Works by Bhattacharyya, Dhananjay

Results: 39

Capturing state-dependent dynamic events of GABA A -receptors: a microscopic look into the structural and functional insights.

Published in:

Journal of Biomolecular Structure & Dynamics, 2016, v. 34, n. 8, p. 1818, doi. 10.1080/07391102.2015.1094410

By:

Payghan, Pavan V.;
Bera, Indrani;
Bhattacharyya, Dhananjay;
Ghoshal, Nanda

Publication type:

Article

MetBP: a software tool for detection of interaction between metal ion–RNA base pairs.

Published in:

Bioinformatics, 2022, v. 38, n. 15, p. 3833, doi. 10.1093/bioinformatics/btac392

By:

Roy, Parthajit;
Bhattacharyya, Dhananjay

Publication type:

Article

Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.

Published in:

BMC Research Notes, 2014, v. 7, n. 1, p. 1, doi. 10.1186/1756-0500-7-83

By:

Kailasam, Senthilkumar;
Bhattacharyya, Dhananjay;
Bansal, Manju

Publication type:

Article

Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies.

Published in:

Journal of Molecular Modeling, 2017, v. 23, n. 11, p. 1, doi. 10.1007/s00894-017-3480-z

By:

Ray, Angana;
Agarwal, Ankita;
Bhattacharyya, Dhananjay

Publication type:

Article

Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation.

Published in:

Journal of Molecular Modeling, 2017, v. 23, n. 10, p. 1, doi. 10.1007/s00894-017-3470-1

By:

Mukherjee, Debasish;
Bhattacharyya, Dhananjay

Publication type:

Article

Melting of polymeric DNA double helix at elevated temperature: a molecular dynamics approach.

Published in:

Journal of Molecular Modeling, 2017, v. 23, n. 8, p. 1, doi. 10.1007/s00894-017-3398-5

By:

Kundu, Sangeeta;
Mukherjee, Sanchita;
Bhattacharyya, Dhananjay

Publication type:

Article

Contribution of phenylalanine side chain intercalation to the TATA-box binding protein–DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies.

Published in:

Journal of Molecular Modeling, 2014, v. 20, n. 11, p. 1, doi. 10.1007/s00894-014-2499-7

By:

Mondal, Manas;
Mukherjee, Sanchita;
Bhattacharyya, Dhananjay

Publication type:

Article

Deciphering the binding mode of Zolpidem to GABA α receptor - insights from molecular dynamics simulation.

Published in:

Journal of Molecular Modeling, 2012, v. 18, n. 4, p. 1345, doi. 10.1007/s00894-011-1142-0

By:

Vijayan, R.;
Bhattacharyya, Dhananjay;
Ghoshal, Nanda

Publication type:

Article

Effect of temperature on DNA double helix: An insight from molecular dynamics simulation.

Published in:

Journal of Biosciences, 2012, v. 37, n. 3, p. 445, doi. 10.1007/s12038-012-9215-5

By:

Kundu, Sangeeta;
Mukherjee, Sanchita;
Bhattacharyya, Dhananjay

Publication type:

Article

Theoretical analysis of noncanonical base pairing interactions in RNA molecules.

Published in:

Journal of Biosciences, 2007, v. 32, n. 5, p. 809, doi. 10.1007/s12038-007-0082-4

By:

BHATTACHARYYA, DHANANJAY;
KORIPELLA, SIV CHAND;
MITRA, ABHIJIT;
RAJENDRAN, VIJAY BABU;
SINHA, BHABDYUTI

Publication type:

Article

Influence of 2′-Deoxy Sugar Moiety on Excited-State Protonation Equilibrium of Adenine and Adenosine with Acridine inside SDS Micelles: A Time-Resolved Study with Quantum Chemical Calculations.

Published in:

ChemPhysChem, 2012, v. 13, n. 2, p. 525, doi. 10.1002/cphc.201100763

By:

Sarangi, Manas Kumar;
Bhattacharyya, Dhananjay;
Basu, Samita

Publication type:

Article

RNABPDB: Molecular Modeling of RNA Structure—From Base Pair Analysis in Crystals to Structure Prediction.

Published in:

Interdisciplinary Sciences: Computational Life Sciences, 2022, v. 14, n. 3, p. 759, doi. 10.1007/s12539-022-00528-w

By:

Mukherjee, Debasish;
Maiti, Satyabrata;
Gouda, Prasanta Kumar;
Sharma, Richa;
Roy, Parthajit;
Bhattacharyya, Dhananjay

Publication type:

Article

RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

Published in:

Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 2, p. 219, doi. 10.1007/s10822-016-0007-0

By:

Bhattacharyya, Dhananjay;
Halder, Sukanya;
Basu, Sankar;
Mukherjee, Debasish;
Kumar, Prasun;
Bansal, Manju

Publication type:

Article

Role of indirect readout mechanism in TATA box binding protein-DNA interaction.

