List of works - Narayanaswamy Srinivasan

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

scientific article published in May 2015

A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases.

scientific article

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis.

scientific article

A short survey on protein blocks.

scientific article

A structural entropy index to analyse local conformations in intrinsically disordered proteins

scientific article published on 21 January 2020

A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications

scientific article published on 01 October 2006

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling

scientific article published on 6 December 2013

An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure

scholarly article by Raghu Bhagavat published in March 2018

Artificial protein sequences enable recognition of vicinal and distant protein functional relationships

scientific article published on 29 July 2020

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

scientific article

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

scientific article

Cis-trans peptide variations in structurally similar proteins

scientific article published on 8 January 2012

Classification of protein kinases on the basis of both kinase and non-kinase regions

scientific article

Clustering of multi-domain protein sequences

scientific article published on 06 May 2018

Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins

scientific article published on 02 August 2021

Comparison of Leptospira interrogans and Leptospira biflexa genomes: analysis of potential leptospiral-host interactions

scientific article published on 15 March 2017

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

scientific article

Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria

scientific article (publication date: 31 May 2016)

Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites.

scientific article

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.

scientific article published on 3 June 2013

Data set of intrinsically disordered proteins analysed at a local protein conformation level

scientific article published on 05 March 2020

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

scientific article

Deciphering common recognition principles of nucleoside mono/di and tri-phosphates binding in diverse proteins via structural matching of their binding sites.

scientific article published on 25 May 2017

Design, Synthesis, and Experimental Validation of Peptide Ligands Targeting Mycobacterium tuberculosis σ Factors.

scientific article

Discrete analyses of protein dynamics

scientific article published on 12 August 2019

DoSA: Database of Structural Alignments

scientific article

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

scientific article

Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold

scientific article published on 12 August 2015

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

scientific article published on 18 July 2017

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

scientific article published on 4 December 2013

Fold combinations in multi-domain proteins

scientific article published on 15 May 2019

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

scientific article

Genome-wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights

scientific article published on 15 July 2020

Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum.

scientific article

How good are comparative models in the understanding of protein dynamics?

scientific article published on 30 January 2020

Hybrid and rogue kinases encoded in the genomes of model eukaryotes

scientific article published on 25 September 2014

Identification of Potential Binders of <i>Mtb</i> Universal Stress Protein (Rv1636) Through an <i>in silico</i> Approach and Insights Into Compound Selection for Experimental Validation

scientific article published on 03 May 2021

Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks

scientific article

Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage

scientific article

Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins

scientific article

In silico prediction of protein flexibility with local structure approach

scientific article published on 01 August 2019

Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions

scientific article published on 15 January 2019

Knowledge-Based Protein Modeling

scientific article (publication date: 1994)

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

scientific article published on 21 November 2017

Length variations amongst protein domain superfamilies and consequences on structure and function

scientific article

Local structural differences in homologous proteins: specificities in different SCOP classes

scientific article

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

scientific article published on 22 April 2021

Mechanism of CcdA-Mediated Rejuvenation of DNA Gyrase

scientific article published on 02 April 2020

NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G

scientific article published on 23 August 2019

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

scientific article

PB-kPRED: Knowledge-Based Prediction Of Protein Backbone Conformation Using A Structural Alphabet

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

scientific article

Protein flexibility in the light of structural alphabets

scientific article

Protein sequence design and its applications

scientific article

Publisher Correction: A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

scientific article published on 19 November 2020

Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins.

scientific article

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

scientific article published on 13 February 2018

Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv.

scientific article

Repurposing Drugs Based on Evolutionary Relationships Between Targets of Approved Drugs and Proteins of Interest

scientific article published on 01 January 2019

Repurposing drugs against the main protease of SARS-CoV-2: mechanism-based insights supported by available laboratory and clinical data

scientific article published on 22 July 2020

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

scientific article

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

scientific article published on 26 March 2012

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis.

