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Ramanathan Sowdhamini

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Mahantesha Naika; Shameer Khader; Ramanjini Gowda; Oommen K Mathew; Ramanathan Sowdhamini
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.
Swati Kaushik; Eshita Mutt; Sandhya Sankaran; Ajithavalli Chellappan; Narayanaswamy Srinivasan; Ramanathan Sowdhamini
Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage.
Malini Manoharan; Matthieu Ng Fuk Chong; Ramanathan Sowdhamini; Aurore Vaïtinadapoulé; Etienne Frumence; Bernard OFFMANN
Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus.

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All Publications

2013: Mahantesha Naika; Shameer Khader; Ramanjini Gowda; Oommen K Mathew; Ramanathan Sowdhamini
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 2013;54(2):e8.
2013: Swati Kaushik; Eshita Mutt; Sandhya Sankaran; Ajithavalli Chellappan; Narayanaswamy Srinivasan; Ramanathan Sowdhamini
Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage.
PloS one 2013;8(2):e56449.
2013: Malini Manoharan; Matthieu Ng Fuk Chong; Ramanathan Sowdhamini; Aurore Vaïtinadapoulé; Etienne Frumence; Bernard OFFMANN
Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus.
Genome biology and evolution 2013;5(1):163-80.
2012: Sankaran Sandhya; Ramanathan Sowdhamini; KR Abhinandan; C Jayadev; R Mudgal; Narayanaswamy Srinivasan
Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins.
Molecular bioSystems 2012;8(8):2076-84.
2012: Divya P Syamaladevi; Margaret S Sunitha; Mohammed Iftekhar; S Kalaimathy; Shaik N Pasha; Chandrashekar C Reddy; Ramanathan Sowdhamini
Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence-structure-function relationships.
Bioinformatics and biology insights 2012;6():247-54.
2012: S Margaret Sunitha; John A Mercer; James A Spudich; Ramanathan Sowdhamini
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 2012;6():203-23.
2012: Margaret S Sunitha; Amol Charya; Kamalakar Jadhav; Sami Mukhopadhyay; Anu G Nair; Ramanathan Sowdhamini
Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins.
BMC research notes 2012;5():530.
2012: Prashant Shingate; Ramanathan Sowdhamini
Analysis of domain-swapped oligomers reveals local sequence preferences and structural imprints at the linker regions and swapped interfaces.
PloS one 2012;7(7):e39305.
2012: Balasubramanian Nagarathnam; Veluchamy Balakrishnan; Singaravelu Kalaimathy; Ramanathan Sowdhamini
Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors.
Evolutionary bioinformatics online 2012;8():229-59.
2012: Sony Malhotra; Ramanathan Sowdhamini
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.
BMC bioinformatics 2012;13():165.
2012: K Harini; Ramanathan Sowdhamini
Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. Melanogaster.
Bioinformatics and biology insights 2012;6():33-47.
2012: Shameer Khader; Ramanathan Sowdhamini
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome.
Journal of clinical bioinformatics 2012;2(1):8.
2012: Divya P Syamaladevi; James A Spudich; Ramanathan Sowdhamini
Structural and functional insights on the Myosin superfamily.
Bioinformatics and biology insights 2012;6():11-21.
2012: Djamel Harbi; Sepehr Ehsani; Deena M A Gendoo; Manish Kumar; Marimuthu Parthiban; Gerold Schmitt-Ulms; Ramanathan Sowdhamini; Paul M Harrison
PrionHome: a database of prions and other sequences relevant to prion phenomena.
PloS one 2012;7(2):e31785.
2011: Shameer Khader; Ganesan Pugalenthi; Krishna Kumar Kandaswamy; Ramanathan Sowdhamini
3dswap-pred: prediction of 3D domain swapping from protein sequence using Random Forest approach.
Protein and peptide letters 2011;18(10):1010-20.
2011: Singarevelu Kalaimathy; Ramanathan Sowdhamini; Kanagarajadurai karuppiah
Critical assessment of structure-based sequence alignment methods at distant relationships.
Briefings in bioinformatics 2011;12(2):163-75.
2011: Pandurangan Sundaramurthy; Raashi Sreenivasan; Sunita Gakkhar; Shameer Khader; Ramanathan Sowdhamini
HORIBALFRE program: Higher Order Residue Interactions Based ALgorithm for Fold REcognition.
Bioinformation 2011;7(7):352-9.
2011: Swati Kaushik; Ramanathan Sowdhamini
Structural analysis of prolyl oligopeptidases using molecular docking and dynamics: insights into conformational changes and ligand binding.
PloS one 2011;6(11):e26251.
2011: Balasubramanian Nagarathnam; Kannan Sankar; Govindaraju Archunan; Veluchamy Balakrishnan; Varadhan Dharnidharka; Ramanathan Sowdhamini
TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences.
Bioinformation 2011;7(5):214-21.
2011: Shameer Khader; Prashant N Shingate; M Karthika; S C P Manjunath; Ganesan Pugalenthi; Ramanathan Sowdhamini
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.
Database : the journal of biological databases and curation 2011;2011():bar042.
2011: Divya P Syamaladevi; Ramanathan Sowdhamini
Evolutionary traces decode molecular mechanism behind fast pace of myosin XI.
BMC structural biology 2011;11():35.
2011: Lalima L Madan; Chilamakuri C S Reddy; Shameer Khader; Ramanathan Sowdhamini; S Veeranna; B Gopal
Modulation of catalytic activity in multi-domain protein tyrosine phosphatases.
PloS one 2011;6(9):e24766.
2011: Balasubramanian Nagarathnam; Govindaraju Archunan; Veluchamy Balakrishnan; Varadhan Dharnidharka; Sankar Kannan; Ramanathan Sowdhamini
Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters.
Bioinformation 2011;7(1):15-20.
2011: Chandra Sekhar Reddy Chilamakuri; Adwait Joshi; Bernard OFFMANN; Sane Sudha Rani; Ramanathan Sowdhamini
Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species.
Comparative and functional genomics 2011;2011():878973.
2010: Ganesan Pugalenthi; Krishna Kumar Kandaswamy; PN Suganthan; Ramanathan Sowdhamini; Thomas Martinetz; Prasanna R Kolatkar
SMpred: a support vector machine approach to identify structural motifs in protein structure without using evolutionary information.
Journal of biomolecular structure & dynamics 2010;28(3):405-14.
2010: Marimuthu Parthiban; Piramanayagam Shanmughavel; Ramanathan Sowdhamini
In silico point mutation and evolutionary trace analysis applied to nicotinic acetylcholine receptors in deciphering ligand-binding surfaces.
Journal of molecular modeling 2010;16(10):1651-70.
2010: C Koshy; M Parthiban; Ramanathan Sowdhamini
100 ns molecular dynamics simulations to study intramolecular conformational changes in Bax.
Journal of biomolecular structure & dynamics 2010;28(1):71-83.
2010: Ganesan Pugalenthi; Krishna Kumar Kandaswamy; PN Suganthan; Govindaraju Archunan; Ramanathan Sowdhamini
Identification of functionally diverse lipocalin proteins from sequence information using support vector machine.
Amino acids 2010;39(3):777-83.
2010: Padmanabhan Anbazhagan; Meera Purushottam; H B Kiran Kumar; Odity Mukherjee; Sanjeev Jain; Ramanathan Sowdhamini
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 2010;27(5):581-98.
2010: Ramalingam Rajkumar; Subramaniya Prakash; Govindaraju Archunan; Ramanathan Sowdhamini
Primary structural documentation of the major urinary protein of the Indian commensal rat (Rattus rattus) using a proteomic platform.
Protein and peptide letters 2010;17(4):449-57.
2010: Shameer Khader; Lalima L Madan; Shivamurthy Veeranna; Balasubramanian Gopal; Ramanathan Sowdhamini
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes.
BMC bioinformatics 2010;11():473.
2010: Khader Shameer; Ganesan Pugalenthi; Krishna Kumar Kandaswamy; Ponnuthurai N Suganthan; Govindaraju Archunan; Ramanathan Sowdhamini
Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach.
Bioinformatics and biology insights 2010;4():33-42.
2010: Chilamakuri Cs Reddy; Sane Sudha Rani; Bernard OFFMANN; Ramanathan Sowdhamini
Systematic search for putative new domain families in Mycoplasma gallisepticum genome.
