sequences relevant to prion phenomena . Nature Precedings. https://doi.org/10.1038/npre.2011.6430.1

[132]    Nagarathnam, B., Sankar, K., Dharnidharka, V., Balakrishnan, V., Archunan, G., & Sowdhamini, R. (2011). TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences. Bioinformation, 7(5), 214–221. https://doi.org/10.6026/97320630007214

[131]    Divya P  Syamaladevi, S. Kalaimathy, Naseer Pasha, S. Subramonian and R. Sowdhamini. (2011) A three-step validation following genome-wide data  mining for myosin family members improves search efficiency. In Procceedings of IEEE ICDM 2011 workshop on Biological Data Mining and its Applications in Healthcare (BioDM). 2011(18):1071-1074

[130]    Mutt, E., Mitra, A., & Sowdhamini, R. (2011). Search for Protein Sequence Homologues that Display Considerable Domain Length Variations. International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 2(2), 55-77. http://doi.org/10.4018/jkdb.2011040104

[129]    Eshita Mutt, Abhijit Mitra and R. Sowdhamini. (2011) Mining protein sequence databases for remote homologues that can display considerable domain length variations. In Procceedings of IEEE ICDM 2011 workshop on Biological Data Mining and its Applications in Healthcare (ICDMW). 2011:1050-1057

[128]    Kaushik, S., & Sowdhamini, R. (2011). Structural analysis of prolyl oligopeptidases using molecular docking and dynamics: insights into conformational changes and ligand binding. PloS one, 6(11), e26251. https://doi.org/10.1371/journal.pone.0026251

[127]    Madan, L. L., Veeranna, S., Shameer, K., Reddy, C. C., Sowdhamini, R., & Gopal, B. (2011). Modulation of catalytic activity in multi-domain protein tyrosine phosphatases. PloS one, 6(9), e24766. https://doi.org/10.1371/journal.pone.0024766

[126]    Shameer, K., Shingate, P. N., Manjunath, S. C., Karthika, M., Pugalenthi, G., & Sowdhamini, R. (2011). 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. Database : the journal of biological databases and curation, 2011, bar042. https://doi.org/10.1093/database/bar042

[125]    Nagarathnam, B., Kannan, S., Dharnidharka, V., Balakrishnan, V., Archunan, G., & Sowdhamini, R. (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), 15–20. https://doi.org/10.6026/97320630007015

[124]    Syamaladevi, D. P., & Sowdhamini, R. (2011). Evolutionary traces decode molecular mechanism behind fast pace of myosin XI. BMC structural biology, 11, 35. https://doi.org/10.1186/1472-6807-11-35

[123]    Kanagarajadurai, K., Kalaimathy, S., Nagarajan, P., & Sowdhamini, R. (2011). PASS2: A Database of Structure-Based Sequence Alignments of Protein Structural Domain Superfamilies. International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 2(4), 53-66. http://doi.org/10.4018/jkdb.2011100104

[122]    Chilamakuri, C. S., Joshi, A., Rani, S. S., Offmann, B., & 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. https://doi.org/10.1155/2011/878973

[121]    Shameer, K., Pugalenthi, G., Kandaswamy, K. K., & Sowdhamini, R. (2011). 3dswap-pred: prediction of 3D domain swapping from protein sequence using Random Forest approach. Protein and peptide letters, 18(10), 1010–1020. https://doi.org/10.2174/092986611796378729

[120]    Kalaimathy, S., Sowdhamini, R., & Kanagarajadurai, K. (2011). Critical assessment of structure-based sequence alignment methods at distant relationships. Briefings in bioinformatics, 12(2), 163–175. https://doi.org/10.1093/bib/bbq025

[119]    Kumar, J., Choudhary, B. C., Metpally, R., Zheng, Q., Nonet, M. L., Ramanathan, S., Klopfenstein, D. R., & Koushika, S. 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. https://doi.org/10.1371/journal.pgen.1001200