Published in:

Journal of Computer-Aided Molecular Design, 2015, v. 29, n. 3, p. 283, doi. 10.1007/s10822-014-9828-x

By:

Mondal, Manas;
Choudhury, Devapriya;
Chakrabarti, Jaydeb;
Bhattacharyya, Dhananjay

Publication type:

Article

Analysis of stacking overlap in nucleic acid structures: algorithm and application.

Published in:

Journal of Computer-Aided Molecular Design, 2014, v. 28, n. 8, p. 851, doi. 10.1007/s10822-014-9767-6

By:

Pingali, Pavan;
Halder, Sukanya;
Mukherjee, Debasish;
Basu, Sankar;
Banerjee, Rahul;
Choudhury, Devapriya;
Bhattacharyya, Dhananjay

Publication type:

Article

Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs.

Published in:

Journal of Computer-Aided Molecular Design, 2014, v. 28, n. 7, p. 735, doi. 10.1007/s10822-014-9755-x

By:

Mukherjee, Sanchita;
Kundu, Sangeeta;
Bhattacharyya, Dhananjay

Publication type:

Article

Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.

Published in:

Journal of Computer-Aided Molecular Design, 2006, v. 20, n. 10/11, p. 629, doi. 10.1007/s10822-006-9083-x

By:

Mukherjee, Shayantani;
Bansal, Manju;
Bhattacharyya, Dhananjay

Publication type:

Article

Structural basis of DNA recognition by anticancer antibiotics, chromomycin A<sub>3</sub>, and mithramycin: Roles of minor groove width and ligand flexibility.

Published in:

Biopolymers, 2000, v. 56, n. 2, p. 85, doi. 10.1002/1097-0282(2000)56:2<85::AID-BIP1054>3.0.CO;2-7

By:

Chakrabarti, Sukanya;
Bhattacharyya, Dhananjay;
Dasgupta, Dipak

Publication type:

Article

Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?

Published in:

Proteins, 2022, v. 90, n. 7, p. 1390, doi. 10.1002/prot.26321

By:

Biswas, Gargi;
Ghosh, Semanti;
Basu, Sankar;
Bhattacharyya, Dhananjay;
Datta, Alok Kumar;
Banerjee, Rahul

Publication type:

Article

Skeletal Muscle Dystrophy mutant of lamin A alters the structure and dynamics of the Ig fold domain.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-32227-2

By:

Dutta, Subarna;
Das, Jitendra K.;
Maganti, Lakshmi;
Bhattacharyya, Maitree;
Bhattacharyya, Dhananjay;
Mukherjee, Sujoy;
Sengupta, Kaushik

Publication type:

Article

Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs.

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 195, doi. 10.1186/1471-2105-12-195

By:

Basu, Sankar;
Bhattacharyya, Dhananjay;
Banerjee, Rahul

Publication type:

Article

Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs.

Published in:

Biopolymers, 2016, v. 105, n. 4, p. 212, doi. 10.1002/bip.22787

By:

Mondal, Manas;
Halder, Sukanya;
Chakrabarti, Jaydeb;
Bhattacharyya, Dhananjay

Publication type:

Article

A comparison of four different conformations adopted by human telomeric G-quadruplex using computer simulations.

Published in:

Biopolymers, 2016, v. 105, n. 2, p. 83, doi. 10.1002/bip.22751

By:

Ray, Angana;
Panigrahi, Swati;
Bhattacharyya, Dhananjay;
Case, David

Publication type:

Article

Stacking geometry for non-canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion-corrected DFT-D study.

Published in:

Biopolymers, 2015, v. 103, n. 6, p. 328, doi. 10.1002/bip.22616

By:

Mondal, Manas;
Mukherjee, Sanchita;
Halder, Sukanya;
Bhattacharyya, Dhananjay;
Woodson, Sarah

Publication type:

Article

Stacking interactions in RNA and DNA: Roll-slide energy hyperspace for ten unique dinucleotide steps.

Published in:

Biopolymers, 2015, v. 103, n. 3, p. 134, doi. 10.1002/bip.22566

By:

Mukherjee, Sanchita;
Kailasam, Senthilkumar;
Bansal, Manju;
Bhattacharyya, Dhananjay

Publication type:

Article

Energy hyperspace for stacking interaction in AU/ AU dinucleotide step: Dispersion-corrected density functional theory study.

Published in:

Biopolymers, 2014, v. 101, n. 1, p. 107, doi. 10.1002/bip.22289

By:

Mukherjee, Sanchita;
Kailasam, Senthilkumar;
Bansal, Manju;
Bhattacharyya, Dhananjay;
Walter, Nils G.

Publication type:

Article

Effect of phosphorothioate chirality on the grooves of DNA double helices: A molecular dynamics study.

Published in:

Biopolymers, 2004, v. 73, n. 2, p. 269, doi. 10.1002/bip.10550

By:

Shayantani Mukherjee;
Dhananjay Bhattacharyya

Publication type:

Article

Contact networks in RNA: a structural bioinformatics study with a new tool.

Published in:

Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 2, p. 131, doi. 10.1007/s10822-021-00438-x

By:

Roy, Parthajit;
Bhattacharyya, Dhananjay

Publication type:

Article

Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 1, p. 83, doi. 10.1007/s10822-019-00268-y

By:

Maganti, Lakshmi;
Bhattacharyya, Dhananjay

Publication type:

Article

Understanding the role of non‐Watson‐Crick base pairs in DNA–protein recognition: Structural and energetic aspects using crystallographic database analysis and quantum chemical calculation.

Published in:

Biopolymers, 2022, v. 113, n. 7, p. 1, doi. 10.1002/bip.23492

By:

Das, Soumi;
Roy, Siddhartha;
Bhattacharyya, Dhananjay

Publication type:

Article

RNABP COGEST: a resource for investigating functional RNAs.

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav011

By:

Bhattacharya, Sohini;
Mittal, Shriyaa;
Panigrahi, Swati;
Sharma, Purshotam;
Preethi S. P.;
Paul, Rahul;
Halder, Sukanya;
Halder, Antarip;
Bhattacharyya, Dhananjay;
Mitra, Abhijit

Publication type:

Article

The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics.

Published in:

PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0142173

By:

Roy, Sourav;
Basu, Sankar;
Dasgupta, Dipak;
Bhattacharyya, Dhananjay;
Banerjee, Rahul

Publication type:

Article

In silico work flow for scaffold hopping in Leishmania.

Published in:

BMC Research Notes, 2014, v. 7, n. 1, p. 1, doi. 10.1186/1756-0500-7-802

By:

Waugh, Barnali;
Ghosh, Ambarnil;
Bhattacharyya, Dhananjay;
Ghoshal, Nanda;
Banerjee, Rahul

Publication type:

Article

Maturation of siRNA by strand separation: Steered molecular dynamics study.

Published in:

Journal of Biomolecular Structure & Dynamics, 2022, v. 40, n. 24, p. 13682, doi. 10.1080/07391102.2021.1994468

By:

Mishra, Rakesh Kumar;
Mukherjee, Sanchita;
Bhattacharyya, Dhananjay

Publication type:

Article

Cross-talk between allosteric and orthosteric binding sites of γ-amino butyric acid type A receptors (GABA<sub>A</sub>-Rs): A computational study revealing the structural basis of selectivity.

Published in:

Journal of Biomolecular Structure & Dynamics, 2019, v. 37, n. 12, p. 3065, doi. 10.1080/07391102.2018.1508367

By:

Payghan, Pavan V.;
Nath Roy, Sudipendra;
Bhattacharyya, Dhananjay;
Ghoshal, Nanda

Publication type:

Article

Plausible blockers of Spike RBD in SARS-CoV2—molecular design and underlying interaction dynamics from high-level structural descriptors.

Published in:

Journal of Molecular Modeling, 2021, v. 27, n. 6, p. 1, doi. 10.1007/s00894-021-04779-0

By:

Basu, Sankar;
Chakravarty, Devlina;
Bhattacharyya, Dhananjay;
Saha, Pampa;
Patra, Hirak K

Publication type:

Article

Twist-dependent stacking energy of base-pair steps in B-DNA geometry: A density functional theory approach.

Published in:

International Journal of Quantum Chemistry, 2008, v. 108, n. 6, p. 1173, doi. 10.1002/qua.21579

By:

Samanta, Sudipta;
Kabir, Mukul;
Sanyal, Biplab;
Bhattacharyya, Dhananjay

Publication type:

Article

Ab initio studies on excited state intramolecular electron transfer in 4-amino-N-methylphthalimide and 3-amino-N-methylphthalimide.

Published in:

International Journal of Quantum Chemistry, 2006, v. 106, n. 4, p. 913, doi. 10.1002/qua.20866

By:

Sen, Kakali;
Basu, Samita;
Bhattacharyya, Dhananjay

Publication type:

Article

Ab Initio QM/MM Study of Excited State Electron Transfer Between Pyrene and 4,4′-Bis(dimethylamino)-diphenylmethane With Different Solvent Systems: Role of Hydrogen Bonding Within Solvent Molecules.

Published in:

International Journal of Quantum Chemistry, 2005, v. 102, n. 4, p. 368, doi. 10.1002/qua.20417

By:

Sen, Kakali;
Basu, Samita;
Bhattacharyya, Dhananjay

Publication type:

Article