Narayanaswamy Srinivasan

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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, 2005, Nucleic Acids Res..

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

Narayanaswamy Srinivasan, Alexandre G. de Brevern, P. Sharma, 2006, Nucleic Acids Res..

Knowledge-based prediction of protein backbone conformation using a structural alphabet

Narayanaswamy Srinivasan, Manoj Tyagi, Frédéric Cadet, 2017, bioRxiv.

A short survey on protein blocks

Bohdan Schneider, L. S. Swapna, Narayanaswamy Srinivasan, 2010, Biophysical Reviews.

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, S. Abhiman, Narayanaswamy Srinivasan, 2002, Nucleic Acids Res..

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Narayanaswamy Srinivasan, Juliette Martin, Mutharasu Gnanavel, 2014, BMC Bioinformatics.

iPBA: a tool for protein structure comparison using sequence alignment strategies

Narayanaswamy Srinivasan, Alexandre G. de Brevern, Jean-Christophe Gelly, 2011, Nucleic Acids Res..

Clustering of multi‐domain protein sequences

Narayanaswamy Srinivasan, Prachi Mehrotra, Vimla Kany G Ami, 2018, Proteins.

HARMONY: a server for the assessment of protein structures

Narayanaswamy Srinivasan, Khader Shameer, Ramanathan Sowdhamini, 2006, Nucleic Acids Res..

DoSA: Database of Structural Alignments

Narayanaswamy Srinivasan, Alexandre G. de Brevern, Bernard O. Offmann, 2013, Database J. Biol. Databases Curation.

SUPFAM: A database of sequence superfamilies of protein domains

S. Balaji, Shashi B. Pandit, Narayanaswamy Srinivasan, 2004, BMC Bioinformatics.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Neil D. Rawlings, Robert D. Finn, Alex Bateman, 2015, Database J. Biol. Databases Curation.

Recognition of sites of functional specialisation in all known eukaryotic protein kinase families

Narayanaswamy Srinivasan, Raju Kalaivani, Raju Reema, 2018, PLoS Comput. Biol..

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins.

Narayanaswamy Srinivasan, Mutharasu Gnanavel, Prachi Mehrotra, 2014, Molecular bioSystems.

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

Narayanaswamy Srinivasan, Alexandre G. de Brevern, Sneha Vishwanath, 2018, PLoS Comput. Biol..

Influence of Genomic and Other Biological Data Sets in the Understanding of Protein Structures, Functions and Interactions

Oruganty Krishnadev, Smita Mohanty, L. S. Swapna, 2011, Int. J. Knowl. Discov. Bioinform..

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, N. Srinivasan, 2008, Silico Biol..

168 Classification of protein sequences with special references to multi-domain systems

Narayanaswamy Srinivasan, Mutharasu Gnanavel, Prachi Mehrotra, 2015, Journal of biomolecular structure & dynamics.

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection

Nagasuma R. Chandra, Narayanaswamy Srinivasan, Ramanathan Sowdhamini, 2014, Nucleic Acids Res..

Identification and analysis of a new family of bacterial serine proteinases

Shashi B. Pandit, Narayanaswamy Srinivasan, S. Pandit, 2004, Silico Biol..

Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures

Shashi B. Pandit, Narayanaswamy Srinivasan, Seema Namboori, 2004, Silico Biol..

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Saikat Chakrabarti, 2006, Nucleic Acids Res..

Prediction of Protein-Protein Interactions Between Human Host and Two Mycobacterial Organisms

Oruganty Krishnadev, Narayanaswamy Srinivasan, Shveta Bisht, 2010, Int. J. Knowl. Discov. Bioinform..

MulPSSM: a database of multiple position-specific scoring matrices of protein domain families

Oruganty Krishnadev, Narayanaswamy Srinivasan, Venkatraman S. Gowri, 2005, Nucleic Acids Res..

Nucleic Acids Research Advance Access published June 21, 2007 PIC: Protein Interactions Calculator

Narayanaswamy Srinivasan, Rana Bhadra, K. G. Tina, 2007 .

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

Narayanaswamy Srinivasan, Venkatraman S. Gowri, Ambrish Roy, 2009, Silico Biol..

PALI - a database of Phylogeny and ALIgnment of homologous protein structures

S. Balaji, Narayanaswamy Srinivasan, S. Sujatha, 2001, Nucleic Acids Res..

PALI: a database of alignments and phylogeny of homologous protein structures

S. Balaji, Narayanaswamy Srinivasan, S. Sujatha, 2001, Bioinform..

Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database

S. Balaji, Shashi B. Pandit, Narayanaswamy Srinivasan, 2003, Nucleic Acids Res..

KinG: a database of protein kinases in genomes

Narayanaswamy Srinivasan, K. R. Abhinandan, A. Krupa, 2004, Nucleic Acids Res..

A New Domain Family in the Superfamily of Alkaline Phosphatases

Shashi B. Pandit, Narayanaswamy Srinivasan, Rana Bhadra, 2005, Silico Biol..

How effective is the data on co-occurrence of domains in multi-domain proteins in prediction of protein-protein interactions?

Smita Mohanty, Narayanaswamy Srinivasan, 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics.

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues

Narayanaswamy Srinivasan, Venkatraman S. Gowri, B. Anand, 2005, Bioinform..

AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

Oruganty Krishnadev, Narayanaswamy Srinivasan, N. Srinivasan, 2011, BMC Bioinformatics.