[118]    V.S. Gowri, Khader Shameer, Chilamakuri Chandra Sekhar Reddy, Prashant Shingate & Ramanathan Sowdhamini (2010).A Sequence Data Mining Protocol to Identify Best Representative Sequence for Protein Domain Families. Proceedings of 2010 IEEE International Conference on Data Mining Workshops (ICDMW 2010) ISBN: 978-0-7695-4257-7

[117]    Shameer, K., Madan, L. L., Veeranna, S., Gopal, B., & Sowdhamini, R. (2010). PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. BMC bioinformatics, 11, 473. https://doi.org/10.1186/1471-2105-11-473

[116]    Sundaramurthy Pandurangan, Shameer Khader, Raashi Sreenivasan, Sunita Gakkhar and Sowdhamini Ramanathan*. (2010) A bioinformatics protocol for the identification of spatial clusters and the calculation of higher order residue interactions in protein structures. Nature Protocols Network (http://www.natureprotocols.com/2010/04/09/a_bioinformatics_protocol_for_1.php )

[115]    Pugalenthi, G., Kandaswamy, K. K., Suganthan, P. N., Sowdhamini, R., Martinetz, T., & Kolatkar, P. R. (2010). SMpred: a support vector machine approach to identify structural motifs in protein structure without using evolutionary information. Journal of biomolecular structure & dynamics, 28(3), 405–414. https://doi.org/10.1080/07391102.2010.10507369

[114]    Rajkumar, R., Prakash, S., Archunan, G., & Sowdhamini, R. (2010). Primary structural documentation of the major urinary protein of the Indian commensal rat (Rattus rattus) using a proteomic platform. Protein and peptide letters, 17(4), 449–457. https://doi.org/10.2174/092986610790963573

[113]    Shameer, K., Pugalenthi, G., Kandaswamy, K. K., Suganthan, P. N., Archunan, G., & Sowdhamini, R. (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, 33–42. https://doi.org/10.4137/bbi.s4464

[112]    Reddy, C. C., Rani, S. S., Offmann, B., & Sowdhamini, R. (2010). Systematic search for putative new domain families in Mycoplasma gallisepticum genome. BMC research notes, 3, 98. https://doi.org/10.1186/1756-0500-3-98

[111]    Pugalenthi, G., Kandaswamy, K. K., 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), 777–783. https://doi.org/10.1007/s00726-010-0520-8

[110]    Koshy, C., Parthiban, M., & Sowdhamini, R. (2010). 100 ns molecular dynamics simulations to study intramolecular conformational changes in Bax. Journal of biomolecular structure & dynamics, 28(1), 71–83. https://doi.org/10.1080/07391102.2010.10507344

[109]    Rajkumar, R., Prakash, S., Archunan, G., & Sowdhamini, R. (2010). Primary structural documentation of the major urinary protein of the Indian commensal rat (Rattus rattus) using a proteomic platform. Protein and peptide letters, 17(4), 449–457. https://doi.org/10.2174/092986610790963573

[108]    Anbazhagan, P., Purushottam, M., Kumar, H. B., Mukherjee, O., Jain, S., & Sowdhamini, R. (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), 581–598. https://doi.org/10.1080/07391102.2010.10508573

[107]    Parthiban, M., Shanmughavel, P., & Sowdhamini, R. (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), 1651–1670. https://doi.org/10.1007/s00894-010-0670-3

[106]    Sundaramurthy, P., Shameer, K., Sreenivasan, R., Gakkhar, S., & Sowdhamini, R. (2010). HORI: a web server to compute Higher Order Residue Interactions in protein structures. BMC bioinformatics, 11 Suppl 1(Suppl 1), S24. https://doi.org/10.1186/1471-2105-11-S1-S24

[105]    Shameer, K., Nagarajan, P., Gaurav, K., & Sowdhamini, R. (2009). 3PFDB--a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach. BioData mining, 2(1), 8. https://doi.org/10.1186/1756-0381-2-8

