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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.
Juma M, Sankaradoss A, Ndombi R, Mwaura P, Damoda T, Nazir J, Pandit A, Khurana R, Masika M, Chirchir R et al.. 2021. Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting. Front. Microbiol.
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.
Sharma A, Krishna S, Sowdhamini R. 2023. Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites.. Mol Biol Evol.
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.
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.
K Shafi 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.
Harini K, Sowdhamini R. 2015. Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening.. PLoS One. 10(7):e0131077.
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
Bheemireddy S, Sandhya S, Srinivasan N, Sowdhamini R. 2022. Computational tools to study RNA-protein complexes.. Front Mol Biosci. 9:954926.
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.
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.
Sarkar SR, Dubey VKumar, Jahagirdar A, Lakshmanan V, Haroon MMohamed, 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.. Dev Biol.
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.
Ahmed A, Mam B, Sowdhamini R. 2021. DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity.. Bioinform Biol Insights. 15:11779322211030364.
Mondal S, K Shafi M, Raizada A, Song H, Badigannavar AM, 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.
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.
Kalmankar NV, Hari H, Sowdhamini R, Venkatesan R. 2021. Disulfide-Rich Cyclic Peptides from Protect against β-Amyloid Toxicity and Oxidative Stress in Transgenic .. J Med Chem.
Malhotra S, Mathew OK, Sowdhamini R. 2015. DOCKSCORE: a webserver for ranking protein-protein docked poses.. BMC Bioinformatics. 16:127.
Kalmankar NV, 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 (Oxford). 2022
Rebehmed J, de Brevern AG, Sowdhamini R, Joseph APraveen. 2022. Editorial: Advances in Molecular Docking and Structure-Based Modelling.. Front Mol Biosci. 9:839826.
Kalmankar NV, Gehi BRajendraku, Sowdhamini R. 2022. Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations.. Front Mol Biosci. 9:986704.
Shingate P, Warwicker J, Sowdhamini R. 2015. Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins.. PLoS One. 10(6):e0127716.
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.
Naika MBN, Sathyanarayanan N, Sajeevan RSivarajan, Bhattacharyya T, Ghosh P, Iyer MS, Jarjapu M, Joshi AG, Harini K, K Shafi M et al.. 2022. Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.).. Sci Rep. 12(1):13534.
Naveenkumar N, Kumar G, Sowdhamini R, Srinivasan N, Vishwanath S. 2019. Fold combinations in multi-domain proteins.. Bioinformation. 15(5):342-350.
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.
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
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.
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.
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.
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.
Verma S, Sowdhamini R. 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.. Biol Direct. 17(1):24.
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.
Iyer MS, Joshi AG, Sowdhamini R. 2018. Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes.. Mol Omics.
Bhattacharyya T, Sowdhamini R. 2021. Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes. Cell Signal. (110009)
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.
Karpe SD, Jain R, Brockmann A, Sowdhamini R. 2016. Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera.. Genome Biol Evol. 8(9):2879-2895.
Sankaradoss A, Jagtap S, Nazir J, Moula S-E, Modak A, Fialho J, Iyer M, Shastri JS, Dias M, Gadepalli R et al.. 2022. Immune profile and responses of a novel Dengue DNA vaccine encoding EDIII-NS1 consensus design based on Indo-African sequences.. Mol Ther.
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.
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.
Chauhan PKumar, Sowdhamini R. 2022. Integrative network analysis interweaves the missing links in cardiomyopathy diseasome.. Sci Rep. 12(1):19670.
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.
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.
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.
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.
Joshi AG, Harini K, Meenakshi I, K Shafi M, Pasha SNaseer, Mahita J, Sajeevan RSivarajan, Karpe SD, Ghosh P, Nitish S et al.. 2020. A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.. MethodsX. 7:101053.
Harini K, Jayashree S, Tiwari V, Vishwanath S, Sowdhamini R. 2021. Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors.. Bioinform Biol Insights. 15:11779322211037769.
Chauhan PKumar, Sowdhamini R. 2022. LIM domain-wide comprehensive virtual mutagenesis provides structural rationale for cardiomyopathy mutations in CSRP3.. Sci Rep. 12(1):3562.
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.
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.
Mam B, Karpe SD, Sowdhamini R. 2023. Minus-C subfamily has diverged from Classic odorant-binding proteins in honeybees. APIDOLOGIE . 54(1):12.
Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. 2019. Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.. Nat Commun. 10(1):4127.
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.
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.
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.
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
Bhattacharyya T, Nayak S, Goswami S, Gadiyaram V, Mathew OK, Sowdhamini R. 2022. PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe.. Database (Oxford). 2022
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.
Mathew OK, Sowdhamini R. 2016. PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.. Bioinform Biol Insights. 10:105-9.
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.
Mahita J, Sowdhamini R. 2018. Probing subtle conformational changes induced by phosphorylation and point mutations in the TIR domains of TLR2 and TLR3.. Proteins.
Sandhya S, Mudgal R, Kumar G, Sowdhamini R, Srinivasan N. 2016. Protein sequence design and its applications.. Curr Opin Struct Biol. 37:71-80.
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.
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.
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.
Manoharan M, Muhammad SAuwn, Sowdhamini R. 2015. Sequence Analysis and Evolutionary Studies of Reelin Proteins.. Bioinform Biol Insights. 9:187-93.
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.
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.
Vishwanath S, Sukhwal A, Sowdhamini R, Srinivasan N. 2017. Specificity and stability of transient protein-protein interactions.. Curr Opin Struct Biol. 44:77-86.
Bhattacharyya T, Ghosh A, Verma S, Raghu P, Sowdhamini R. 2023. Structural rationale to understand the effect of disease-associated mutations on Myotubularin.. Curr Res Struct Biol. 5:100100.
Naveenkumar N, Prabantu VManjveekar, Vishwanath S, Sowdhamini R, Srinivasan N. 2022. Structures of distantly-related interacting protein homologues are less divergent than non-interacting homologues.. FEBS Open Bio.
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.
Tiwari V, Karpe SD, Sowdhamini R. 2019. Topology prediction of insect olfactory receptors.. Curr Opin Struct Biol. 55:194-203.
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.
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.
K Shafi M, Sajeevan RSivarajan, Kouser S, Vishnuprasad CN, Sowdhamini R. 2022. Transcriptome profiling of two Moringa species and insights into their antihyperglycemic activity.. BMC Plant Biol. 22(1):561.
Kalmankar NV, Venkatesan R, Balaram P, Sowdhamini R. 2020. Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis.. Sci Rep. 10(1):12658.
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.