Ramanathan Sowdhamini

发表

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

Joel Dudley, Krishna R. Kalari, Khader Shameer, 2016, Briefings Bioinform..

HORIBALFRE program: Higher Order Residue Interactions Based ALgorithm for Fold REcognition

Ramanathan Sowdhamini, Pandurangan Sundaramurthy, Raashi Sreenivasan, 2011, Bioinformation.

A Sequence Data Mining Protocol to Identify Best Representative Sequence for Protein Domain Families

Khader Shameer, Ramanathan Sowdhamini, Venkatraman S. Gowri, 2010, 2010 IEEE International Conference on Data Mining Workshops.

Bioinformatics and Biology Insights

Ramanathan Sowdhamini, Khader Shameer, Mahantesha BN Naika, 2022 .

GenDiS: Genomic Distribution of protein structural domain Superfamilies

Ramanathan Sowdhamini, Ganesan Pugalenthi, Anirban Bhaduri, 2004, Nucleic Acids Res..

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

Shashi B. Pandit, S. Abhiman, Narayanaswamy Srinivasan, 2002, Nucleic Acids Res..

Poster: HORIBALFRE: Higher Order Residue Interactions Based ALgorithm for Fold REcognition

Khader Shameer, Ramanathan Sowdhamini, Pandurangan Sundaramurthy, 2011, 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

MegaMotifBase: a database of structural motifs in protein families and superfamilies

Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Ganesan Pugalenthi, 2008, Nucleic Acids Res..

PURE: A webserver for the prediction of domains in unassigned regions in proteins

Khader Shameer, Ramanathan Sowdhamini, Chilamakuri Chandra Sekhar Reddy, 2008, BMC Bioinformatics.

DDBASE2.0: updated domain database with improved identification of structural domains

Jiye Shi, Ramanathan Sowdhamini, Tom L. Blundell, 2003, Bioinform..

Bioinformatics and Biology Insights

Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Khader Shameer, 2022 .

Critical assessment of structure-based sequence alignment methods at distant relationships

Ramanathan Sowdhamini, Singaravelu Kalaimathy, Karuppiah Kanagarajadurai, 2011, Briefings Bioinform..

PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies

Ramanathan Sowdhamini, Arumugam Gandhimathi, Anu G. Nair, 2011, Nucleic Acids Res..

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information

Ramanathan Sowdhamini, Pritha Ghosh, Oommen K. Mathew, 2016, BMC Bioinformatics.

A glance into the evolution of template-free protein structure prediction methodologies.

Ramanathan Sowdhamini, Bernard Offmann, Surbhi Dhingra, 2020, Biochimie.

HARMONY: a server for the assessment of protein structures

Narayanaswamy Srinivasan, Khader Shameer, Ramanathan Sowdhamini, 2006, Nucleic Acids Res..

3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families

Ramanathan Sowdhamini, Prashant Shingate, Agnel Praveen Joseph, 2014, Database J. Biol. Databases Curation.

PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

Ramanathan Sowdhamini, Pritha Ghosh, Sridhar Hariharaputran, 2015, Nucleic Acids Res..

3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach

Khader Shameer, Ramanathan Sowdhamini, Kumar Gaurav, 2009, BioData Mining.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Neil D. Rawlings, Robert D. Finn, Alex Bateman, 2015, Database J. Biol. Databases Curation.

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

Nagasuma R. Chandra, Ramanathan Sowdhamini, Tom L. Blundell, 2015, Database J. Biol. Databases Curation.

iMOT: an interactive package for the selection of spatially interacting motifs

Ramanathan Sowdhamini, Nitin Gupta, Ganesan Pugalenthi, 2004, Nucleic Acids Res..

Computational biology: More than just a set of techniques

Alok Bhattacharya, Ramanathan Sowdhamini, Narayanaswamy Srinivasan, 2007 .

3dswap-pred: prediction of 3D domain swapping from protein sequence using Random Forest approach.

Ramanathan Sowdhamini, Khader Shameer, Ganesan Pugalenthi, 2011, Protein and peptide letters.

iMOTdb—a comprehensive collection of spatially interacting motifs in proteins

Ramanathan Sowdhamini, Ganesan Pugalenthi, Anirban Bhaduri, 2006, Nucleic Acids Res..

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection

Nagasuma R. Chandra, Narayanaswamy Srinivasan, Ramanathan Sowdhamini, 2014, Nucleic Acids Res..