[104]    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 (http://www.natureprotocols.com/2009/09/03/a_bioinformatics_protocol_for.php)

[103]    Kanagarajadurai, K., Malini, M., Bhattacharya, A., Panicker, M. M., & Sowdhamini, R. (2009). Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding. Molecular bioSystems, 5(12), 1877–1888. https://doi.org/10.1039/b906391a

[102]    Shameer, K., Ambika, S., Varghese, S. M., Karaba, N., Udayakumar, M., & Sowdhamini, R. (2009). STIFDB-Arabidopsis Stress Responsive Transcription Factor DataBase. International journal of plant genomics, 2009, 583429. https://doi.org/10.1155/2009/583429

[101]    Doodhi, H., Ghosal, D., Krishnamurthy, M., Jana, S. C., Shamala, D., Bhaduri, A., Sowdhamini, R., & Ray, K. (2009). KAP, the accessory subunit of kinesin-2, binds the predicted coiled-coil stalk of the motor subunits. Biochemistry, 48(10), 2248–2260. https://doi.org/10.1021/bi8018338

[100]    Sandhya, S., Rani, S. S., Pankaj, B., Govind, M. K., Offmann, B., Srinivasan, N., & Sowdhamini, R. (2009). Length variations amongst protein domain superfamilies and consequences on structure and function. PloS one, 4(3), e4981. https://doi.org/10.1371/journal.pone.0004981

[99]    Bhaduri, A., Kalaimathy, S., & Sowdhamini, R. (2009). Conservation and divergence among Salmonella enterica subspecies. Infectious disorders drug targets, 9(3), 248–256. https://doi.org/10.2174/1871526510909030248

[98]    Sundaramurthy, P., Gakkhar, S., & Sowdhamini, R. (2009). Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each other: a systems approach. Bioinformation, 3(6), 244–249. https://doi.org/10.6026/97320630003244

[97]    Sundaramurthy, P., Gakkhar, S., & Sowdhamini, R. (2009). Computational prediction and analysis of impact of the cross-talks between JNK and P38 kinase cascades. Bioinformation, 3(6), 250–254. https://doi.org/10.6026/97320630003250

[96]    Thangudu, R. R., 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 structural biology, 8, 55. https://doi.org/10.1186/1472-6807-8-55

[95]    Tripathi, L. 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, 549. https://doi.org/10.1186/1471-2164-9-549

[94]    Sundar, A. S., Varghese, S. M., Shameer, K., Karaba, N., Udayakumar, M., & Sowdhamini, R. (2008). STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. Bioinformation, 2(10), 431–437. https://doi.org/10.6026/97320630002431

[93]    Anbazhagan, P., Purushottam, M., Kumar, H. B., Kubendran, S., Mukherjee, O., Brahmachari, S. K., Jain, S., & Sowdhamini, R. (2008). Evolutionary analysis of PHLPP1 gene in humans and non-human primates. Bioinformation, 2(10), 471–474. https://doi.org/10.6026/97320630002471

[92]    Reddy, C. C., Shameer, K., Offmann, B. O., & Sowdhamini, R. (2008). PURE: a webserver for the prediction of domains in unassigned regions in proteins. BMC bioinformatics, 9, 281. https://doi.org/10.1186/1471-2105-9-281

[91]    Vyas, N., Goswami, D., Manonmani, A., Sharma, P., Ranganath, H. A., VijayRaghavan, K., Shashidhara, L. S., Sowdhamini, R., & Mayor, S. (2008). Nanoscale organization of hedgehog is essential for long-range signaling. Cell, 133(7), 1214–1227. https://doi.org/10.1016/j.cell.2008.05.026

[90]    Kanagarajadurai, K., & Sowdhamini, R. (2008). Sequence and structural analyses of interleukin-8-like chemokine superfamily. In silico biology, 8(3-4), 307–330.

[89]    Sandhya, S., Pankaj, B., Govind, M. K., 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 structural biology, 8, 28. https://doi.org/10.1186/1472-6807-8-28

[88]    Alva, V., Syamala Devi, D. P., & Sowdhamini, R. (2008). COILCHECK: an interactive server for the analysis of interface regions in coiled coils. Protein and peptide letters, 15(1), 33–38. https://doi.org/10.2174/092986608783330314

[87]    Pugalenthi, G., Suganthan, P. N., Sowdhamini, R., & Chakrabarti, S. (2008). MegaMotifBase: a database of structural motifs in protein families and superfamilies. Nucleic acids research, 36(Database issue), D218–D221. https://doi.org/10.1093/nar/gkm794

[86]    Shah, P. K., Tripathi, L. P., Jensen, L. J., Gahnim, M., Mason, C., Furlong, E. E., Rodrigues, V., White, K. P., Bork, P., & 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), 199–215. https://doi.org/10.1016/j.gene.2007.10.012

[85]    N.Srinivasan, R.Sowdhamini and Alok Bhattacharya. (2007). Computational biology:More than just a set of techniques. J.Biosci.32:(1),1-2

[84]    Pugalenthi, G., Tang, K., 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. https://doi.org/10.1186/1471-2105-8-351

[83]    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 (http://www.natureprotocols.com/2007/11/01/pure_a_web_server_for_querying.php)

[82]    Shameer, K., & Sowdhamini, R. (2007). IWS: integrated web server for protein sequence and structure analysis. Bioinformation, 2(3), 86–90. https://doi.org/10.6026/97320630002086

[81]    Lokesh P. Tripathi and Ramanathan Sowdhamini (2007) Genome-wide survey of protein families and superfamilies. Biobytes

[80]    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), 207–218. https://doi.org/10.1080/07391102.2007.10507170

[79]    Parikh, N., Koshy, C., Dhayabaran, V., Perumalsamy, L. R., 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. https://doi.org/10.1186/1471-2121-8-16

[78]    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

[77]    Pugalenthi, G., Suganthan, P. N., Sowdhamini, R., & Chakrabarti, S. (2007). SMotif: a server for structural motifs in proteins. Bioinformatics (Oxford, England), 23(5), 637–638. https://doi.org/10.1093/bioinformatics/btl679

[76]    Metpally, R. P., Vigneshwar, R., & Sowdhamini, R. (2007). Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis. Journal of biosciences, 32(1), 43–50. https://doi.org/10.1007/s12038-007-0005-4

[75]    Gadkari, R. A., Sandhya, S., Sowdhamini, R., & Dighe, R. 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, 23–32. https://doi.org/10.1016/j.mce.2006.07.006

[74]    Khajamohiddin, S., Babu, P. S., Chakka, D., Merrick, M., Bhaduri, A., Sowdhamini, R., & Siddavattam, D. (2006). A novel meta-cleavage product hydrolase from Flavobacterium sp. ATCC27551. Biochemical and biophysical research communications, 351(3), 675–681. https://doi.org/10.1016/j.bbrc.2006.10.080

[73]    Tripathi, L. P., & Sowdhamini, R. (2006). Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC genomics, 7, 200. https://doi.org/10.1186/1471-2164-7-200

[72]    Chakrabarti, S., Manohari, G., Pugalenthi, G., & Sowdhamini, R. (2006). SSToSS--sequence-structural templates of single-member superfamilies. In silico biology, 6(4), 311–319.

[71]    Pugalenthi, G., Bhaduri, A., & Sowdhamini, R. (2006). iMOTdb--a comprehensive collection of spatially interacting motifs in proteins. Nucleic acids research, 34(Database issue), D285–D286. https://doi.org/10.1093/nar/gkj125

[70]    Reddy, C. S., Manonmani, A., Babu, M., & Sowdhamini, R. (2006). Enhanced structure prediction of gene products containing class III adenylyl cyclase domains. In silico biology, 6(5), 351–362.

[69]    Chakrabarti, S., Manohari, G., Pugalenthi, G., & Sowdhamini, R. (2006). SSToSS--sequence-structural templates of single-member superfamilies. In silico biology, 6(4), 311–319.

[68]    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(Web Server issue), W143–W146. https://doi.org/10.1093/nar/gkl157

[67]    Pugalenthi, G., Shameer, K., Srinivasan, N., & Sowdhamini, R. (2006). HARMONY: a server for the assessment of protein structures. Nucleic acids research, 34(Web Server issue), W231–W234. https://doi.org/10.1093/nar/gkl314

[66]    Pugalenthi, G., Bhaduri, A., & Sowdhamini, R. (2006). iMOTdb--a comprehensive collection of spatially interacting motifs in proteins. Nucleic acids research, 34(Database issue), D285–D286. https://doi.org/10.1093/nar/gkj125

[65]    Bhaduri, A., & Sowdhamini, R. (2006). Domain architectural census of eukaryotic gene products containing O-protein phosphatases. Gene, 366(2), 246–255. https://doi.org/10.1016/j.gene.2005.07.040

[64]    Sandhya, S., Jayadev, C., Abhinandan, K.R., Chakrabarti, S., Sowdhamini, R. and Srinivasan, N. Relating protein families in sequence space through multiple intermediates in Mathematical Biology: Recent trends Peeyush Chandra and B.V. Rathish Kumar (Eds) (2006) Copyright © 2006 Anamaya Publishers, New Delhi, India

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[62]    Gaurav, K., Gupta, N., & Sowdhamini, R. (2005). FASSM: enhanced function association in whole genome analysis using sequence and structural motifs. In silico biology, 5(5-6), 425–438.

[61]    Metpally, R. P., & 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. https://doi.org/10.1186/1471-2164-6-106

[60]    Bhaduri, A., & Sowdhamini, R. (2005). Genome-wide survey of prokaryotic O-protein phosphatases. Journal of molecular biology, 352(3), 736–752. https://doi.org/10.1016/j.jmb.2005.07.004

[59]    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. Journal of biomolecular structure & dynamics, 23(3), 283–298. https://doi.org/10.1080/07391102.2005.10507066

[58]    Metpally, R. P., & Sowdhamini, R. (2005). Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis. BMC evolutionary biology, 5, 41. https://doi.org/10.1186/1471-2148-5-41

[57]    Chakrabarti, S., Anand, A. P., Bhardwaj, N., Pugalenthi, G., & Sowdhamini, R. (2005). SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs. Nucleic acids research, 33(Web Server issue), W274–W276. https://doi.org/10.1093/nar/gki493

[56]    Pugalenthi, G., Archunan, G., & Sowdhamini, R. (2005). DIAL: a web-based server for the automatic identification of structural domains in proteins. Nucleic acids research, 33(Web Server issue), W130–W132. https://doi.org/10.1093/nar/gki427

[55]    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. Journal of molecular modeling, 11(6), 489–502. https://doi.org/10.1007/s00894-005-0258-5

[54]    Pugalenthi, G., Bhaduri, A., & Sowdhamini, R. (2005). GenDiS: Genomic Distribution of protein structural domain Superfamilies. Nucleic acids research, 33(Database issue), D252–D255. https://doi.org/10.1093/nar/gki087

[53]    Thangudu, R. R., 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, 58(4), 866–879. https://doi.org/10.1002/prot.20369

[52]    Blaise, M. C., 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. Journal of biomolecular structure & dynamics, 22(4), 399–410. https://doi.org/10.1080/07391102.2005.10507012

[51]    Chakrabarti, S., Bhardwaj, N., Anand, P. A., & Sowdhamini, R. (2004). Improvement of alignment accuracy utilizing sequentially conserved motifs. BMC bioinformatics, 5, 167. https://doi.org/10.1186/1471-2105-5-167

[50]    Blaise, M. C., Sowdhamini, R., Rao, M. R., & Pradhan, N. (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), 305–316. https://doi.org/10.1007/s00894-004-0196-7

[49]    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(1-3), 31–36. https://doi.org/10.1016/j.febslet.2004.05.028

[48]    Bhaduri, A., Pugalenthi, G., Gupta, N., & Sowdhamini, R. (2004). iMOT: an interactive package for the selection of spatially interacting motifs. Nucleic acids research, 32(Web Server issue), W602–W605. https://doi.org/10.1093/nar/gkh375

[47]    Bhaduri, A., Pugalenthi, G., & Sowdhamini, R. (2004). PASS2: an automated database of protein alignments organised as structural superfamilies. BMC bioinformatics, 5, 35. https://doi.org/10.1186/1471-2105-5-35

[46]    Innis, C. A., Anand, A. P., & Sowdhamini, R. (2004). Prediction of functional sites in proteins using conserved functional group analysis. Journal of molecular biology, 337(4), 1053–1068. https://doi.org/10.1016/j.jmb.2004.01.053

[45]    Bhaduri, A., Pugalenthi, G. & Sowdhamini, R.(2004) PASS2 Nucleic Acids Research , (http://www3.oup.co.uk/nar/database/summary/275(Web publication)

[44]    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).

[43]    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(1), 69–75. https://doi.org/10.1007/s00894-003-0169-2

[42]    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, 54(4), 657–670. https://doi.org/10.1002/prot.10638

[41]    Vinayagam, A., Pugalenthi, G., Rajesh, R., & Sowdhamini, R. (2004). DSDBASE: a consortium of native and modelled disulphide bonds in proteins. Nucleic acids research, 32(Database issue), D200–D202. https://doi.org/10.1093/nar/gkh026

[40]    Bhaduri, A., & Sowdhamini, R. (2003). A genome-wide survey of human tyrosine phosphatases. Protein engineering, 16(12), 881–888. https://doi.org/10.1093/protein/gzg144

[39]    Chakrabarti, S., Venkatramanan, K., & Sowdhamini, R. (2003). SMoS: a database of structural motifs of protein superfamilies. Protein engineering, 16(11), 791–793. https://doi.org/10.1093/protein/gzg110

[38]    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), 225–230. https://doi.org/10.1016/s0014-5793(03)00929-3

[37]    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 (Oxford, England), 19(14), 1760–1764. https://doi.org/10.1093/bioinformatics/btg233

[36]    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).

[35]    Chakrabarti, S., & Sowdhamini, R. (2003). Functional sites and evolutionary connections of acylhomoserine lactone synthases. Protein engineering, 16(4), 271–278. https://doi.org/10.1093/proeng/gzg031

[34]    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).

[33]    Bhaduri, A., Krishnaswamy, L., Ullal, G. R., Panicker, M. M., & Sowdhamini, R. (2003). Fold prediction and comparative modeling of Bdm1: a probable alpha/beta hydrolase associated with hot water epilepsy. Journal of molecular modeling, 9(1), 3–8. https://doi.org/10.1007/s00894-002-0102-0

[32]    Bhaduri, A., Mallika, V., & Sowdhamini, R. (2002). Genome Analysis of Pass2 a Semi-Automated Database of Protein Alignments Organised as Structural Superfamilies. TheScientificWorldJournal, 2, 9–10. https://doi.org/10.1100/tsw.2002.5

[31]    Mallika, V., Bhaduri, A., & Sowdhamini, R. (2002). PASS2: a semi-automated database of protein alignments organised as structural superfamilies. Nucleic acids research, 30(1), 284–288. https://doi.org/10.1093/nar/30.1.284

[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. S., Mhatre, N. 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), 289–293. https://doi.org/10.1093/nar/30.1.289

[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, 45(4), 408–420. https://doi.org/10.1002/prot.10010