BMC research notes 2010;3():98.
2010: Pandurangan Sundaramurthy; Shameer Khader; Raashi Sreenivasan; Sunita Gakkhar; Ramanathan Sowdhamini
HORI: a web server to compute Higher Order Residue Interactions in protein structures.
BMC bioinformatics 2010;11 Suppl 1():S24.
2009: Kanagarajadurai karuppiah; Manoharan Malini; Aditi Bhattacharya; Mitradas M Panicker; Ramanathan Sowdhamini
Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding.
Molecular bioSystems 2009;5(12):1877-88.
2009: Anirban Bhaduri; S Kalaimathy; Ramanathan Sowdhamini
Conservation and divergence among Salmonella enterica subspecies.
Infectious disorders drug targets 2009;9(3):248-56.
2009: Khader Shameer; Paramasivam Nagarajan; Kumar Gaurav; Ramanathan Sowdhamini
3PFDB--a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach.
BioData mining 2009;2(1):8.
2009: Shameer Khader; S Ambika; Susan Mary Varghese; N Karaba; Makarla Udayakumar; Ramanathan Sowdhamini
STIFDB-Arabidopsis Stress Responsive Transcription Factor DataBase.
International journal of plant genomics 2009;2009():583429.
2009: Sankaran Sandhya; Saane Sudha Rani; pankaj bagul; Madabosse Kande Govind; Bernard OFFMANN; Narayanaswamy Srinivasan; Ramanathan Sowdhamini
Length variations amongst protein domain superfamilies and consequences on structure and function.
PloS one 2009;4(3):e4981.
2009: Pandurangan Sundaramurthy; Sunita Gakkhar; Ramanathan Sowdhamini
Computational prediction and analysis of impact of the cross-talks between JNK and P38 kinase cascades.
Bioinformation 2009;3(6):250-4.
2009: Pandurangan Sundaramurthy; Sunita Gakkhar; Ramanathan Sowdhamini
Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each other: a systems approach.
Bioinformation 2009;3(6):244-9.
2008: Parantu K Shah; Lokesh P Tripathi; Lars Jensen; Murad Gahnim; Christopher Mason; Eileen E M Furlong; Veronica Rodrigues; Kevin P White; Peer Bork; Ramanathan Sowdhamini
Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.
Gene 2008;407(1-2):199-215.
2008: Ratna R Thangudu; Malini Manoharan; Narayanaswamy Srinivasan; Frédéric Cadet; Ramanathan Sowdhamini; Bernard OFFMANN
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families.
BMC structural biology 2008;8():55.
2008: Kanagarajadurai karuppiah; Ramanathan Sowdhamini
Sequence and structural analyses of interleukin-8-like chemokine superfamily.
In silico biology 2008;8(3-4):307-30.
2008: Padmanabhan Anbazhagan; Meera Purushottam; H B Kiran Kumar; Shobana Kubendran; Odity Mukherjee; Samir K Brahmachari; Sanjeev Jain; Ramanathan Sowdhamini
Evolutionary analysis of PHLPP1 gene in humans and non-human primates.
Bioinformation 2008;2(10):471-4.
2008: Ambika Shyam Sundar; Susan Mary Varghese; Khader Shameer; Nataraja Karaba; Makarla Udayakumar; Ramanathan Sowdhamini
STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana.
Bioinformation 2008;2(10):431-7.
2008: Chilamakuri C S Reddy; Shameer Khader; Bernard OFFMANN; Ramanathan Sowdhamini
PURE: a webserver for the prediction of domains in unassigned regions in proteins.
BMC bioinformatics 2008;9():281.
2008: Sankaran Sandhya; pankaj bagul; Madabosse Kande Govind; Bernard OFFMANN; Narayanaswamy Srinivasan; Ramanathan Sowdhamini
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 2008;8():28.
2008: Ganesan Pugalenthi; PN Suganthan; Ramanathan Sowdhamini; Saikat Chakrabarti
MegaMotifBase: a database of structural motifs in protein families and superfamilies.
Nucleic acids research 2008;36(Database issue):D218-21.
2007: M Vijayalakshmi; GV Shivashankar; Ramanathan Sowdhamini
Simulations of SIN mutations and histone variants in human nucleosomes reveal altered protein-DNA and core histone interactions.