SDBASE: a consortium of native and modelled disulphide bonds in proteins

Ramanathan Sowdhamini, Ganesan Pugalenthi, A. Vinayagam, 2004, Nucleic Acids Res..

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Saikat Chakrabarti, 2006, Nucleic Acids Res..

DOCKSCORE: a webserver for ranking protein-protein docked poses

Ramanathan Sowdhamini, Oommen K. Mathew, Sony Malhotra, 2015, BMC Bioinformatics.

PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

Khader Shameer, Ramanathan Sowdhamini, Lalima L. Madan, 2010, BMC Bioinformatics.

DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity

Ramanathan Sowdhamini, Asad Ahmed, Bhavika Mam, 2020 .

Key challenges for the creation and maintenance of specialist protein resources

Bernard Henrissat, Ramanathan Sowdhamini, Gert Vriend, 2015, Proteins.

3DSwap: curated knowledgebase of proteins involved in 3D domain swapping

Khader Shameer, Ramanathan Sowdhamini, Prashant Shingate, 2011, Database J. Biol. Databases Curation.

SSToSS - Sequence-Structural Templates of Single-Member Superfamilies

Ramanathan Sowdhamini, Ganesan Pugalenthi, Saikat Chakrabarti, 2006, Silico Biol..

Re-visiting protein-centric two-tier classification of existing DNA-protein complexes

Ramanathan Sowdhamini, Sony Malhotra, R. Sowdhamini, 2012, BMC Bioinformatics.

172 Computational analysis and prediction of proteins that undergo domain swapping

Ramanathan Sowdhamini, Prashant Shingate, Atul Upadhyay, 2015, Journal of biomolecular structure & dynamics.

A machine learning approach for the identification of odorant binding proteins from sequence-derived properties

Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Ganesan Pugalenthi, 2007, BMC Bioinformatics.

HORI: a web server to compute Higher Order Residue Interactions in protein structures

Khader Shameer, Ramanathan Sowdhamini, Pandurangan Sundaramurthy, 2010, BMC Bioinformatics.

DIAL: a web-based server for the automatic identification of structural domains in proteins

Ramanathan Sowdhamini, Ganesan Pugalenthi, Govindaraju Archunan, 2005, Nucleic Acids Res..

Enhanced Structure Prediction of Gene Products Containing Class III Adenylyl Cyclase Domains

Ramanathan Sowdhamini, Arunachalam Manonmani, Chandrashekar Reddy, 2006, Silico Biol..

Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies

Ramanathan Sowdhamini, Sudha Rani, Eshita Mutt, 2012, BioData Mining.

hRBPome: a central repository of all known human RNA-binding proteins

Ramanathan Sowdhamini, Pritha Ghosh, Pavalam Murugavel, 2018, bioRxiv.

SMotif: a server for structural motifs in proteins

Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Ganesan Pugalenthi, 2007, Bioinform..

A Three-Step Validation Following Genome-Wide Data Mining for Myosin Family Members Improves Search Efficiency

Ramanathan Sowdhamini, Singaravelu Kalaimathy, Divya P. Syamaladevi, 2011, 2011 IEEE 11th International Conference on Data Mining Workshops.

An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins

Ramanathan Sowdhamini, Adwait Joshi, Divya P Syamaladevi, 2013, Bioinformation.

ECMIS: computational approach for the identification of hotspots at protein-protein interfaces

Ramanathan Sowdhamini, Prashant Shingate, Malini Manoharan, 2014, BMC Bioinformatics.

PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies

Ramanathan Sowdhamini, Anirban Bhaduri, V. Mallika, 2002, Nucleic Acids Res..

Improvement of alignment accuracy utilizing sequentially conserved motifs

Ramanathan Sowdhamini, Nitin Bhardwaj, Saikat Chakrabarti, 2004, BMC Bioinformatics.

SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs

Ramanathan Sowdhamini, Nitin Bhardwaj, Ganesan Pugalenthi, 2005, Nucleic Acids Res..

GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies

Ramanathan Sowdhamini, Meenakshi S. Iyer, Kartik Bhargava, 2019, Database J. Biol. Databases Curation.

PPCheck: A Webserver for the Quantitative Analysis of Protein–Protein Interfaces and Prediction of Residue Hotspots

Ramanathan Sowdhamini, Anshul Sukhwal, R. Sowdhamini, 2015, Bioinformatics and biology insights.

