Bandyopadhyay P - Search Results

1

A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion.

Hasnain S, McClendon CL, Hsu MT, Jacobson MP, Bandyopadhyay P. Hasnain S, et al. Among authors: bandyopadhyay p. PLoS One. 2014 Sep 2;9(9):e106466. doi: 10.1371/journal.pone.0106466. eCollection 2014. PLoS One. 2014. PMID: 25180859 Free PMC article.

2

An analytical correlated random walk model and its application to understand subdiffusion in crowded environment.

Hasnain S, Bandyopadhyay P. Hasnain S, et al. Among authors: bandyopadhyay p. J Chem Phys. 2015 Sep 21;143(11):114104. doi: 10.1063/1.4930275. J Chem Phys. 2015. PMID: 26395684

3

How Mg²⁺ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study.

Shanker S, Bandyopadhyay P. Shanker S, et al. Among authors: bandyopadhyay p. J Biomol Struct Dyn. 2017 Aug;35(10):2103-2122. doi: 10.1080/07391102.2016.1213186. Epub 2016 Aug 2. J Biomol Struct Dyn. 2017. PMID: 27426235

4

Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics.

Jaiswal AK, Srivastava R, Pandey P, Bandyopadhyay P. Jaiswal AK, et al. Among authors: bandyopadhyay p. PLoS One. 2018 Nov 14;13(11):e0206359. doi: 10.1371/journal.pone.0206359. eCollection 2018. PLoS One. 2018. PMID: 30427849 Free PMC article.

5

Calculation of salt-dependent free energy of binding of β-lactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and three-dimensional reference interaction site model (3D-RISM): diffuse salt ions and non-polar interactions between the monomers favor the dimer formation.

Srivastava R, Chattopadhyaya M, Bandyopadhyay P. Srivastava R, et al. Among authors: bandyopadhyay p. Phys Chem Chem Phys. 2020 Jan 28;22(4):2142-2156. doi: 10.1039/c9cp05578a. Epub 2020 Jan 8. Phys Chem Chem Phys. 2020. PMID: 31912070

6

Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation.

Basit A, Yadav AK, Bandyopadhyay P. Basit A, et al. Among authors: bandyopadhyay p. J Chem Inf Model. 2022 Jun 13;62(11):2821-2834. doi: 10.1021/acs.jcim.2c00428. Epub 2022 May 24. J Chem Inf Model. 2022. PMID: 35608259

7

Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.

Bandyopadhyay P, Kuntz ID. Bandyopadhyay P, et al. Biopolymers. 2009 Jan;91(1):68-77. doi: 10.1002/bip.21083. Biopolymers. 2009. PMID: 18781627

8

Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, molecular dynamics simulation and quantum mechanical calculation.

Sharma S, Bandyopadhyay P. Sharma S, et al. Among authors: bandyopadhyay p. J Mol Model. 2012 Feb;18(2):481-92. doi: 10.1007/s00894-011-1087-3. Epub 2011 May 4. J Mol Model. 2012. PMID: 21541744

9

Molecular dynamics simulations indicate that tyrosineB10 limits motions of distal histidine to regulate CO binding in soybean leghemoglobin.

Sharma S, Kumar A, Kundu S, Bandyopadhyay P. Sharma S, et al. Among authors: bandyopadhyay p. Proteins. 2015 Oct;83(10):1836-48. doi: 10.1002/prot.24867. Epub 2015 Aug 13. Proteins. 2015. PMID: 26211916

10

Determination of low-energy structures of a small RNA hairpin using Monte Carlo-based techniques.

Shanker S, Bandyopadhyay P. Shanker S, et al. Among authors: bandyopadhyay p. J Biosci. 2012 Jul;37(3):533-8. doi: 10.1007/s12038-012-9209-3. J Biosci. 2012. PMID: 22750989

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