List of works - Sandeep Chakraborty

A computational module assembled from different protease family motifs identifies PI PLC from Bacillus cereus as a putative prolyl peptidase with a serine protease scaffold

scientific article

A measure of the broad substrate specificity of enzymes based on 'duplicate' catalytic residues

scientific article

A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity

scientific article

A single amino acid substitution in the Ω-like loop of E. coli PBP5 disrupts its ability to maintain cell shape and intrinsic beta-lactam resistance

scientific article

Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase

scientific article

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions

scientific article

Chromosome territories reposition during DNA damage-repair response

scientific article published on 13 December 2013

Correlating the ability of VP24 protein from Ebola and Marburg viruses to bind human karyopherin to their immune suppression mechanism and pathogenicity using computational methods

Corrigendum: The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines.

scientific article published on 25 February 2016

Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues

scientific article

Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template

scientific article published on 9 September 2014

Genomic Variation Among and Within Six Juglans Species.

scientific article

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

scientific article published on 01 May 2020

IMACULAT - an open access package for the quantitative analysis of chromosome localization in the nucleus

scientific article

Inhibition of a cold-active alkaline phosphatase by imipenem revealed by in silico modeling of metallo-β-lactamase active sites.

scientific article published on 11 September 2012

Molecular Profiling of Pierce's Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection.

scientific article

PAGAL - Properties and corresponding graphics of alpha helical structures in proteins

scientific article

PAGAL - Properties and corresponding graphics of alpha helical structures in proteins

PREMONITION - Preprocessing motifs in protein structures for search acceleration

Promiscuity-based enzyme selection for rational directed evolution experiments

scientific article published on 01 January 2013

Promiscuous scaffolds in proteins - non-native, non-additive and non-trivial

Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

scientific article

Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa.

scientific article published on 24 May 2016

Sequencing a × hybrid yields high-quality genome assemblies of parental species

scientific article published on 25 March 2019

Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator

scientific article

The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens

scientific article

The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa

scientific article published on 5 August 2016

The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines.

scientific article

The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins.

scientific article

The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

scientific article

The plant-based chimeric antimicrobial protein SlP14a-PPC20 protects tomato against bacterial wilt disease caused by Ralstonia solanacearum

scientific article published on 29 November 2018

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

scientific article published on 3 May 2016

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

scientific article

YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools

scientific article

List of works by Sandeep Chakraborty

A computational module assembled from different protease family motifs identifies PI PLC from Bacillus cereus as a putative prolyl peptidase with a serine protease scaffold

A measure of the broad substrate specificity of enzymes based on 'duplicate' catalytic residues

A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity

A single amino acid substitution in the Ω-like loop of E. coli PBP5 disrupts its ability to maintain cell shape and intrinsic beta-lactam resistance

Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions

Chromosome territories reposition during DNA damage-repair response

Correlating the ability of VP24 protein from Ebola and Marburg viruses to bind human karyopherin to their immune suppression mechanism and pathogenicity using computational methods

Correlating the ability of VP24 protein from Ebola and Marburg viruses to bind human karyopherin to their immune suppression mechanism and pathogenicity using computational methods

Corrigendum: The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines.

Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues

Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template

Genomic Variation Among and Within Six Juglans Species.

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

IMACULAT - an open access package for the quantitative analysis of chromosome localization in the nucleus

Inhibition of a cold-active alkaline phosphatase by imipenem revealed by in silico modeling of metallo-β-lactamase active sites.

Molecular Profiling of Pierce's Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection.

PAGAL - Properties and corresponding graphics of alpha helical structures in proteins

PAGAL - Properties and corresponding graphics of alpha helical structures in proteins

PREMONITION - Preprocessing motifs in protein structures for search acceleration

Promiscuity-based enzyme selection for rational directed evolution experiments

Promiscuous scaffolds in proteins - non-native, non-additive and non-trivial

Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa.

Sequencing a × hybrid yields high-quality genome assemblies of parental species

Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator

The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens

The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa

The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines.

The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins.

The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

The plant-based chimeric antimicrobial protein SlP14a-PPC20 protects tomato against bacterial wilt disease caused by Ralstonia solanacearum

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools