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Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N et al.. 2015. Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.. BMC Plant Biol. 15:212.
Malhotra S, Mathew OK, Sowdhamini R. 2015. DOCKSCORE: a webserver for ranking protein-protein docked poses.. BMC Bioinformatics. 16:127.
Malhotra S, Sowdhamini R. 2015. Collation and analyses of DNA-binding protein domain families from sequence and structural databanks.. Mol Biosyst. 11(4):1110-8.
Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N et al.. 2015. Key challenges for the creation and maintenance of specialist protein resources.. Proteins. 83(6):1005-13.
Gupte TM, Haque F, Gangadharan B, Sunitha MS, Mukherjee S, Anandhan S, Rani DSelvi, Mukundan N, Jambekar A, Thangaraj K et al.. 2015. Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies.. J Biol Chem. 290(11):7003-15.
Mudgal R, Sandhya S, Kumar G, Sowdhamini R, Chandra NR, Srinivasan N. 2015. NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.. Nucleic Acids Res. 43(Database issue):D300-5.
Ramakrishnan G, Ochoa-Montaño B, Raghavender US, Mudgal R, Joshi AG, Chandra NR, Sowdhamini R, Blundell TL, Srinivasan N. 2015. Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.. Tuberculosis (Edinb). 95(1):14-25.
Harini K, Sowdhamini R. 2015. Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening.. PLoS One. 10(7):e0131077.
Metri R, Hariharaputran S, Ramakrishnan G, Anand P, Raghavender US, Ochoa-Montaño B, Higueruelo AP, Sowdhamini R, Chandra NR, Blundell TL et al.. 2015. SInCRe-structural interactome computational resource for Mycobacterium tuberculosis.. Database (Oxford). 2015:bav060.
Shingate P, Upadhyay A, Khader S, Sowdhamini R. 2015. 172 Computational analysis and prediction of proteins that undergo domain swapping.. J Biomol Struct Dyn. 33 Suppl 1:112-3.
Shingate P, Warwicker J, Sowdhamini R. 2015. Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins.. PLoS One. 10(6):e0127716.
Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJinan, Craik DJ, Finn RD, Gloriam D, Haft DH et al.. 2015. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.. Database (Oxford). 2015:bav063.
Sukhwal A, Sowdhamini R. 2015. PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots.. Bioinform Biol Insights. 9:141-51.
Raghavender US, Sowdhamini R. 2015. Mechanistic Basis Of Peptide-Protein Interaction In AtPep1-PEPR1 Complex In Arabidopsis thaliana.. Protein Pept Lett. 22(7):618-27.
Kaushik S, Nair AG, Mutt E, Subramanian HPrasanna, Sowdhamini R. 2016. Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space.. Bioinformatics. 32(3):338-44.
Dhanyalakshmi KH, Naika MBN, Sajeevan RS, Mathew OK, K Shafi M, Sowdhamini R, Nataraja KN. 2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.. PLoS One. 11(3):e0151323.
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.
Mathew OKaleeckal, Sowdhamini R. 2016. PIMA: Protein-Protein interactions in Macromolecular Assembly - a web server for its Analysis and Visualization.. Bioinformation. 12(1):9-11.
Sandhya S, Mudgal R, Kumar G, Sowdhamini R, Srinivasan N. 2016. Protein sequence design and its applications.. Curr Opin Struct Biol. 37:71-80.
Barah P, N MNaika B, Jayavelu NDoni, Sowdhamini R, Shameer K, Bones AM. 2016. Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.. Nucleic Acids Res. 44(7):3147-64.
Upadhyay AKumar, 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.
Mathew OK, Sowdhamini R. 2016. PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.. Bioinform Biol Insights. 10:105-9.
Pasha SNaseer, Meenakshi I, Sowdhamini R. 2016. Revisiting Myosin Families Through Large-scale Sequence Searches Leads to the Discovery of New Myosins.. Evol Bioinform Online. 12:201-11.
Rao RM, Pasha SNaseer, Sowdhamini R. 2016. Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes.. BMC Genomics. 17(1):742.
Mahita J, Harini K, Pichika MRao, Sowdhamini R. 2016. An in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway.. J Biomol Struct Dyn. 34(6):1345-62.
Ghosh P, Mathew OK, 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.
Vinekar RS, Sowdhamini R. 2016. 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.. Curr Neuropharmacol.
Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R. 2016. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.. Brief Bioinform. 17(5):841-62.
Vishwanath S, Sukhwal A, Sowdhamini R, Srinivasan N. 2017. Specificity and stability of transient protein-protein interactions.. Curr Opin Struct Biol. 44:77-86.
Mahita J, Sowdhamini R. 2017. Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-β (TRIF) provides insights into its autoinhibited state.. Biol Direct. 12(1):9.
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.
Gangadharan B, Sunitha MS, Mukherjee S, Chowdhury RRoy, Haque F, Sekar N, Sowdhamini R, Spudich JA, Mercer JA. 2017. Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region.. Proc Natl Acad Sci U S A.
Mahita J, Sowdhamini R. 2018. Probing subtle conformational changes induced by phosphorylation and point mutations in the TIR domains of TLR2 and TLR3.. Proteins.
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.
Pandey RKumar, Dahiya S, Mahita J, Sowdhamini R, Prajapati VKumar. 2019. Vaccination and immunization strategies to design Aedes aegypti salivary protein based subunit vaccine tackling Flavivirus infection.. Int J Biol Macromol. 122:1203-1211.
Shameer K, Naika MBN, K Shafi M, Sowdhamini R. 2019. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production.. Prog Biophys Mol Biol. 145:19-39.
Upadhyay AKumar, Sowdhamini R. 2019. Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: .. Bioinform Biol Insights. 13:1177932218821362.
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.. Biol Direct. 14(1):1.
Ghosh P, Bhattacharyya T, Mathew OK, Sowdhamini R. 2019. PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe.. Database (Oxford). 2019
Iyer MS, Bhargava K, Pavalam M, Sowdhamini R. 2019. GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies.. Database (Oxford). 2019
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.. Evol Bioinform Online. 15:1176934319840289.
Batra S, Corcoran J, Zhang D-D, Pal P, P UK, Kulkarni R, Löfstedt C, Sowdhamini R, Olsson SB. 2019. A Functional Agonist of Insect Olfactory Receptors: Behavior, Physiology and Structure.. Front Cell Neurosci. 13:134.
Tiwari V, Karpe SD, Sowdhamini R. 2019. Topology prediction of insect olfactory receptors.. Curr Opin Struct Biol. 55:194-203.
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.
Pasha SNaseer, K Shafi M, Joshi AG, Meenakshi I, Harini K, Mahita J, Sajeevan RSivarajan, Karpe SD, Ghosh P, Nitish S et al.. 2020. The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera).. Genomics. 112(1):621-628.
Sellamuthu G, Jegadeeson V, Sajeevan RSivarajan, Rajakani R, Parthasarathy P, Raju K, Shabala L, Chen Z-H, Zhou M, Sowdhamini R et al.. 2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species.. Front Plant Sci. 11:267.
K Shafi M, Joshi AG, Meenakshi I, Pasha SNaseer, Harini K, Mahita J, Sajeevan RSivarajan, Karpe SD, Ghosh P, Nitish S et al.. 2020. Dataset for the combined transcriptome assembly of and functional annotation.. Data Brief. 30:105416.
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.
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.. J Biosci. 45