Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
Abstract Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …
Rnabpdb: Molecular modeling of rna structure—From base pair analysis in crystals to structure prediction
The stable three-dimensional structure of RNA is known to play several important
biochemical roles, from post-transcriptional gene regulation to enzymatic action. These …
biochemical roles, from post-transcriptional gene regulation to enzymatic action. These …
RNA secondary structure prediction with pseudoknots using chemical reaction optimization algorithm
RNA molecules play a significant role in cell function especially including pseudoknots. In
past decades, several methods have been developed to predict RNA secondary structure …
past decades, several methods have been developed to predict RNA secondary structure …
Non-canonical base pairing
D Bhattacharyya, A Mitra - WikiJournal of Science, 2023 - search.informit.org
Non-canonical base pairs are planar hydrogen bonded pairs of nucleobases, having
hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base …
hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base …
Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches
L Maganti, D Bhattacharyya - Journal of computer-aided molecular design, 2020 - Springer
DNA is an essential target for the treatment of various pathologies, especially cancer. Hence
targeting DNA double helix for alteration of its function has been attempted by several ways …
targeting DNA double helix for alteration of its function has been attempted by several ways …
Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction
Background Molecular modeling of RNA double helices is possible using most probable
values of basepair parameters obtained from crystal structure database. The A: A w: wC non …
values of basepair parameters obtained from crystal structure database. The A: A w: wC non …
Stacking interactions involving non-Watson–Crick basepairs: dispersion corrected density functional theory studies
S Maiti, D Bhattacharyya - Physical Chemistry Chemical Physics, 2017 - pubs.rsc.org
The G: A basepair, stabilized by hydrogen bonding through the sugar edge of guanine and
Hoogsteen edge of adenine in trans orientation (G: AS: HT), appears very frequently in the …
Hoogsteen edge of adenine in trans orientation (G: AS: HT), appears very frequently in the …
DNA base sequence specificity through partial intercalation: DFT-D based energy analysis of molecular dynamics snapshots
S Das, S Roy, D Bhattacharyya - Journal of Molecular Graphics and …, 2020 - Elsevier
It had been observed that in some DNA-binding proteins, hydrophobic amino acid side-
chains intercalate between two base pairs of the DNA, often leading to curvature or kink …
chains intercalate between two base pairs of the DNA, often leading to curvature or kink …
[PDF][PDF] Canonical and non-canonical base pairs in DNA or RNA: Structure, function and dynamics
D Bhattacharyya, A Mitra - osf.io
Non-canonical base pairs are planar hydrogen bonded pairs of nucleobases, having
hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base …
hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base …
[PDF][PDF] WikiJournal of Science/Non-canonical Base Pairing
D Bhattacharyya¹, A Mitra - upload.wikimedia.org
Non-canonical base pairs are planar hydrogen-bonded pairs of nucleobases, having
hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base …
hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base …