Journal of biomolecular structure & dynamics 2007;25(3):207-18.
2007: Ganesan Pugalenthi; PN Suganthan; Ramanathan Sowdhamini; Saikat Chakrabarti
SMotif: a server for structural motifs in proteins.
Bioinformatics (Oxford, England) 2007;23(5):637-8.
2007: Shameer Khader; Ramanathan Sowdhamini
IWS: integrated web server for protein sequence and structure analysis.
Bioinformation 2007;2(3):86-90.
2007: Ganesan Pugalenthi; Ke Tang; PN Suganthan; Govindaraju Archunan; Ramanathan Sowdhamini
A machine learning approach for the identification of odorant binding proteins from sequence-derived properties.
BMC bioinformatics 2007;8():351.
2007: Raghu Metpally; Ramakrishnan Vigneshwar; Ramanathan Sowdhamini
Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis.
Journal of biosciences 2007;32(1):43-50.
2006: Syed Khajamohiddin; Pakala Suresh Babu; Deviprasanna Chakka; Mike Merrick; Anirban Bhaduri; Ramanathan Sowdhamini; Dayananda Siddavattam
A novel meta-cleavage product hydrolase from Flavobacterium sp. ATCC27551.
Biochemical and biophysical research communications 2006;351(3):675-81.
2006: Ganesan Pugalenthi; Shameer Khader; N Srinivasan; Ramanathan Sowdhamini
HARMONY: a server for the assessment of protein structures.
Nucleic acids research 2006;34(Web Server issue):W231-4.
2006: Anirban Bhaduri; Ramanathan Sowdhamini
Domain architectural census of eukaryotic gene products containing O-protein phosphatases.
Gene 2006;366(2):246-55.
2006: Chandrashekar S Reddy; Arunachalam Manonmani; Meenakshi Babu; Ramanathan Sowdhamini
Enhanced structure prediction of gene products containing class III adenylyl cyclase domains.
In silico biology 2006;6(5):351-62.
2006: Saikat Chakrabarti; Gowri Manohari; Ganesan Pugalenthi; Ramanathan Sowdhamini
SSToSS--sequence-structural templates of single-member superfamilies.
In silico biology 2006;6(4):311-9.
2006: Lokesh P Tripathi; Ramanathan Sowdhamini
Cross genome comparisons of serine proteases in Arabidopsis and rice.
BMC genomics 2006;7():200.
2006: Ganesan Pugalenthi; Anirban Bhaduri; Ramanathan Sowdhamini
iMOTdb--a comprehensive collection of spatially interacting motifs in proteins.
Nucleic acids research 2006;34(Database issue):D285-6.
2005: Mathias-Costa Blaise; Ramanathan Sowdhamini; Nithyananda Pradhan
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 2005;11(6):489-502.
2005: Anirban Bhaduri; Ramanathan Sowdhamini
Genome-wide survey of prokaryotic O-protein phosphatases.
Journal of molecular biology 2005;352(3):736-52.
2005: Saikat Chakrabarti; A Prem Anand; Nitin Bhardwaj; Ganesan Pugalenthi; Ramanathan Sowdhamini
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs.
Nucleic acids research 2005;33(Web Server issue):W274-6.
2005: Ganesan Pugalenthi; Govindaraju Archunan; Ramanathan Sowdhamini
DIAL: a web-based server for the automatic identification of structural domains in proteins.
Nucleic acids research 2005;33(Web Server issue):W130-2.
2005: Ratna Rajesh Thangudu; Arunachalam Vinayagam; Ganesan Pugalenthi; A Manonmani; Bernard OFFMANN; Ramanathan Sowdhamini
Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides.
Proteins 2005;58(4):866-79.
2005: Mathias-Costa Blaise; Dananjay Bhattacharyya; Ramanathan Sowdhamini; Nithyananda Pradhan
Structural consequences of D481N/K483Q mutation at glycine binding site of NMDA ionotropic glutamate receptors: a molecular dynamics study.
Journal of biomolecular structure & dynamics 2005;22(4):399-410.
2005: Kumar Gaurav; Nitin Gupta; Ramanathan Sowdhamini
FASSM: enhanced function association in whole genome analysis using sequence and structural motifs.