Computational Methods and Tools for Repurposing of Drugs Against Coronaviruses

Narayanaswamy Srinivasan, Sohini Chakraborti, Sneha Bheemireddy, 2021 .

Master Blaster: an approach to sensitive identification of remotely related proteins

Narayanaswamy Srinivasan, V. S. Gowri, Chintalapati Janaki, 2021, Scientific Reports.

Protein sequence design and its applications.

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Sankaran Sandhya, 2016, Current opinion in structural biology.

Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes

L. S. Swapna, Narayanaswamy Srinivasan, N. Srinivasan, 2015, Protein science : a publication of the Protein Society.

Evolution of domain combinations in protein kinases and its implications for functional diversity.

Narayanaswamy Srinivasan, Krishanpal Anamika, N. Srinivasan, 2010, Progress in biophysics and molecular biology.

Frontiers in Protein and Peptide Sciences

Wei Chen, Hui Ding, Kuo-Chen Chou, 2014 .

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles.

Ruth Nussinov, Narayanaswamy Srinivasan, R. Nussinov, 2014, Progress in biophysics and molecular biology.

Prediction of protein-protein interactions between Helicobacter pylori and a human host.

Oruganty Krishnadev, Narayanaswamy Srinivasan, Nidhi Tyagi, 2009, Molecular bioSystems.

Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Eshita Mutt, 2013, PloS one.

Alpha-Turns In Protein Structures

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, R. Sowdhamini, 1995 .

Resolving protein structure‐function‐binding site relationships from a binding site similarity network perspective

Narayanaswamy Srinivasan, Nagasuma Chandra, Richa Mudgal, 2017, Proteins.

Roles of residues in the interface of transient protein-protein complexes before complexation

L. S. Swapna, Narayanaswamy Srinivasan, Lakshmipuram S. Swapna, 2012, Scientific Reports.

Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Narayanaswamy Srinivasan, Mutharasu Gnanavel, Ramaswamy Rakshambikai, 2015 .

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Narayanaswamy Srinivasan, Krishanpal Anamika, Juliette Martin, 2010, PloS one.

From workstations to workbenches: Towards predicting physicochemically viable protein–protein interactions across a host and a pathogen

Narayanaswamy Srinivasan, Gayatri Ramakrishnan, N. Chandra, 2014, IUBMB life.

Exploring anti-malarial potential of FDA approved drugs: an in silico approach

Narayanaswamy Srinivasan, Nagasuma Chandra, Gayatri Ramakrishnan, 2017, Malaria Journal.

Creating a specialist protein resource network

Neil D. Rawlings, Alex Bateman, Bernard Henrissat, 2015 .

Understanding the role of domain–domain linkers in the spatial orientation of domains in multi-domain proteins

Narayanaswamy Srinivasan, Alexandre G de Brevern, N. Srinivasan, 2013, Journal of biomolecular structure & dynamics.

Structural Insights into Saccharomyces cerevisiae Msh4–Msh5 Complex Function Using Homology Modeling

Narayanaswamy Srinivasan, Ramaswamy Rakshambikai, K. T. Nishant, 2013, PloS one.

Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting.

L. S. Swapna, Narayanaswamy Srinivasan, Lakshmipuram S. Swapna, 2016, Journal of structural biology.

Dynamics of Protein-Protein Interaction Network in Plasmodium Falciparum

Shashi B. Pandit, Narayanaswamy Srinivasan, Smita Mohanty, 2009 .

Length Variations amongst Protein Domain Superfamilies and Consequences on Structure and Function

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Bernard Offmann, 2009, PloS one.

Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility

Narayanaswamy Srinivasan, Ananya Chatterjee, Arindam Maitra, 2020, Journal of Biosciences.

Characterization of Conformational Patterns in Active and Inactive Forms of Kinases Using Protein Blocks Approach

Narayanaswamy Srinivasan, Alexandre G. de Brevern, A. G. Brevern, 2010 .

Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold

Narayanaswamy Srinivasan, Balasubramanian Gopal, N. Srinivasan, 2009, PloS one.

Characterization of the Entamoeba histolytica Ornithine Decarboxylase-Like Enzyme

Alok Bhattacharya, Narayanaswamy Srinivasan, Krishanpal Anamika, 2008, PLoS neglected tropical diseases.

Functional diversity of human protein kinase splice variants marks significant expansion of human kinome

Narayanaswamy Srinivasan, Krishanpal Anamika, N. Srinivasan, 2009, BMC Genomics.

Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins

L. S. Swapna, Narayanaswamy Srinivasan, Alexandre G de Brevern, 2012, BMC Structural Biology.

The origins of the evolutionary signal used to predict protein-protein interactions

L. S. Swapna, Narayanaswamy Srinivasan, David L Robertson, 2012, BMC Evolutionary Biology.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Bernardo Ochoa-Montaño, 2015, Tuberculosis.

α-Turns in protein structure

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, R. Sowdhamini, 1995 .

CUSP : an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Bernard Offmann, 2008 .

Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability.

Narayanaswamy Srinivasan, Ramanathan Sowdhamini, Nagasuma Chandra, 2014, Journal of molecular biology.

Classification of Protein Kinases Influenced by Conservation of Substrate Binding Residues.

Narayanaswamy Srinivasan, Chintalapati Janaki, N. Srinivasan, 2016, Methods in molecular biology.

Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

Narayanaswamy Srinivasan, R. Gadkari, Rupali A Gadkari, 2010, BMC Structural Biology.