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ORCIDRamanathan Sowdhamini
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2020 – today
- 2022
[j48]Teerna Bhattacharyya
, Soumya Nayak, Smit Goswami, Vasundhara Gadiyaram, Oommen K. Mathew, Ramanathan Sowdhamini:
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. Database J. Biol. Databases Curation 2022(2022) (2022)- [j47]Neha V. Kalmankar, Murugavel Pavalam, Sowmya Indrakumar, Narayanaswamy Srinivasan, Ramanathan Sowdhamini:
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins. Database J. Biol. Databases Curation 2022(2022) (2022) - [j46]M. Michael Gromiha, Christine A. Orengo, Ramanathan Sowdhamini, Janet M. Thornton:
Srinivasan (1962-2021) in Bioinformatics and beyond. Bioinform. 38(8): 2377-2379 (2022)
2010 – 2019
- 2019
- [j45]Pritha Ghosh, Teerna Bhattacharyya, Oommen K. Mathew, Ramanathan Sowdhamini:
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. Database J. Biol. Databases Curation 2019: baz028 (2019) - [j44]Meenakshi S. Iyer, Kartik Bhargava, Murugavel Pavalam, Ramanathan Sowdhamini:
GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies. Database J. Biol. Databases Curation 2019: baz042 (2019) - 2016
- [j43]Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini:
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. Briefings Bioinform. 17(5): 841-862 (2016) - [j42]Swati Kaushik, Anu G. Nair, Eshita Mutt, Hari Prasanna Subramanian, Ramanathan Sowdhamini:
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space. Bioinform. 32(3): 338-344 (2016) - [j41]Pritha Ghosh, Oommen K. Mathew, Ramanathan Sowdhamini:
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. BMC Bioinform. 17: 411 (2016) - [j40]Arumugam Gandhimathi, Pritha Ghosh, Sridhar Hariharaputran, Oommen K. Mathew, Ramanathan Sowdhamini:
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. Nucleic Acids Res. 44(Database-Issue): 410-414 (2016) - 2015
- [j39]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:
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database J. Biol. Databases Curation 2015 (2015) - [j38]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:
SInCRe - structural interactome computational resource for Mycobacterium tuberculosis. Database J. Biol. Databases Curation 2015 (2015) - [j37]Sony Malhotra, Oommen K. Mathew, Ramanathan Sowdhamini:
DOCKSCORE: a webserver for ranking protein-protein docked poses. BMC Bioinform. 16: 127:1-127:6 (2015) - [j36]Richa Mudgal, Sankaran Sandhya, Gayatri Kumar, Ramanathan Sowdhamini, Nagasuma R. Chandra, Narayanaswamy Srinivasan:
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. Nucleic Acids Res. 43(Database-Issue): 300-305 (2015) - 2014
- [j35]Agnel Praveen Joseph, Prashant Shingate, Atul Kumar Upadhyay, Ramanathan Sowdhamini:
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. Database J. Biol. Databases Curation 2014 (2014) - [j34]Prashant Shingate, Malini Manoharan, Anshul Sukhwal, Ramanathan Sowdhamini:
ECMIS: computational approach for the identification of hotspots at protein-protein interfaces. BMC Bioinform. 15: 303 (2014) - [j33]Eshita Mutt, Oommen K. Mathew, Ramanathan Sowdhamini:
LenVarDB: database of length-variant protein domains. Nucleic Acids Res. 42(Database-Issue): 246-250 (2014) - 2013
- [j32]Eshita Mutt, Sudha Rani, Ramanathan Sowdhamini:
Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies. BioData Min. 6: 20 (2013) - 2012
- [j31]Sony Malhotra, Ramanathan Sowdhamini:
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. BMC Bioinform. 13: 165 (2012) - [j30]Khader Shameer, Ramanathan Sowdhamini:
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. J. Clin. Bioinform. 2: 8 (2012) - [j29]Arumugam Gandhimathi, Anu G. Nair, Ramanathan Sowdhamini:
PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Res. 40(Database-Issue): 531-534 (2012) - 2011
- [j28]Singaravelu Kalaimathy, Ramanathan Sowdhamini, Karuppiah Kanagarajadurai:
Critical assessment of structure-based sequence alignment methods at distant relationships. Briefings Bioinform. 12(2): 163-175 (2011) - [j27]Khader Shameer, Prashant Shingate, S. C. P. Manjunath, M. Karthika, Ganesan Pugalenthi, Ramanathan Sowdhamini:
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. Database J. Biol. Databases Curation 2011 (2011) - [j26]Eshita Mutt, Abhijit Mitra, Ramanathan Sowdhamini:
Search for Protein Sequence Homologues that Display Considerable Domain Length Variations. Int. J. Knowl. Discov. Bioinform. 2(2): 55-77 (2011) - [j25]Karuppiah Kanagarajadurai, Singaravelu Kalaimathy, Paramasivam Nagarajan, Ramanathan Sowdhamini:
PASS2: A Database of Structure-Based Sequence Alignments of Protein Structural Domain Superfamilies. Int. J. Knowl. Discov. Bioinform. 2(4): 53-66 (2011) - [c4]Pandurangan Sundaramurthy, Raashi Sreenivasan, Khader Shameer, Sunita Gakkhar, Ramanathan Sowdhamini:
Poster: HORIBALFRE: Higher Order Residue Interactions Based ALgorithm for Fold REcognition. ICCABS 2011: 262 - [c3]Eshita Mutt, Abhijit Mitra, Ramanathan Sowdhamini:
Mining Protein Sequence Databases for Remote Homologues That Can Display Considerable Domain Length Variations. ICDM Workshops 2011: 1050-1057 - [c2]Divya P. Syamaladevi, Singaravelu Kalaimathy, Naseer Pasha, S. Subramonian, Ramanathan Sowdhamini:
A Three-Step Validation Following Genome-Wide Data Mining for Myosin Family Members Improves Search Efficiency. ICDM Workshops 2011: 1071-1074 - 2010
- [j24]Pandurangan Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar, Ramanathan Sowdhamini:
HORI: a web server to compute Higher Order Residue Interactions in protein structures. BMC Bioinform. 11(S-1): 24 (2010) - [j23]Khader Shameer, 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 Bioinform. 11: 473 (2010) - [c1]V. S. Gowri, Khader Shameer, Chilamakuri Chandra Sekhar Reddy, Prashant Shingate, Ramanathan Sowdhamini:
A Sequence Data Mining Protocol to Identify Best Representative Sequence for Protein Domain Families. ICDM Workshops 2010: 703-710
2000 – 2009
- 2009
- [j22]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 Min. 2: 8 (2009) - 2008
- [j21]Chilamakuri Chandra Sekhar Reddy, Khader Shameer, Bernard O. Offmann, Ramanathan Sowdhamini:
PURE: A webserver for the prediction of domains in unassigned regions in proteins. BMC Bioinform. 9 (2008) - [j20]Karuppiah Kanagarajadurai, Ramanathan Sowdhamini:
Sequence and Structural Analyses of Interleukin-8-Like Chemokine Superfamily. Silico Biol. 8(3-4): 307-330 (2008) - [j19]Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti:
MegaMotifBase: a database of structural motifs in protein families and superfamilies. Nucleic Acids Res. 36(Database-Issue): 218-221 (2008) - 2007
- [j18]Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti:
SMotif: a server for structural motifs in proteins. Bioinform. 23(5): 637-638 (2007) - [j17]Ganesan Pugalenthi, E. Ke Tang, Ponnuthurai N. Suganthan, Govindaraju Archunan, Ramanathan Sowdhamini:
A machine learning approach for the identification of odorant binding proteins from sequence-derived properties. BMC Bioinform. 8 (2007) - 2006
- [j16]Saikat Chakrabarti, Gowri Manohari, Ganesan Pugalenthi, Ramanathan Sowdhamini:
SSToSS - Sequence-Structural Templates of Single-Member Superfamilies. Silico Biol. 6(4): 311-319 (2006) - [j15]Chandrashekar Reddy, Arunachalam Manonmani, Meenakshi Babu, Ramanathan Sowdhamini:
Enhanced Structure Prediction of Gene Products Containing Class III Adenylyl Cyclase Domains. Silico Biol. 6(5): 351-362 (2006) - [j14]Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
iMOTdb - a comprehensive collection of spatially interacting motifs in proteins. Nucleic Acids Res. 34(Database-Issue): 285-286 (2006) - [j13]Rana Bhadra, Sankaran Sandhya, K. R. Abhinandan, Saikat Chakrabarti, Ramanathan Sowdhamini, Narayanaswamy Srinivasan:
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. Nucleic Acids Res. 34(Web-Server-Issue): 143-146 (2006) - [j12]Ganesan Pugalenthi, Khader Shameer, Narayanaswamy Srinivasan, Ramanathan Sowdhamini:
HARMONY: a server for the assessment of protein structures. Nucleic Acids Res. 34(Web-Server-Issue): 231-234 (2006) - 2005
- [j11]Kumar Gaurav, Nitin Gupta, Ramanathan Sowdhamini:
FASSM: Enhanced Function Association in Whole Genome Analysis Using Sequence and Structural Motifs. Silico Biol. 5(5-6): 425-438 (2005) - [j10]Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
GenDiS: Genomic Distribution of protein structural domain Superfamilies. Nucleic Acids Res. 33(Database-Issue): 252-255 (2005) - [j9]Ganesan Pugalenthi, Govindaraju Archunan, Ramanathan Sowdhamini:
DIAL: a web-based server for the automatic identification of structural domains in proteins. Nucleic Acids Res. 33(Web-Server-Issue): 130-132 (2005) - [j8]Saikat Chakrabarti, Prem A. Anand, Nitin Bhardwaj, Ganesan Pugalenthi, Ramanathan Sowdhamini:
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs. Nucleic Acids Res. 33(Web-Server-Issue): 274-276 (2005) - 2004
- [j7]Anirban Bhaduri, Ganesan Pugalenthi, Ramanathan Sowdhamini:
PASS2: an automated database of protein alignments organised as structural superfamilies. BMC Bioinform. 5: 35 (2004) - [j6]Saikat Chakrabarti, Nitin Bhardwaj, Prem A. Anand, Ramanathan Sowdhamini:
Improvement of alignment accuracy utilizing sequentially conserved motifs. BMC Bioinform. 5: 167 (2004) - [j5]A. Vinayagam, Ganesan Pugalenthi, R. Rajesh, Ramanathan Sowdhamini:
SDBASE: a consortium of native and modelled disulphide bonds in proteins. Nucleic Acids Res. 32(Database-Issue): 200-202 (2004) - [j4]Anirban Bhaduri, Ganesan Pugalenthi, Nitin Gupta, Ramanathan Sowdhamini:
iMOT: an interactive package for the selection of spatially interacting motifs. Nucleic Acids Res. 32(Web-Server-Issue): 602-605 (2004) - 2003
- [j3]A. Vinayagam, Jiye Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini:
DDBASE2.0: updated domain database with improved identification of structural domains. Bioinform. 19(14): 1760-1764 (2003) - 2002
- [j2]V. Mallika, Anirban Bhaduri, Ramanathan Sowdhamini:
PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies. Nucleic Acids Res. 30(1): 284-288 (2002) - [j1]Shashi B. Pandit, Dilip Gosar, S. Abhiman, S. Sujatha, Sayali S. Dixit, Natasha S. Mhatre, Ramanathan Sowdhamini, Narayanaswamy Srinivasan:
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. 30(1): 289-293 (2002)
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