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List of works by Nagasuma Chandra

13 Influence of iron on iron dependent repressor (IdeR) activation and DNA binding

scientific article published in May 2015

A K52Q substitution in the globular domain of histone H1t modulates its nucleosome binding properties

scientific article published on 05 October 2006

A Strategic Target Rescues Trimethoprim Sensitivity in Escherichia coli

scientific article published on 16 March 2020

A Systems Perspective of Signalling Networks in Host–Pathogen Interactions

A combined immuno-informatics and structure-based modeling approach for prediction of T cell epitopes of secretory proteins of Mycobacterium tuberculosis

article

A comparative analysis of the DNA recombination repair pathway in mycobacterial genomes

scientific article published on 4 May 2016

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

scientific article

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

scientific article

A molecular systems approach to modelling human skin pigmentation: identifying underlying pathways and critical components

scientific article published on 29 April 2015

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

scientific article

A systems perspective of host–pathogen interactions: predicting disease outcome in tuberculosis

scientific article published on 14 December 2009

ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex.

scientific article published on 9 September 2014

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

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

scientific article

Architectural plan of transcriptional regulation in Mycobacterium tuberculosis

scientific article published on 17 February 2015

Biophysical and biochemical characterization of Rv3405c, a tetracycline repressor protein from Mycobacterium tuberculosis

scientific article published on 30 January 2018

CHEXVIS: a tool for molecular channel extraction and visualization

scientific article

CancerLectinDB: a database of lectins relevant to cancer

scientific article

Cd Conformational And Modeling Studies Of A Synthetic Peptide Vpdlladllk In Different Media

Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection

scientific article published on 15 September 2014

Cloning, expression, purification, and biochemical characterisation of the FIC motif containing protein of Mycobacterium tuberculosis.

scientific article published on 13 September 2012

Common recognition principles across diverse sequence and structural families of sialic acid binding proteins.

scientific article published on 16 September 2013

Common scaffolds, diverse recognition profiles.

scientific article

Complete Genome Sequences of a Mycobacterium smegmatis Laboratory Strain (MC2 155) and Isoniazid-Resistant (4XR1/R2) Mutant Strains.

scientific article published on 5 February 2015

Complete Genome Sequences of an Escherichia coli Laboratory Strain and Trimethoprim-Resistant (TMP32XR) Mutant Strains.

scientific article published on 10 December 2015

Computational analysis of multivalency in lectins: structures of garlic lectin-oligosaccharide complexes and their aggregates.

scientific article

Computational analysis of proteome of H5N1 avian influenza virus to define T cell epitopes with vaccine potential.

scientific article published on 12 September 2007

Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria.

scientific article published on 19 December 2017

Computational approaches for drug target identification in pathogenic diseases ⬇️

scientific article published on August 22, 2011

Computational framework to integrate the effect of antigen recognition on disease epidemiology outcome: Multi-scale approach

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

scientific article (publication date: 31 May 2016)

Computational systems approach for drug target discovery ⬇️

scientific article published on December 1, 2009

Conformation of gramicidin-A in CTAB micellar media.

scientific article published in May 2003

Conformationally locked thiosugars as potent alpha-mannosidase inhibitors: synthesis, biochemical and docking studies.

scientific article published on 8 June 2007

Correction: The multifunctional PE_PGRS11 protein from Mycobacterium tuberculosis plays a role in regulating resistance to oxidative stress

scientific article published on 01 December 2019

Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis

scientific article

Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity

scientific article

Crystallization and preliminary crystallographic studies on the mannose-specific lectin from garlic

scientific article published on 01 November 1997

Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA Additional role of RuvB-binding domain and inter species variability

scientific article

Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.

scientific article published on 28 April 2006

Curcumin Reduces the Motility of Salmonella enterica Serovar Typhimurium by Binding to the Flagella, Thereby Leading to Flagellar Fragility and Shedding

scientific article published on 18 April 2016

Current trends in modeling host-pathogen interactions

Cytoview: development of a cell modelling framework

scientific article published on August 2007

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

Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping

scientific article published on 24 February 2015

Defining putative T cell epitopes from PE and PPE families of proteins of Mycobacterium tuberculosis with vaccine potential

scientific article published on 01 January 2005

Delta-aminolevulinic acid dehydratase from Plasmodium falciparum: indigenous versus imported.

