Items where Author is "Chakraborty, Sandeep"

Article

Chakraborty, Sandeep ; Nascimento, Rafael ; Zaini, Paulo A. ; Gouran, Hossein ; Rao, Basuthkar J. ; Goulart, Luiz R. ; Dandekar, Abhaya M. (2016) 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 PeerJ, 4 . Article ID e2007, 25 pages. ISSN 2167-8359

Nascimento, Rafael ; Gouran, Hossein ; Chakraborty, Sandeep ; Gillespie, Hyrum W. ; Almeida-Souza, Hebreia O. ; Tu, Aye ; Rao, Basuthkar J. ; Feldstein, Paul A. ; Bruening, George ; Goulart, Luiz R. ; Dandekar, Abhaya M. (2016) The type II secreted lipase/esterase LesA is a key virulence factor required for Xylella fastidiosa pathogenesis in grapevines Scientific Reports, 6 (1). Article ID 18598, 17 pages. ISSN 2045-2322

Chakraborty, Sandeep ; Rao, Basuthkar J. ; Asgeirsson, Bjarni ; Dandekar, Abhaya M. (2015) Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions F1000Research, 3 . pp. Article ID 251-16 pages. ISSN 2046-1402

Chakraborty, Sandeep ; Phu, My ; de Morais, Tamara Prado ; Nascimento, Rafael ; Goulart, Luiz Ricardo ; Rao, Basuthkar J. ; Asgeirsson, Bjarni ; Dandekar, Abhaya M. (2015) The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens F1000Research, 3 . Article ID 295, 15 pages. ISSN 2046-1402

Chakraborty, Sandeep ; Britton, Monica ; Wegrzyn, Jill ; Butterfield, Timothy ; Martínez-García, Pedro José ; Reagan, Russell L. ; Rao, Basuthkar J. ; Leslie, Charles A. ; Aradhaya, Mallikarjuna ; Neale, David ; Woeste, Keith ; Dandekar, Abhaya M. (2015) YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut F1000Research, 4 . Article ID 155, 15 pages. ISSN 2046-1402

Chakraborty, Sandeep ; Rendón-Ramírez, Adela ; Ásgeirsson, Bjarni ; Dutta, Mouparna ; Ghosh, Anindya S. ; Oda, Masataka ; Venkatramani, Ravindra ; Rao, Basuthkar J. ; Dandekar, Abhaya M. ; Goni, Felix M. (2015) The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins F1000Research, 2 . Article ID 286, 26 pages. ISSN 2046-1402

Gouran, Hossein ; Chakraborty, Sandeep ; Rao, Basuthkar J. ; Asgeirsson, Bjarni ; Dandekar, Abhaya M. (2014) Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template F1000Research, 3 . Article 215, 11 pages. ISSN 2046-1402

Chakraborty, Sandeep ; Venkatramani, Ravindra ; Rao, Basuthkar J. ; Asgeirsson, Bjarni ; Dandekar, Abhaya M. (2014) The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment F1000Research, 2 . pp. Article ID 243-18 pages. ISSN 2046-1402

Mehta, Ishita S ; Kulashreshtha, Mugdha ; Chakraborty, Sandeep ; Kolthur-Seetharam, Ullas ; Rao, Basuthkar J (2013) Chromosome territories reposition during DNA damage-repair response Genome Biology, 14 (12). R135. ISSN 1465-6906

Mehta, Ishita S. ; Kulashreshtha, Mugdha ; Chakraborty, Sandeep ; Kolthur-Seetharam, Ullas ; Rao, Basuthkar J. (2013) Chromosome territories reposition during DNA damage-repair response Genome Biology, 14 (12). Article ID R135, 15 pages. ISSN 1465-6906

Mehta, Ishita ; Chakraborty, Sandeep ; Rao, Basuthkar J. (2013) IMACULAT - an open access package for the quantitative analysis of chromosome localization in the nucleus PLoS ONE, 8 (4). Article ID e61386, 7 pages. ISSN 1932-6203

Chakraborty, Sandeep ; Venkatramani, Ravindra ; Rao, Basuthkar J. ; Asgeirsson, Bjarni ; Dandekar, Abhaya M. (2013) Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms F1000Research, 2 . Article ID 211, 12 pages. ISSN 2046-1402

Chakraborty, Sandeep ; Rao, Basuthkar J. ; Baker, Nathan ; Ásgeirsson, Bjarni (2013) Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator Intrinsically Disordered Proteins, 1 (1). Article ID e25463, 14 pages. ISSN 2169-0707

Rendón-Ramírez, Adela ; Shukla, Manish ; Oda, Masataka ; Chakraborty, Sandeep ; Minda, Renu ; Dandekar, Abhaya M. ; Ásgeirsson, Bjarni ; Goñi, Félix M. ; Rao, Basuthkar J. (2013) 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 PLoS ONE, 8 (8). Article ID e70923, 9 pages. ISSN 1932-6203

Chakraborty, Sandeep ; Ásgeirsson, Bjarni ; Minda, Renu ; Salaye, Lipika ; Frère, Jean-Marie ; Rao, Basuthkar J. (2012) Inhibition of a cold-active alkaline phosphatase by imipenem revealed by in silico modeling of metallo-β-lactamase active sites FEBS Letters, 586 (20). pp. 3710-3715. ISSN 0014-5793

Chakraborty, Sandeep ; Ásgeirsson, Bjarni ; Rao, Basuthkar J. (2012) A measure of the broad substrate specificity of enzymes based on 'duplicate' catalytic residues PLoS One, 7 (11). Article ID e49313, 10 pages. ISSN 1932-6203

Chakraborty, Sandeep ; Rao, Basuthkar J. (2012) A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity PLoS One, 7 (2). Article ID e32011, 10 pages. ISSN 1932-6203

Chakraborty, Sandeep ; Minda, Renu ; Salaye, Lipika ; Bhattacharjee, Swapan K. ; Rao, Basuthkar J. (2011) Active site detection by spatial conformity and electrostatic analysis—unravelling a proteolytic function in shrimp alkaline phosphatase PLoS One, 6 (12). Article ID e28470, 14 pages. ISSN 1932-6203