List of works - Nagarajan Vaidehi

5-Formyluracil-induced perturbations of DNA function

scientific article

Advanced techniques for constrained internal coordinate molecular dynamics

scientific article

Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors

scientific article

Alkylation of cysteine 468 in Stat3 defines a novel site for therapeutic development

scientific article

Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1.

scientific article

Allosteric communication pipelines in G-protein-coupled receptors

scientific article

Atomic-level simulations of seeman DNA nanostructures: the paranemic crossover in salt solution

scientific article

Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor.

scientific article published in April 2010

Computational method to identify druggable binding sites that target protein-protein interactions.

scientific article

Conserved Mechanism of Conformational Stability and Dynamics in G-Protein-Coupled Receptors

scientific article published on 06 October 2016

Cooperation of neurotrophin receptor TrkB and Her2 in breast cancer cells facilitates brain metastases

scientific article published on 26 April 2017

Critical analysis of the successes and failures of homology models of G protein-coupled receptors.

scientific article published on 14 February 2013

Differences in allosteric communication pipelines in the inactive and active states of a GPCR.

scientific article

Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα.

scientific article published on 15 August 2017

Dynamic Role of the G Protein in Stabilizing the Active State of the Adenosine A Receptor

Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor.

scientific article published on 17 March 2014

Elucidation of binding sites of dual antagonists in the human chemokine receptors CCR2 and CCR5.

scientific article published on 18 March 2009

Exploring the molecular mechanism for color distinction in humans.

scientific article published in August 2006

Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations

scientific article published on 3 March 2006

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

scientific article

Folding of Small Proteins Using Constrained Molecular Dynamics ⬇️

scientific article published on May 18, 2011

Functional selectivity of dopamine D1 receptor agonists in regulating the fate of internalized receptors

scientific article

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

scientific article published in January 2004

How Can Mutations Thermostabilize G-Protein-Coupled Receptors?

scientific article

How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins?

scientific article

Human breast cancer metastases to the brain display GABAergic properties in the neural niche

scientific article

Identifying Functional Hotspot Residues for Biased Ligand Design in G-protein-coupled Receptors.

scientific article published on 24 January 2018

Importance of receptor flexibility in binding of cyclam compounds to the chemokine receptor CXCR4.

scientific article published on 15 December 2010

Interaction of E. coli outer-membrane protein A with sugars on the receptors of the brain microvascular endothelial cells

scientific article

LITiCon: a discrete conformational sampling computational method for mapping various functionally selective conformational states of transmembrane helical proteins

scientific article published on January 2012

Leflunomide regulates c-Myc expression in myeloma cells through PIM targeting

Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activation

scientific article

Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors

scientific article published in May 2004

Mapping conformational dynamics of proteins using torsional dynamics simulations

scientific article published on May 2013

Mechanism for antibody catalysis of the oxidation of water by singlet dioxygen

scientific article

Modeling the human PTC bitter-taste receptor interactions with bitter tastants

scientific article

Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3.

scientific article published on 6 September 2009

Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface

scientific article

Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptors.

scientific article published on January 2011

N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias

scientific article published on 22 June 2015

Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction

scientific article published on 20 February 2009

Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparison of predicted odor recognition profiles with experiment

scientific article

Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists

scholarly article

Prediction of structure and function of G protein-coupled receptors

scientific article

Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site

scientific article

Prediction of the 3D structure and dynamics of human DP G-protein coupled receptor bound to an agonist and an antagonist

scientific article published on 11 August 2007

Prediction of the 3D structure of FMRF-amide neuropeptides bound to the mouse MrgC11 GPCR and experimental validation

scientific article published in September 2007

Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation

scientific article published on 12 July 2006

Protein dynamics in a family of laboratory evolved thermophilic enzymes

scientific article published in March 2003

Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors.

scientific article

Receptor conformations involved in dopamine D(2L) receptor functional selectivity induced by selected transmembrane-5 serine mutations

scientific article

Role of specific cations and water entropy on the stability of branched DNA motif structures.

scientific article

Selectivity and specificity of substrate binding in methionyl-tRNA synthetase.

scientific article

Stereoselective synthesis, biological evaluation, and modeling of novel bile acid-derived G-protein coupled bile acid receptor 1 (GP-BAR1, TGR5) agonists

scientific article published on 11 February 2015

Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers

article

Structural dynamics and thermostabilization of neurotensin receptor 1

scientific article

Structural insights into conformational stability of wild-type and mutant beta1-adrenergic receptor.

scientific article published on July 2010

Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method ⬇️

scientific article published on February 16, 2012

Structure and dynamics of G-protein coupled receptors

scientific article published on January 2014

Structure and dynamics of a constitutively active neurotensin receptor

scientific article published on 07 December 2016

Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine

scientific article

Test of the Binding Threshold Hypothesis for olfactory receptors: explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912-93.

scientific article published on March 2005

The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals.

scientific article

The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists.

scholarly article

The predicted 3D structures of the human M1 muscarinic acetylcholine receptor with agonist or antagonist bound

scientific article published in August 2006

The role of conformational ensembles in ligand recognition in G-protein coupled receptors.

scientific article

The role of conformational ensembles of seven transmembrane receptors in functional selectivity ⬇️

scientific article published on December 1, 2010

The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number

scientific article published on 18 November 2004

Thermostabilization of the β1-adrenergic receptor correlates with increased entropy of the inactive state

scientific article published on 05 June 2013

Variable G protein determinants of GPCR coupling selectivity.

scientific article published on 29 May 2019

List of works by Nagarajan Vaidehi

5-Formyluracil-induced perturbations of DNA function

Advanced techniques for constrained internal coordinate molecular dynamics

Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors

Alkylation of cysteine 468 in Stat3 defines a novel site for therapeutic development

Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1.

Allosteric communication pipelines in G-protein-coupled receptors

Atomic-level simulations of seeman DNA nanostructures: the paranemic crossover in salt solution

Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor.

Computational method to identify druggable binding sites that target protein-protein interactions.

Conserved Mechanism of Conformational Stability and Dynamics in G-Protein-Coupled Receptors

Cooperation of neurotrophin receptor TrkB and Her2 in breast cancer cells facilitates brain metastases

Critical analysis of the successes and failures of homology models of G protein-coupled receptors.

Differences in allosteric communication pipelines in the inactive and active states of a GPCR.

Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα.

Dynamic Role of the G Protein in Stabilizing the Active State of the Adenosine A Receptor

Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor.

Elucidation of binding sites of dual antagonists in the human chemokine receptors CCR2 and CCR5.

Exploring the molecular mechanism for color distinction in humans.

Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

Folding of Small Proteins Using Constrained Molecular Dynamics ⬇️

Functional selectivity of dopamine D1 receptor agonists in regulating the fate of internalized receptors

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

How Can Mutations Thermostabilize G-Protein-Coupled Receptors?

How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins?

Human breast cancer metastases to the brain display GABAergic properties in the neural niche

Identifying Functional Hotspot Residues for Biased Ligand Design in G-protein-coupled Receptors.

Importance of receptor flexibility in binding of cyclam compounds to the chemokine receptor CXCR4.

Interaction of E. coli outer-membrane protein A with sugars on the receptors of the brain microvascular endothelial cells

LITiCon: a discrete conformational sampling computational method for mapping various functionally selective conformational states of transmembrane helical proteins

Leflunomide regulates c-Myc expression in myeloma cells through PIM targeting

Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activation

Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors

Mapping conformational dynamics of proteins using torsional dynamics simulations

Mechanism for antibody catalysis of the oxidation of water by singlet dioxygen

Modeling the human PTC bitter-taste receptor interactions with bitter tastants

Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3.

Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface

Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptors.

N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias

Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction

Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparison of predicted odor recognition profiles with experiment

Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists

Prediction of structure and function of G protein-coupled receptors

Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site

Prediction of the 3D structure and dynamics of human DP G-protein coupled receptor bound to an agonist and an antagonist

Prediction of the 3D structure of FMRF-amide neuropeptides bound to the mouse MrgC11 GPCR and experimental validation

Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation

Protein dynamics in a family of laboratory evolved thermophilic enzymes

Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors.

Receptor conformations involved in dopamine D(2L) receptor functional selectivity induced by selected transmembrane-5 serine mutations

Role of specific cations and water entropy on the stability of branched DNA motif structures.

Selectivity and specificity of substrate binding in methionyl-tRNA synthetase.

Stereoselective synthesis, biological evaluation, and modeling of novel bile acid-derived G-protein coupled bile acid receptor 1 (GP-BAR1, TGR5) agonists

Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers

Structural dynamics and thermostabilization of neurotensin receptor 1

Structural insights into conformational stability of wild-type and mutant beta1-adrenergic receptor.

Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method ⬇️

Structure and dynamics of G-protein coupled receptors

Structure and dynamics of a constitutively active neurotensin receptor

Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine

Test of the Binding Threshold Hypothesis for olfactory receptors: explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912-93.

The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals.

The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists.

The predicted 3D structures of the human M1 muscarinic acetylcholine receptor with agonist or antagonist bound

The role of conformational ensembles in ligand recognition in G-protein coupled receptors.

The role of conformational ensembles of seven transmembrane receptors in functional selectivity ⬇️

The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number

Thermostabilization of the β1-adrenergic receptor correlates with increased entropy of the inactive state

Variable G protein determinants of GPCR coupling selectivity.