List of works - Nilesh Banavali

A low affinity ground state conformation for the Dynein microtubule binding domain

scientific article

Analyzing the relationship between single base flipping and strand slippage near DNA duplex termini

scientific article

Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck

scholarly article by Nilesh Banavali published in March 2007

Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids

Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase

scientific article published on 23 July 2004

Characterizing structural transitions using localized free energy landscape analysis

scientific article

Chemical activation of adenylyl cyclase Rv1625c inhibits growth of Mycobacterium tuberculosis on cholesterol and modulates intramacrophage signaling.

scientific article published on 02 May 2017

Computational exploration of structural hypotheses for an additional sequence in a mammalian mitochondrial protein

scientific article

Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix

scientific article published on June 2006

Cytosine unstacking and strand slippage at an insertion-deletion mutation sequence in an overhang-containing DNA duplex

scientific article

DNA bending induced by carbocyclic sugar analogs constrained to the north conformation

scientific article published on April 2007

Development and current status of the CHARMM force field for nucleic acids.

scientific article

Electrostatic free energy calculations using the generalized solvent boundary potential method

Existing drugs as broad-spectrum and potent inhibitors for Zika virus by targeting NS2B-NS3 interaction

scientific article published on 07 July 2017

Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases

scientific article published on February 2009

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

scientific article published in 2005

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

scientific article published in May 2002

General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing

scientific article published on 07 November 2019

Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

scientific article

Identification and Characterization of Novel Broad-Spectrum Inhibitors of the Flavivirus Methyltransferase

scientific article

Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites.

scientific article

Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1

scientific article

Insights into Structural Basis of Mammalian Mitochondrial Translation

article published in 2013

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

scientific article

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

scientific article

Modeling a ryanodine receptor N-terminal domain connecting the central vestibule and the corner clamp region

scientific article published on 30 November 2012

Molecular evidence for β-tubulin neofunctionalization in Retaria (Foraminifera and radiolarians).

scientific article published on 4 September 2013

Novel Broad Spectrum Inhibitors Targeting the Flavivirus Methyltransferase

scientific article

Partial base flipping is sufficient for strand slippage near DNA duplex termini

scientific article published on 21 May 2013

Post-translational environmental switch of RadA activity by extein-intein interactions in protein splicing

scientific article published on 22 June 2015

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

scientific article

RNA approaches the B-form in stacked single strand dinucleotide contexts

scientific article

Reevaluation of Stereoelectronic Contributions to the Conformational Properties of the Phosphodiester and N3‘-Phosphoramidate Moieties of Nucleic Acids

scientific article published on 01 July 2001

S-adenosyl-homocysteine is a weakly bound inhibitor for a flaviviral methyltransferase

scientific article

Selective inhibition of the West Nile virus methyltransferase by nucleoside analogs

scientific article published on 22 December 2012

Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing

scientific article published on 10 October 2019

Sterol A-ring plasticity in hedgehog protein cholesterolysis supports a primitive substrate selectivity mechanism

scientific article published on 01 February 2019

Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching

scientific article published on 22 January 2018

Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation

scientific article published on 31 July 2020

The Mechanism of Cholesterol Modification of Hedgehog Ligand

scientific article published on 14 November 2019

The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation

scientific article

The extent of B-form structure in a 6S RNA variant that mimics DNA to bind to the Escherichia coli RNA Polymerase

Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets To Probe the Mechanism of Base Flipping byHhaI DNA (Cytosine C5)-methyltransferase

article by Peiyuan Wang et al published December 2000 in Journal of the American Chemical Society

List of works by Nilesh Banavali

A low affinity ground state conformation for the Dynein microtubule binding domain

Analyzing the relationship between single base flipping and strand slippage near DNA duplex termini

Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck

Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids

Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase

Characterizing structural transitions using localized free energy landscape analysis

Chemical activation of adenylyl cyclase Rv1625c inhibits growth of Mycobacterium tuberculosis on cholesterol and modulates intramacrophage signaling.

Computational exploration of structural hypotheses for an additional sequence in a mammalian mitochondrial protein

Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix

Cytosine unstacking and strand slippage at an insertion-deletion mutation sequence in an overhang-containing DNA duplex

DNA bending induced by carbocyclic sugar analogs constrained to the north conformation

Development and current status of the CHARMM force field for nucleic acids.

Electrostatic free energy calculations using the generalized solvent boundary potential method

Existing drugs as broad-spectrum and potent inhibitors for Zika virus by targeting NS2B-NS3 interaction

Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing

Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

Identification and Characterization of Novel Broad-Spectrum Inhibitors of the Flavivirus Methyltransferase

Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites.

Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1

Insights into Structural Basis of Mammalian Mitochondrial Translation

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

Modeling a ryanodine receptor N-terminal domain connecting the central vestibule and the corner clamp region

Molecular evidence for β-tubulin neofunctionalization in Retaria (Foraminifera and radiolarians).

Novel Broad Spectrum Inhibitors Targeting the Flavivirus Methyltransferase

Partial base flipping is sufficient for strand slippage near DNA duplex termini

Post-translational environmental switch of RadA activity by extein-intein interactions in protein splicing

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

RNA approaches the B-form in stacked single strand dinucleotide contexts

Reevaluation of Stereoelectronic Contributions to the Conformational Properties of the Phosphodiester and N3‘-Phosphoramidate Moieties of Nucleic Acids

S-adenosyl-homocysteine is a weakly bound inhibitor for a flaviviral methyltransferase

Selective inhibition of the West Nile virus methyltransferase by nucleoside analogs

Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing

Sterol A-ring plasticity in hedgehog protein cholesterolysis supports a primitive substrate selectivity mechanism

Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching

Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation

The Mechanism of Cholesterol Modification of Hedgehog Ligand

The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation

The extent of B-form structure in a 6S RNA variant that mimics DNA to bind to the Escherichia coli RNA Polymerase

Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets To Probe the Mechanism of Base Flipping byHhaI DNA (Cytosine C5)-methyltransferase