Ramanathan Sowdhamini

56 papers Journal 52Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
Cascade PSI-BLAST 2.0: a fast-searching parallelized remote homology detection tool and development of Cascade web server 2.0.
BMC Bioinform.
Soumya Nayak, Dheemanth Reddy Regati, Murugavel Pavalam, Ramanathan Sowdhamini
2025 J jnl
From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering.
CoRR
Wen-ran Li, Xavier F. Cadet, David Medina-Ortiz, Mehdi D. Davari, Ramanathan Sowdhamini, Cedric Damour, Yu Li, Alain Miranville, Frédéric Cadet
2025 J jnl
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database.
Database J. Biol. Databases Curation
Sarthak Joshi, Shailendu Mohapatra, Dhwani Kumar, Adwait Joshi, Meenakshi S. Iyer, Ramanathan Sowdhamini
2025 J jnl
PASS2: update of database of structure-based sequence alignments.
Database J. Biol. Databases Curation
Revathy Menon, Soumya Nayak, Rama Rajesh, Ramanathan Sowdhamini
2022 J jnl
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins.
Database J. Biol. Databases Curation
Neha V. Kalmankar, Murugavel Pavalam, Sowmya Indrakumar, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
2022 J jnl
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe.
Database J. Biol. Databases Curation
Teerna Bhattacharyya, Soumya Nayak, Smit Goswami, Vasundhara Gadiyaram, Oommen K. Mathew, Ramanathan Sowdhamini
2022 J jnl
Srinivasan (1962-2021) in Bioinformatics and beyond.
Bioinform.
M. Michael Gromiha, Christine A. Orengo, Ramanathan Sowdhamini, Janet M. Thornton
2019 J jnl
GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies.
Database J. Biol. Databases Curation
Meenakshi S. Iyer, Kartik Bhargava, Murugavel Pavalam, Ramanathan Sowdhamini
2019 J jnl
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe.
Database J. Biol. Databases Curation
Pritha Ghosh, Teerna Bhattacharyya, Oommen K. Mathew, Ramanathan Sowdhamini
2016 J jnl
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.
Briefings Bioinform.
Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini
2016 J jnl
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.
Nucleic Acids Res.
Arumugam Gandhimathi, Pritha Ghosh, Sridhar Hariharaputran, Oommen K. Mathew, Ramanathan Sowdhamini
2016 J jnl
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.
BMC Bioinform.
Pritha Ghosh, Oommen K. Mathew, Ramanathan Sowdhamini
2016 J jnl
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space.
Bioinform.
Swati Kaushik, Anu G. Nair, Eshita Mutt, Hari Prasanna Subramanian, Ramanathan Sowdhamini
2015 J jnl
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Database J. Biol. Databases Curation
Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend
2015 J jnl
DOCKSCORE: a webserver for ranking protein-protein docked poses.
BMC Bioinform.
Sony Malhotra, Oommen K. Mathew, Ramanathan Sowdhamini
2015 J jnl
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.
Nucleic Acids Res.
Richa Mudgal, Sankaran Sandhya, Gayatri Kumar, Ramanathan Sowdhamini, Nagasuma R. Chandra, Narayanaswamy Srinivasan
2015 J jnl
SInCRe - structural interactome computational resource for
Database J. Biol. Databases Curation
Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S. Raghavender, Bernardo Ochoa-Montaño, Alicia P. Higueruelo, Ramanathan Sowdhamini, Nagasuma R. Chandra, Tom L. Blundell, Narayanaswamy Srinivasan
2014 J jnl
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families.
Database J. Biol. Databases Curation
Agnel Praveen Joseph, Prashant Shingate, Atul Kumar Upadhyay, Ramanathan Sowdhamini
2014 J jnl
ECMIS: computational approach for the identification of hotspots at protein-protein interfaces.
BMC Bioinform.
Prashant Shingate, Malini Manoharan, Anshul Sukhwal, Ramanathan Sowdhamini
2014 J jnl
LenVarDB: database of length-variant protein domains.
Nucleic Acids Res.
Eshita Mutt, Oommen K. Mathew, Ramanathan Sowdhamini
2013 J jnl
Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies.
BioData Min.
Eshita Mutt, Sudha Rani, Ramanathan Sowdhamini
2012 J jnl
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome.
J. Clin. Bioinform.
Khader Shameer, Ramanathan Sowdhamini
2012 J jnl
PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies.
Nucleic Acids Res.
Arumugam Gandhimathi, Anu G. Nair, Ramanathan Sowdhamini
2012 J jnl
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.
BMC Bioinform.
Sony Malhotra, Ramanathan Sowdhamini
2011 J jnl
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.
Database J. Biol. Databases Curation
Khader Shameer, Prashant Shingate, S. C. P. Manjunath, M. Karthika, Ganesan Pugalenthi, Ramanathan Sowdhamini
2011 — conf
A Three-Step Validation Following Genome-Wide Data Mining for Myosin Family Members Improves Search Efficiency.
ICDM Workshops
Divya P. Syamaladevi, Singaravelu Kalaimathy, Naseer Pasha, S. Subramonian, Ramanathan Sowdhamini
2011 J jnl
Critical assessment of structure-based sequence alignment methods at distant relationships.
Briefings Bioinform.
Singaravelu Kalaimathy, Ramanathan Sowdhamini, Karuppiah Kanagarajadurai
2011 — conf
Mining Protein Sequence Databases for Remote Homologues That Can Display Considerable Domain Length Variations.
ICDM Workshops
Eshita Mutt, Abhijit Mitra, Ramanathan Sowdhamini
2011 J jnl
PASS2: A Database of Structure-Based Sequence Alignments of Protein Structural Domain Superfamilies.
