Publications by authors named "Indrajit Deb"

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N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation.
Jeremy Monroe, Daniel E Eyler, Lili Mitchell, Indrajit Deb, Abigail Bojanowski

Nat Commun· September 2024

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Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and 1-methylpseudouridine within RNA duplexes.
Nivedita Dutta, Joanna Sarzynska, Indrajit Deb, Ansuman Lahiri

Phys Chem Chem Phys· January 2024

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How Robust Is the Ligand Binding Transition State?
Samik Bose, Samuel D Lotz, Indrajit Deb, Megan Shuck, Kin Sing Stephen Lee

J Am Chem Soc· November 2023

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Comparative analysis of RNA secondary structure accuracy on predicted RNA 3D models.
Mandar Kulkarni, Jayaraman Thangappan, Indrajit Deb, Sangwook Wu

PLoS One· September 2023

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Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand.
Adrien Chauvier, Jason C Porta, Indrajit Deb, Emily Ellinger, Katarina Meze

Nat Struct Mol Biol· July 2023

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LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations.
Rupak Pal, Indrajit Deb, Joanna Sarzynska, Ansuman Lahiri

J Biomol Struct Dyn· April 2023

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Bell-Evans model and steered molecular dynamics in uncovering the dissociation kinetics of ligands targeting G-protein-coupled receptors.
Muhammad Jan Akhunzada, Hyun Jung Yoon, Indrajit Deb, Abdennour Braka, Sangwook Wu

Sci Rep· September 2022

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Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA.
Nivedita Dutta, Indrajit Deb, Joanna Sarzynska, Ansuman Lahiri

Prog Biophys Mol Biol· April 2022

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Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives.
Nivedita Dutta, Indrajit Deb, Joanna Sarzynska, Ansuman Lahiri

J Comput Aided Mol Des· March 2022

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Quantum Mechanics Helps Uncover Atypical Recognition Features in the Flavin Mononucleotide Riboswitch.
Indrajit Deb, Hazel Wong, Colleen Tacubao, Aaron T Frank

J Phys Chem B· August 2021

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Accelerating Rare Dissociative Processes in Biomolecules Using Selectively Scaled MD Simulations.
Indrajit Deb, Aaron T Frank

J Chem Theory Comput· November 2019

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Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.
Indrajit Deb, Łukasz Popenda, Joanna Sarzyńska, Magdalena Małgowska, Ansuman Lahiri

Sci Rep· November 2019

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Reparameterizations of the χ Torsion and Lennard-Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines.
Indrajit Deb, Rupak Pal, Joanna Sarzynska, Ansuman Lahiri

J Comput Chem· June 2016

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Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations.
Indrajit Deb, Joanna Sarzynska, Lennart Nilsson, Ansuman Lahiri

Biopolymers· October 2014

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Conformational preferences of modified uridines: comparison of AMBER derived force fields.
Indrajit Deb, Joanna Sarzynska, Lennart Nilsson, Ansuman Lahiri

J Chem Inf Model· April 2014

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