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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
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
Srinivasan (1962-2021) in Bioinformatics and beyond. Bioinform. 38(8): 2377-2379 (2022)
2010 – 2019
- 2019
- [j45]Pritha Ghosh
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
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
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space. Bioinform. 32(3): 338-344 (2016) - [j41]Pritha Ghosh
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
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
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
SInCRe - structural interactome computational resource for Mycobacterium tuberculosis. Database J. Biol. Databases Curation 2015 (2015) - [j37]Sony Malhotra, Oommen K. Mathew
DOCKSCORE: a webserver for ranking protein-protein docked poses. BMC Bioinform. 16: 127:1-127:6 (2015) - [j36]Richa Mudgal, Sankaran Sandhya
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
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
LenVarDB: database of length-variant protein domains. Nucleic Acids Res. 42(Database-Issue): 246-250 (2014) - 2013
- [j32]Eshita Mutt
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
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
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
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
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
Poster: HORIBALFRE: Higher Order Residue Interactions Based ALgorithm for Fold REcognition. ICCABS 2011: 262 - [c3]Eshita Mutt, Abhijit Mitra
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
HORI: a web server to compute Higher Order Residue Interactions in protein structures. BMC Bioinform. 11(S-1): 24 (2010) - [j23]Khader Shameer
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
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
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
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
MegaMotifBase: a database of structural motifs in protein families and superfamilies. Nucleic Acids Res. 36(Database-Issue): 218-221 (2008) - 2007
- [j18]Ganesan Pugalenthi
SMotif: a server for structural motifs in proteins. Bioinform. 23(5): 637-638 (2007) - [j17]Ganesan Pugalenthi
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
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
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
GenDiS: Genomic Distribution of protein structural domain Superfamilies. Nucleic Acids Res. 33(Database-Issue): 252-255 (2005) - [j9]Ganesan Pugalenthi
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
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
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
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
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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