Int. J. Knowl. Discov. Bioinform.
Karuppiah Kanagarajadurai, Singaravelu Kalaimathy, Paramasivam Nagarajan, Ramanathan Sowdhamini
2011 — conf
Poster: HORIBALFRE: Higher Order Residue Interactions Based ALgorithm for Fold REcognition.
ICCABS
Pandurangan Sundaramurthy, Raashi Sreenivasan, Khader Shameer, Sunita Gakkhar, Ramanathan Sowdhamini
2011 J jnl
Search for Protein Sequence Homologues that Display Considerable Domain Length Variations.
Int. J. Knowl. Discov. Bioinform.
Eshita Mutt, Abhijit Mitra, Ramanathan Sowdhamini
2010 — conf
A Sequence Data Mining Protocol to Identify Best Representative Sequence for Protein Domain Families.
ICDM Workshops
V. S. Gowri, Khader Shameer, Chilamakuri Chandra Sekhar Reddy, Prashant Shingate, Ramanathan Sowdhamini
2010 J jnl
HORI: a web server to compute Higher Order Residue Interactions in protein structures.
BMC Bioinform.
Pandurangan Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar, Ramanathan Sowdhamini
2010 J jnl
PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes.
BMC Bioinform.
Khader Shameer, Lalima L. Madan, Shivamurthy Veeranna, Balasubramanian Gopal, Ramanathan Sowdhamini
2009 J jnl
3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach.
BioData Min.
Khader Shameer, Paramasivam Nagarajan, Kumar Gaurav, Ramanathan Sowdhamini
2008 J jnl
MegaMotifBase: a database of structural motifs in protein families and superfamilies.
Nucleic Acids Res.
Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti
2008 J jnl
PURE: A webserver for the prediction of domains in unassigned regions in proteins.
BMC Bioinform.
Chilamakuri Chandra Sekhar Reddy, Khader Shameer, Bernard O. Offmann, Ramanathan Sowdhamini
2008 J jnl
Sequence and Structural Analyses of Interleukin-8-Like Chemokine Superfamily.
Silico Biol.
Karuppiah Kanagarajadurai, Ramanathan Sowdhamini
2007 J jnl
A machine learning approach for the identification of odorant binding proteins from sequence-derived properties.
BMC Bioinform.
Ganesan Pugalenthi, E. Ke Tang, Ponnuthurai N. Suganthan, Govindaraju Archunan, Ramanathan Sowdhamini
2007 J jnl
SMotif: a server for structural motifs in proteins.
Bioinform.
Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti
2006 J jnl
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains.
Nucleic Acids Res.
Rana Bhadra, Sankaran Sandhya, K. R. Abhinandan, Saikat Chakrabarti, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
2006 J jnl
Enhanced Structure Prediction of Gene Products Containing Class III Adenylyl Cyclase Domains.
Silico Biol.
Chandrashekar Reddy, Arunachalam Manonmani, Meenakshi Babu, Ramanathan Sowdhamini
2006 J jnl
HARMONY: a server for the assessment of protein structures.
Nucleic Acids Res.
Ganesan Pugalenthi, Khader Shameer, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
2006 J jnl
SSToSS - Sequence-Structural Templates of Single-Member Superfamilies.
Silico Biol.
Saikat Chakrabarti, Gowri Manohari, Ganesan Pugalenthi, Ramanathan Sowdhamini
2006 J jnl
iMOTdb - a comprehensive collection of spatially interacting motifs in proteins.
Nucleic Acids Res.
Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini
2005 J jnl
DIAL: a web-based server for the automatic identification of structural domains in proteins.
Nucleic Acids Res.
Ganesan Pugalenthi, Govindaraju Archunan, Ramanathan Sowdhamini
2005 J jnl
FASSM: Enhanced Function Association in Whole Genome Analysis Using Sequence and Structural Motifs.
Silico Biol.
Kumar Gaurav, Nitin Gupta, Ramanathan Sowdhamini
2005 J jnl
GenDiS: Genomic Distribution of protein structural domain Superfamilies.
Nucleic Acids Res.
Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini
2005 J jnl
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs.
Nucleic Acids Res.
Saikat Chakrabarti, Prem A. Anand, Nitin Bhardwaj, Ganesan Pugalenthi, Ramanathan Sowdhamini
2004 J jnl
Improvement of alignment accuracy utilizing sequentially conserved motifs.
BMC Bioinform.
Saikat Chakrabarti, Nitin Bhardwaj, Prem A. Anand, Ramanathan Sowdhamini
2004 J jnl
PASS2: an automated database of protein alignments organised as structural superfamilies.
BMC Bioinform.
Anirban Bhaduri, Ganesan Pugalenthi, Ramanathan Sowdhamini
2004 J jnl
SDBASE: a consortium of native and modelled disulphide bonds in proteins.
Nucleic Acids Res.
A. Vinayagam, Ganesan Pugalenthi, R. Rajesh, Ramanathan Sowdhamini
2004 J jnl
iMOT: an interactive package for the selection of spatially interacting motifs.
Nucleic Acids Res.
Anirban Bhaduri, Ganesan Pugalenthi, Nitin Gupta, Ramanathan Sowdhamini
2003 J jnl
DDBASE2.0: updated domain database with improved identification of structural domains.
Bioinform.
A. Vinayagam, Jiye Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini
2002 J jnl
PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies.
Nucleic Acids Res.
V. Mallika, Anirban Bhaduri, Ramanathan Sowdhamini
2002 J jnl
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 Res.
Shashi B. Pandit, Dilip Gosar, S. Abhiman, S. Sujatha, Sayali S. Dixit, Natasha S. Mhatre, Ramanathan Sowdhamini, Narayanaswamy Srinivasan