scientific article published on 24 November 2003

DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions

scientific article

Design of a heme-binding peptide motif adopting a β-hairpin conformation

scientific article

Detection of hydrogen-bond signature patterns in protein families

scientific article published in January 2003

Determinants of histamine recognition: implications for the design of antihistamines.

scientific article published in September 2003

Development and Characterization of a Potent Tumor Necrosis Factor-Alpha-Blocking Agent

scientific article published on 15 July 2019

Diagnosis and therapy of oral squamous cell carcinoma.

scientific article published on March 2007

Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics

article

Dissecting the structural and functional features of the Luteinizing hormone receptor using receptor specific single chain fragment variables.

scientific article published on 29 February 2016

Editorial overview: Carbohydrate-protein interactions and glycosylation: integrating structural biology, informatics and systems modelling to understand glycan structure and glycan-protein interactions.

scientific article published on 26 November 2016

Efficacy of β-lactam/β-lactamase inhibitor combination is linked to WhiB4-mediated changes in redox physiology of Mycobacterium tuberculosis.

scientific article published on 26 May 2017

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

scientific article

EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks

scientific article

EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks

article published in 2015

Evolutionary insights from suffix array-based genome sequence analysis

scientific article published in August 2007

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

scientific article published on 18 July 2017

Extracting hydrogen-bond signature patterns from protein structure data.

scientific article

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

Flux balance analysis of biological systems: applications and challenges.

scientific article published on 15 March 2009

Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs

scientific article

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

scientific article

Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis

scientific journal article

Functional interaction of diphenols with polyphenol oxidase

scientific article published on 25 July 2007

Gene expression profiles of wild-type and isoniazid-resistant strains of Mycobacterium smegmatis.

scientific article published on 27 May 2015

Grouping of large populations into few CTL immune 'response-types' from influenza H1N1 genome analysis

scientific article published on 8 August 2014

HLA-A*0201-restricted Cytotoxic T-cell Epitopes in Three PE/PPE Family Proteins of Mycobacterium tuberculosis

scientific article published on 01 February 2008

HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials

scientific article published on 29 March 2016

Hallmarks of mycolic acid biosynthesis: a comparative genomics study.

scientific article

Heat shock protein 70 on Neuro2a cells is a putative receptor for Japanese encephalitis virus

scientific article

High IL-6 and low IL-15 levels mark the presence of TB infection: A preliminary study.

scientific article

Hypothetical protein Rv3423.1 of Mycobacterium tuberculosis is a histone acetyltransferase

scientific journal article

Identification of a 34 amino acid stretch within the C-terminus of histone H1 as the DNA-condensing domain by site-directed mutagenesis.

scientific article

Identification of a co-target for enhancing efficacy of sorafenib in HCC through a quantitative modeling approach

scientific article published on 06 September 2018

Identification of a gene signature for discriminating metastatic from primary melanoma using a molecular interaction network approach. ⬇️

scientific article published on 11 December 2017

Identifying and Tackling Emergent Vulnerability in Drug-Resistant Mycobacteria.

scientific article

Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions.

scientific article

In-silico pharmacodynamics: correlation of adverse effects of H2-antihistamines with histamine N-methyl transferase binding potential

scientific article published in January 2006

Inferring biochemical routes from biochemical networks

Interaction of coumarin derivatives with human serum albumin: investigation by fluorescence spectroscopic technique and modeling studies.

scientific article published in April 2001

Interaction profiling of T-cell epitopes with MHC-class I molecules

scientific article published on 01 January 2007

Interrogation of genome-wide networks in biology: comparison of knowledge-based and statistical methods

scientific article published in 2019

Lectindb: a plant lectin database.

scientific article published on 16 June 2006

Localisation of Plasmodium falciparum uroporphyrinogen III decarboxylase of the heme-biosynthetic pathway in the apicoplast and characterisation of its catalytic properties

scientific article (publication date: April 2009)

MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

scientific article published on 12 January 2016

Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure

article

Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study

scientific article

Meta-analysis of host response networks identifies a common core in tuberculosis.

scientific article

Methionine synthase is localized to the nucleus in Pichia pastoris and Candida albicans and to the cytoplasm in Saccharomyces cerevisiae

scientific article published on 12 July 2017

Mining large-scale response networks reveals 'topmost activities' in Mycobacterium tuberculosis infection

scientific article published on January 2013

Modeling metabolic adjustment in Mycobacterium tuberculosis upon treatment with isoniazid

scientific article published on December 2010

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction.

scientific article

Molecular dissection of Mycobacterium tuberculosis integration host factor reveals novel insights into the mode of DNA binding and nucleoid compaction

scientific article

Molecular mechanism of dimerization of Bowman-Birk inhibitors. Pivotal role of ASP76 in the dimerzation

scientific article published on 28 April 2004

Mycobacterium tuberculosis FtsZ requires at least one arginine residue at the C-terminal end for polymerization in vitro

scientific article published in January 2010

Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction ⬇️

scientific article published on March 21, 2012

Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance

scientific article

Network approaches to drug discovery

scientific article

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

scientific article

Open source drug discovery--a new paradigm of collaborative research in tuberculosis drug development.

scientific article published on 22 July 2011

PLIC: protein-ligand interaction clusters

scientific article published on 23 April 2014

Parallel implementation ofAutoDock

Perpetuation of immunological memory through common MHC-I binding modes of peptidomimic and antigenic peptides

scientific article published on 12 October 2007

PocketAlign a novel algorithm for aligning binding sites in protein structures.

scientific article

PocketAnnotate: towards site-based function annotation.

scientific article

PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins.

scientific article

PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites

PocketMatch: a new algorithm to compare binding sites in protein structures

scientific article

Prediction of an HMG-box fold in the C-terminal domain of histone H1: insights into its role in DNA condensation.

scientific article published on October 2002

Probing the Druggability Limits for Enzymes of the NAD Biosynthetic Network in Glioma.

scientific article published on 09 March 2016

Projections for fast protein structure retrieval

scientific article

Protein tagging, destruction and infection

scientific article

Protein-protein interaction networks suggest different targets have different propensities for triggering drug resistance

scientific article

Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

scientific article published on 18 July 2012

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

scientific article

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

scientific article

Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza. ⬇️

scientific article published on 21 March 2018

Rule-based modelling of iron homeostasis in tuberculosis

scholarly article by Soma Ghosh et al published 2011 in Molecular BioSystems

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis.

scientific article published on 30 June 2015

Scanning the Genome of Mycobacterium tuberculosis to Identify Potential Lectins

scientific article published on 01 January 2007

Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA

scientific article

Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis.

scientific article published in December 2009

Structural Annotation of the Mycobacterium tuberculosis Proteome

scientific article published on April 2014

Structural alignment based kernels for protein structure classification

Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities.

scientific article

Structural annotation of Mycobacterium tuberculosis proteome

scientific article

Structural basis for the function of anti-idiotypic antibody in immune memory

scientific article published on 20 January 2009

Structural bioinformatics: deriving biological insights from protein structures.

scientific article published on 12 December 2010

Structural biology of Mycobacterium tuberculosis proteins: the Indian efforts

scientific article published on 22 April 2011

Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination

scientific article

Support Vector Machine Classifier for Predicting Drug Binding to P-glycoprotein

Synthesis, docking and anti-tumor activity of beta-L-1,3-thiazolidine pyrimidine nucleoside analogues

scientific article

Systems biology

Systems biology of tuberculosis

scientific article published on April 2011

The multifunctional PE_PGRS11 protein from Mycobacterium tuberculosis plays a role in regulating resistance to oxidative stress

scientific journal article

Unbiased Identification of Blood-based Biomarkers for Pulmonary Tuberculosis by Modeling and Mining Molecular Interaction Networks

scientific article published on 21 December 2016

Virtual screening, identification and experimental testing of novel inhibitors of PBEF1/Visfatin/NMPRTase for glioma therapy

scientific article

Xray Studies on Crystalline Complexes Involving Amino Acids and Peptides XXXIV. Novel Mode of Aggregation, Interaction Patterns and Chiral Effects in the Maleic Acid Complexes of DL- and L- Arginine ⬇️

scientific article published on June 1, 1998

targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

scientific article

Ω76: A designed antimicrobial peptide to combat carbapenem- and tigecycline-resistant Acinetobacter baumannii

scientific article published on 24 July 2019

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