PALI: a database of alignments and phylogeny of homologous protein structures. - S. Sujatha; S. Balaji; Narayanaswamy Srinivasan (Bioinform., 2001)

PALI - a database of Phylogeny and ALIgnment of homologous protein structures. - S. Balaji; S. Sujatha; S. Sai Chetan Kumar; Narayanaswamy Srinivasan (Nucleic Acids Res., 2001)

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; Dilip Gosar; S. Abhiman; S. Sujatha; Sayali S. Dixit; Natasha S. Mhatre; Ramanathan Sowdhamini; Narayanaswamy Srinivasan (Nucleic Acids Res., 2002)

Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. - V. S. Gowri; Shashi B. Pandit; P. S. Karthik; Narayanaswamy Srinivasan; S. Balaji (Nucleic Acids Res., 2003)

SUPFAM: A database of sequence superfamilies of protein domains. - Shashi B. Pandit; Rana Bhadra; V. S. Gowri; S. Balaji; B. Anand; Narayanaswamy Srinivasan (BMC Bioinform., 2004)

Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures. - Seema Namboori; Narayanaswamy Srinivasan; Shashi B. Pandit (Silico Biol., 2004)

Identification and analysis of a new family of bacterial serine proteinases. - Shashi B. Pandit; Narayanaswamy Srinivasan (Silico Biol., 2004)

KinG: a database of protein kinases in genomes. - A. Krupa; K. R. Abhinandan; Narayanaswamy Srinivasan (Nucleic Acids Res., 2004)

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues. - B. Anand; V. S. Gowri; Narayanaswamy Srinivasan (Bioinform., 2005)

A New Domain Family in the Superfamily of Alkaline Phosphatases. - Rana Bhadra; Narayanaswamy Srinivasan; Shashi B. Pandit (Silico Biol., 2005)

PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. - Oruganty Krishnadev; N. Rekha; Shashi B. Pandit; S. Abhiman; Smita Mohanty; L. S. Swapna; Swanand P. Gore; Narayanaswamy Srinivasan (Nucleic Acids Res., 2005)

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. - Rana Bhadra; Sankaran Sandhya; K. R. Abhinandan; Saikat Chakrabarti 001; Ramanathan Sowdhamini; Narayanaswamy Srinivasan (Nucleic Acids Res., 2006)

MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. - V. S. Gowri; Oruganty Krishnadev; C. S. Swamy; Narayanaswamy Srinivasan (Nucleic Acids Res., 2006)

HARMONY: a server for the assessment of protein structures. - Ganesan Pugalenthi; Khader Shameer; Narayanaswamy Srinivasan; Ramanathan Sowdhamini (Nucleic Acids Res., 2006)

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. - Manoj Tyagi; P. Sharma; C. S. Swamy; F. Cadet; Narayanaswamy Srinivasan; Alexandre G. de Brevern; Bernard O. Offmann (Nucleic Acids Res., 2006)

PIC: Protein Interactions Calculator. - K. G. Tina; Rana Bhadra; Narayanaswamy Srinivasan (Nucleic Acids Res., 2007)

A Data Integration Approach to Predict Host-Pathogen Protein-Protein Interactions: Application to Recognize Protein Interactions between Human and a Malarial Parasite. - Oruganty Krishnadev; Narayanaswamy Srinivasan (Silico Biol., 2008)

How effective is the data on co-occurrence of domains in multi-domain proteins in prediction of protein-protein interactions? - Smita Mohanty; Narayanaswamy Srinivasan (GENSiPS, 2009)

Molecular and Structural Basis of Drift in the Functions of Closely-Related Homologous Enzyme Domains: Implications for Function Annotation Based on Homology Searches and Structural Genomics. - Ambrish Roy; Narayanaswamy Srinivasan; Venkatraman S. Gowri (Silico Biol., 2009)

Prediction of Protein-Protein Interactions Between Human Host and Two Mycobacterial Organisms. - Oruganty Krishnadev; Shveta Bisht; Narayanaswamy Srinivasan (Int. J. Knowl. Discov. Bioinform., 2010)

AlignHUSH : Alignment of HMMs Using Structure and Hydrophobicity information. - Oruganty Krishnadev; Narayanaswamy Srinivasan (BMC Bioinform., 2011)

Influence of Genomic and Other Biological Data Sets in the Understanding of Protein Structures, Functions and Interactions. - Narayanaswamy Srinivasan; Garima Agarwal; Ramachandra M. Bhaskara; Rupali A. Gadkari; Oruganty Krishnadev; B. Lakshmi; Swapnil Mahajan; Smita Mohanty; Richa Mudgal; R. Rakshambikai; Sankaran Sandhya; G. Sudha; et al. (Int. J. Knowl. Discov. Bioinform., 2011)

iPBA: a tool for protein structure comparison using sequence alignment strategies. - Jean-Christophe Gelly; Agnel Praveen Joseph; Narayanaswamy Srinivasan; Alexandre G. de Brevern (Nucleic Acids Res., 2011)

DoSA: Database of Structural Alignments. - Swapnil Mahajan; Garima Agarwal; Mohammed Iftekhar; Bernard O. Offmann; Alexandre G. de Brevern; Narayanaswamy Srinivasan (Database J. Biol. Databases Curation, 2013)

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins. - Mutharasu Gnanavel; Prachi Mehrotra; Ramaswamy Rakshambikai; Juliette Martin; Narayanaswamy Srinivasan; Ramachandra M. Bhaskara (BMC Bioinform., 2014)

Repertoire of protein kinases Encoded in the genome of zebrafish shows remarkably Large Population of PIM kinases. - R. Rakshambikai; Narayanaswamy Srinivasan; Rupali A. Gadkari (J. Bioinform. Comput. Biol., 2014)

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. - 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; et al. (Database J. Biol. Databases Curation, 2015)

SInCRe - structural interactome computational resource for Mycobacterium tuberculosis. - 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 (Database J. Biol. Databases Curation, 2015)

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. - Richa Mudgal; Sankaran Sandhya; Gayatri Kumar; Ramanathan Sowdhamini; Nagasuma R. Chandra; Narayanaswamy Srinivasan (Nucleic Acids Res., 2015)

Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. - Raju Kalaivani; Raju Reema; Narayanaswamy Srinivasan (PLoS Comput. Biol., 2018)

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains. - Sneha Vishwanath; Alexandre G. de Brevern; Narayanaswamy Srinivasan (PLoS Comput. Biol., 2018)

iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach. - Guilhem Faure; Agnel Praveen Joseph; Pierrick Craveur; Tarun J. Narwani; Narayanaswamy Srinivasan; Jean-Christophe Gelly; Joseph Rebehmed; Alexandre G. de Brevern (Source Code Biol. Medicine, 2019)

DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins. - Neha V. Kalmankar; Murugavel Pavalam; Sowmya Indrakumar; Narayanaswamy Srinivasan; Ramanathan Sowdhamini (Database J. Biol. Databases Curation, 2022)

Shaking the β-Bulges. - Pierrick Craveur; Tarun J. Narwani; Narayanaswamy Srinivasan; Jean-Christophe Gelly; Joseph Rebehmed; Alexandre G. de Brevern (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)