scientific article published on 30 June 2015

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

scientific article published on 12 February 2018

Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family

scientific article published on 30 September 2019

Specificity and stability of transient protein-protein interactions

scientific article published on 11 January 2017

Stability of domain structures in multi-domain proteins ⬇️

scientific article published on July 18, 2011

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

scientific article (publication date: 2 October 2016)

Structural insights into Saccharomyces cerevisiae Msh4-Msh5 complex function using homology modeling

scientific article

Structural variations within proteins can be as large as variations observed across their homologues

scientific article published on 24 September 2019

Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold

scientific article

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

scientific article

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

scientific article published on May 2014

Transient association between proteins elicits alteration of dynamics at sites far away from interfaces

scientific article published on 30 November 2020

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

scientific article

Use of a structural alphabet to find compatible folds for amino acid sequences

scientific article

Use of designed sequences in protein structure recognition.

scientific article published on 9 May 2018

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

scientific article published on 18 July 2016

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

scientific article published on 27 August 2015

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

scientific article

iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach

scientific article published on 02 November 2019

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

scientific article

List of works by Narayanaswamy Srinivasan

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

A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases.

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis.

A short survey on protein blocks.

A structural entropy index to analyse local conformations in intrinsically disordered proteins

A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling

An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure

Artificial protein sequences enable recognition of vicinal and distant protein functional relationships

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

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

Cis-trans peptide variations in structurally similar proteins

Classification of protein kinases on the basis of both kinase and non-kinase regions

Clustering of multi-domain protein sequences

Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins

Comparison of Leptospira interrogans and Leptospira biflexa genomes: analysis of potential leptospiral-host interactions

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

Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria

Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites.

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.

Data set of intrinsically disordered proteins analysed at a local protein conformation level

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Deciphering common recognition principles of nucleoside mono/di and tri-phosphates binding in diverse proteins via structural matching of their binding sites.

Design, Synthesis, and Experimental Validation of Peptide Ligands Targeting Mycobacterium tuberculosis σ Factors.

Discrete analyses of protein dynamics

DoSA: Database of Structural Alignments

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

Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold

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

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

Fold combinations in multi-domain proteins

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

Genome-wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights

Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum.

How good are comparative models in the understanding of protein dynamics?

Hybrid and rogue kinases encoded in the genomes of model eukaryotes

Identification of Potential Binders of <i>Mtb</i> Universal Stress Protein (Rv1636) Through an <i>in silico</i> Approach and Insights Into Compound Selection for Experimental Validation

Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks

Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage

Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins

In silico prediction of protein flexibility with local structure approach

Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions

Knowledge-Based Protein Modeling

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

Length variations amongst protein domain superfamilies and consequences on structure and function

Local structural differences in homologous proteins: specificities in different SCOP classes

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

Mechanism of CcdA-Mediated Rejuvenation of DNA Gyrase

NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G

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

PB-kPRED: Knowledge-Based Prediction Of Protein Backbone Conformation Using A Structural Alphabet

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

Protein flexibility in the light of structural alphabets

Protein sequence design and its applications

Publisher Correction: A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins.

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

Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv.

Repurposing Drugs Based on Evolutionary Relationships Between Targets of Approved Drugs and Proteins of Interest

Repurposing drugs against the main protease of SARS-CoV-2: mechanism-based insights supported by available laboratory and clinical data

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

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

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis.

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

Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family

Specificity and stability of transient protein-protein interactions

Stability of domain structures in multi-domain proteins ⬇️

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

Structural insights into Saccharomyces cerevisiae Msh4-Msh5 complex function using homology modeling

Structural variations within proteins can be as large as variations observed across their homologues

Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold

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

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

Transient association between proteins elicits alteration of dynamics at sites far away from interfaces

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

Use of a structural alphabet to find compatible folds for amino acid sequences

Use of designed sequences in protein structure recognition.

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

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