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Ramanathan 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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