[25]    Shah, P. K., & Sowdhamini, R. (2001). Structural understanding of the transmembrane domains of inositol triphosphate receptors and ryanodine receptors towards calcium channeling. Protein engineering, 14(11), 867–874. https://doi.org/10.1093/protein/14.11.867

[24]    Pullinger, G. D., Sowdhamini, R., & Lax, A. J. (2001). Localization of functional domains of the mitogenic toxin of Pasteurella multocida. Infection and immunity, 69(12), 7839–7850. https://doi.org/10.1128/IAI.69.12.7839-7850.2001

[23]    Sowdhamini, R., Burke, D. F., Huang, J. F., Mizuguchi, K., Nagarajaram, H. A., Srinivasan, N., Steward, R. E., & Blundell, T. L. (1998). CAMPASS: a database of structurally aligned protein superfamilies. Structure (London, England : 1993), 6(9), 1087–1094. https://doi.org/10.1016/s0969-2126(98)00110-5

[22]    Sowdhamini, R., Burke, D. F., Deane, C., Huang, J. F., 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, Biological crystallography, 54(Pt 6 Pt 1), 1168–1177. https://doi.org/10.1107/s0907444998007148

[21]    Chirgadze, D. Y., Hepple, J., Byrd, R. A., Sowdhamini, R., Blundell, T. L., & Gherardi, E. (1998). Insights into the structure of hepatocyte growth factor/scatter factor (HGF/SF) and implications for receptor activation. FEBS letters, 430(1-2), 126–129. https://doi.org/10.1016/s0014-5793(98)00558-4

[20]    Sowdhamini, R., Mitchell, T. J., Andrew, P. W., & Morgan, P. J. (1997). Structural and functional analogy between pneumolysin and proaerolysin. Protein engineering, 10(3), 207–215. https://doi.org/10.1093/protein/10.3.207

[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 & design, 1(3), 209–220. https://doi.org/10.1016/S1359-0278(96)00032-6

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

[16]    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.

[15]    Sowdhamini, R., & Blundell, T. L. (1995). An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein science : a publication of the Protein Society, 4(3), 506–520. https://doi.org/10.1002/pro.5560040317

[14]    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.

[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 HGF1/MSP). Protein science : a publication of the Protein Society, 3(12), 2378–2394. https://doi.org/10.1002/pro.5560031222

[12]    Srinivasan, N., Anuradha, V. S., Ramakrishnan, C., Sowdhamini, R., & Balaram, P. (1994). Conformational characteristics of asparaginyl residues in proteins. International journal of peptide and protein research, 44(2), 112–122. https://doi.org/10.1111/j.1399-3011.1994.tb00565.x

[11]    May, A. C., 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. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 344(1310), 373–381. https://doi.org/10.1098/rstb.1994.0076

[10]    Johnson, M. S., Srinivasan, N., Sowdhamini, R., & Blundell, T. L. (1994). Knowledge-based protein modeling. Critical reviews in biochemistry and molecular biology, 29(1), 1–68. https://doi.org/10.3109/10409239409086797

[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. Biochemical Society transactions, 21 ( Pt 3)(3), 597–604. https://doi.org/10.1042/bst0210597

[8]    Sowdhamini, R., Ramakrishnan, C., & Balaram, P. (1993). Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of alpha-conotoxin GI and endothelin I. Protein engineering, 6(8), 873–882. https://doi.org/10.1093/protein/6.8.873

[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(1), 79–83. https://doi.org/10.1016/0014-5793(93)80625-5

[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 beta beta motifs in proteins. Journal of molecular biology, 223(4), 845–851. https://doi.org/10.1016/0022-2836(92)90246-g

[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. International journal of peptide and protein research, 36(2), 147–155. https://doi.org/10.1111/j.1399-3011.1990.tb00958.x

[2]    Sowdhamini, R., Srinivasan, N., Shoichet, B., Santi, D. V., Ramakrishnan, C., & Balaram, P. (1989). Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis. Protein engineering, 3(2), 95–103. https://doi.org/10.1093/protein/3.2.95

[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.