PASS2: A Database of Structure-Based Sequence Alignments of Protein Structural Domain Superfamilies

Ramanathan Sowdhamini, Singaravelu Kalaimathy, Karuppiah Kanagarajadurai, 2011, Int. J. Knowl. Discov. Bioinform..

Search for Protein Sequence Homologues that Display Considerable Domain Length Variations

Abhijit Mitra, Ramanathan Sowdhamini, Eshita Mutt, 2011, Int. J. Knowl. Discov. Bioinform..

Comparison of Structure Based Sequence Alignment Programs for Protein Domain Superfamilies with Multiple Members

Ramanathan Sowdhamini, Anu G. Nair, A. Gandhimathi, 2012 .

Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome

Khader Shameer, Ramanathan Sowdhamini, R. Sowdhamini, 2012, Journal of Clinical Bioinformatics.

Mining Protein Sequence Databases for Remote Homologues That Can Display Considerable Domain Length Variations

Abhijit Mitra, Ramanathan Sowdhamini, Eshita Mutt, 2011, 2011 IEEE 11th International Conference on Data Mining Workshops.

Sequence and Structural Analyses of Interleukin-8-Like Chemokine Superfamily

Ramanathan Sowdhamini, Karuppiah Kanagarajadurai, R. Sowdhamini, 2008, Silico Biol..

PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe

Ramanathan Sowdhamini, Pritha Ghosh, Oommen K. Mathew, 2019, Database J. Biol. Databases Curation.

BMC Bioinformatics BioMed Central Database

Ramanathan Sowdhamini, Ganesan Pugalenthi, Anirban Bhaduri, 2004 .

FASSM: Enhanced Function Association in Whole Genome Analysis Using Sequence and Structural Motifs

Ramanathan Sowdhamini, Nitin Gupta, Kumar Gaurav, 2005, Silico Biol..

LenVarDB: database of length-variant protein domains

Ramanathan Sowdhamini, Oommen K. Mathew, Eshita Mutt, 2013, Nucleic Acids Res..

IWS: Integrated web server for protein sequence and structure analysis

Ramanathan Sowdhamini, Khader Shameer, 2007, Bioinformation.

Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening

Ramanathan Sowdhamini, K. Harini, R. Sowdhamini, 2015, PloS one.

Protein sequence design and its applications.

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Sankaran Sandhya, 2016, Current opinion in structural biology.

Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-β (TRIF) provides insights into its autoinhibited state

Ramanathan Sowdhamini, Jarjapu Mahita, 2017, Biology Direct.

Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Eshita Mutt, 2013, PloS one.

TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences

Ramanathan Sowdhamini, Govindaraju Archunan, Kannan Sankar, 2011, Bioinformation.

Alpha-Turns In Protein Structures

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, R. Sowdhamini, 1995 .

Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes.

Ramanathan Sowdhamini, R. Sowdhamini, Meenakshi S Iyer, 2018, Molecular omics.

Creating a specialist protein resource network

Neil D. Rawlings, Alex Bateman, Bernard Henrissat, 2015 .

Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis

Ramanathan Sowdhamini, R. Sowdhamini, R. Metpally, 2005, BMC Evolutionary Biology.

Length Variations amongst Protein Domain Superfamilies and Consequences on Structure and Function

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Bernard Offmann, 2009, PloS one.

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

Khader Shameer, Ramanathan Sowdhamini, Oommen K. Mathew, 2013, Plant & cell physiology.

Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters

Ramanathan Sowdhamini, Govindaraju Archunan, Balasubramanian Nagarathnam, 2011, Bioinformation.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Bernardo Ochoa-Montaño, 2015, Tuberculosis.

α-Turns in protein structure

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, R. Sowdhamini, 1995 .

Phylogenetic Analysis and Selection Pressures of 5-HT Receptors in Human and Non-human Primates: Receptor of an Ancient Neurotransmitter

Ramanathan Sowdhamini, Sanjeev Jain, Padmanabhan Anbazhagan, 2010, Journal of biomolecular structure & dynamics.

CUSP : an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Bernard Offmann, 2008 .

Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability.

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Nagasuma Chandra, 2014, Journal of molecular biology.

Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding

Ramanathan Sowdhamini, R. Sowdhamini, Swati Kaushik, 2011, PloS one.

Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses

Khader Shameer, Ramanathan Sowdhamini, Naresh Doni Jayavelu, 2015, Nucleic acids research.