In silico biology 2005;5(5-6):425-38.
2005: Raghu Metpally; Ramanathan Sowdhamini
Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors.
BMC genomics 2005;6():106.
2005: Raghu Metpally; Ramanathan Sowdhamini
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.
BMC evolutionary biology 2005;5():41.
2005: Ganesan Pugalenthi; Anirban Bhaduri; Ramanathan Sowdhamini
GenDiS: Genomic Distribution of protein structural domain Superfamilies.
Nucleic acids research 2005;33(Database issue):D252-5.
2004: Mathias-Costa Blaise; Ramanathan Sowdhamini; Metpally Raghu Prasad Rao; Nithyananda Pradhan
Evolutionary trace analysis of ionotropic glutamate receptor sequences and modeling the interactions of agonists with different NMDA receptor subunits.
Journal of molecular modeling 2004;10(5-6):305-16.
2004: Saikat Chakrabarti; Nitin Bhardwaj; Prem A Anand; Ramanathan Sowdhamini
Improvement of alignment accuracy utilizing sequentially conserved motifs.
BMC bioinformatics 2004;5():167.
2004: Saikat Chakrabarti; Ramanathan Sowdhamini
Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships.
FEBS letters 2004;569(1-3):31-6.
2004: Anirban Bhaduri; Ganesan Pugalenthi; N Gupta; Ramanathan Sowdhamini
iMOT: an interactive package for the selection of spatially interacting motifs.
Nucleic acids research 2004;32(Web Server issue):W602-5.
2004: Anirban Bhaduri; Ganesan Pugalenthi; Ramanathan Sowdhamini
PASS2: an automated database of protein alignments organised as structural superfamilies.
BMC bioinformatics 2004;5():35.
2004: C Axel Innis; A Prem Anand; Ramanathan Sowdhamini
Prediction of functional sites in proteins using conserved functional group analysis.
Journal of molecular biology 2004;337(4):1053-68.
2004: Anirban Bhaduri; R Ravishankar; Ramanathan Sowdhamini
Conserved spatially interacting motifs of protein superfamilies: application to fold recognition and function annotation of genome data.
Proteins 2004;54(4):657-70.
2004: Saikat Chakrabarti; Jaisurya John; Ramanathan Sowdhamini
Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints.
Journal of molecular modeling 2004;10(1):69-75.
2004: Arunachalam Vinayagam; Ganesan Pugalenthi; R Rajesh; Ramanathan Sowdhamini
DSDBASE: a consortium of native and modelled disulphide bonds in proteins.
Nucleic acids research 2004;32(Database issue):D200-2.
2003: Anirban Bhaduri; Ramanathan Sowdhamini
A genome-wide survey of human tyrosine phosphatases.
Protein engineering 2003;16(12):881-8.
2003: Arunachalam Vinayagam; Jiye Shi; Ganesan Pugalenthi; B Meenakshi; T L Blundell; Ramanathan Sowdhamini
DDBASE2.0: updated domain database with improved identification of structural domains.
Bioinformatics (Oxford, England) 2003;19(14):1760-4.
2003: Saikat Chakrabarti; Ramanathan Sowdhamini
Functional sites and evolutionary connections of acylhomoserine lactone synthases.
Protein engineering 2003;16(4):271-8.
2003: Anirban Bhaduri; Lakshminarasimhan Krishnaswamy; Gautam R Ullal; Mitradas M Panicker; Ramanathan Sowdhamini
Fold prediction and comparative modeling of Bdm1: a probable alpha/beta hydrolase associated with hot water epilepsy.
Journal of molecular modeling 2003;9(1):3-8.
2002: V Mallika; Anirban Bhaduri; Ramanathan Sowdhamini
PASS2: a semi-automated database of protein alignments organised as structural superfamilies.
Nucleic acids research 2002;30(1):284-8.
2001: P K Shah; C M Buslje; Ramanathan Sowdhamini
Structural determinants of binding and specificity in transforming growth factor-receptor interactions.
Proteins 2001;45(4):408-20.
2001: P K Shah; Ramanathan Sowdhamini
Structural understanding of the transmembrane domains of inositol triphosphate receptors and ryanodine receptors towards calcium channeling.
Protein engineering 2001;14(11):867-74.