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List of works by Ivet Bahar

"Only a Life Lived for Others Is Worth Living": redox signaling by oxygenated phospholipids in cell fate decisions

journal article published in 2018

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations

scientific article published on December 2009

A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/γ-butyrobetaine antiporter CaiT ⬇️

scientific article published on July 29, 2012

A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α1-antitrypsin deficiency

scientific article

A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry <i>in vitro</i>

scientific article published on 24 November 2020

A stable three enzyme creatinine biosensor. 2. Analysis of the impact of silver ions on creatine amidinohydrolase

scientific article published on 29 December 2004

A stable three-enzyme creatinine biosensor. 1. Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase

scientific article published on 29 December 2004

ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones

scientific article

Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions.

scientific article

Adaptability of protein structures to enable functional interactions and evolutionary implications

scientific article published on 06 August 2015

Allosteric Modulation of Intact γ-Secretase Structural Dynamics

scientific article published in December 2017

Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation

scientific article published on 06 July 2020

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

scientific article

An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates

scientific article published on September 2012

An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research

scientific article published on January 2006

Analysis of correlated mutations in HIV-1 protease using spectral clustering

scientific article

Author Correction: Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD.

scientific article

BalestraWeb: efficient online evaluation of drug-target interactions

scientific article

Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions

scientific article published on September 2015

Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells

journal article published in 2013

Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members

scientific article

Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.

scientific article published on 28 February 2019

Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings

scientific article

ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution

scientific article

Coarse-grained normal mode analysis in structural biology

scientific article

Common mechanism of pore opening shared by five different potassium channels

scientific article

Comparative Dynamics of NMDA- and AMPA-Glutamate Receptor N-Terminal Domains ⬇️

scientific article published on September 6, 2012

Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution

scientific article published on 19 February 2015

Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel

scientific article published on 06 April 2020

Complete mapping of substrate translocation highlights the role of LeuT N-terminal segment in regulating transport cycle

scientific article (publication date: October 2014)

Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments ⬇️

scientific article published on January 1, 2011

Computational insights on the competing effects of nitric oxide in regulating apoptosis

scientific article

Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding

scientific article

Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington's Disease Model through the Application of Quantitative Systems Pharmacology.

scientific article published on 19 December 2017

Constraints Imposed by the Membrane Selectively Guide the Alternating Access Dynamics of the Glutamate Transporter GltPh ⬇️

scientific article published on March 20, 2012

Coupled Global and Local Changes Direct Substrate Translocation by Neurotransmitter-Sodium Symporter Ortholog LeuT ⬇️

scientific article published on August 6, 2013

Coupling between catalytic loop motions and enzyme global dynamics

scientific article

Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

scientific article

Coupling between neurotransmitter translocation and protonation state of a titratable residue during Na ⁺-coupled transport

scientific article published on June 2014

Decoding of persistent multiscale structures in complex biological networks

scientific article published on 18 June 2020

Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids

journal article published in 2014

Development of Small-Molecule PUMA Inhibitors for Mitigating Radiation-Induced Cell Death ⬇️

scientific article published on January 1, 2011

Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase

scientific article

Discovery of novel Myc-Max heterodimer disruptors with a three-dimensional pharmacophore model

scientific article published on March 2009

Domain swapping proceeds via complete unfolding: a 19F- and 1H-NMR study of the Cyanovirin-N protein

scientific article published on 22 February 2012

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

scientific article

DynOmics: dynamics of structural proteome and beyond

scientific article published on 3 May 2017

Dynamics and allosteric potential of the AMPA receptor N-terminal domain ⬇️

scientific article published on February 11, 2011

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

scientific article

EIF3H orchestrates Hippo pathway-mediated oncogenesis via catalytic control of YAP stability

scientific article published on 08 April 2020

Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow

scientific article published on 31 May 2022

Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies

scientific article

Empowerment of 15-Lipoxygenase Catalytic Competence in Selective Oxidation of Membrane ETE-PE to Ferroptotic Death Signals, HpETE-PE

scientific article published on 17 December 2018

Energy landscape of LeuT from molecular simulations

scientific article published in December 2015

Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data

scientific article

Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model

scientific article (publication date: April 2014)

Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

scientific article

FlexE: Using elastic network models to compare models of protein structure.

scientific article

Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer

scientific article published on 06 January 2014

Functional motions of influenza virus hemagglutinin: a structure-based analytical approach

scientific article published on February 2002

Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules

scientific article

Global dynamics of proteins: bridging between structure and function

scientific article published on January 2010

Global motions of the nuclear pore complex: insights from elastic network models

scientific article

Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase

scientific article published on October 2013

High-efficiency bypass of DNA damage by human DNA polymerase Q

scientific article

Identification of Motions in Membrane Proteins by Elastic Network Models and Their Experimental Validation ⬇️

scientific article published on January 1, 2012

Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome

scientific article published on 09 November 2020

Identification of core amino acids stabilizing rhodopsin

scientific article

Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions

scientific article published on 17 February 2022

Improved Total-Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways

scientific article published on 15 November 2017

In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase

scientific article

Inflammatory modulation of hepatocyte apoptosis by nitric oxide: in vivo, in vitro, and in silico studies

scientific article

Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation

scientific article

Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase

scientific article

Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways

scientific article published on 12 July 2016

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions

scientific article

Insights into the Modulation of Dopamine Transporter Function by Amphetamine, Orphenadrine, and Cocaine Binding

scientific article

Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis

scientific article

Intracellular Gating in an Inward-facing State of Aspartate Transporter GltPh Is Regulated by the Movements of the Helical Hairpin HP2 ⬇️

scientific article published on February 5, 2013

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

scientific article published on 27 November 2019

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

scientific article

Large collective motions regulate the functional properties of glutamate transporter trimers

scientific article

Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion

scientific article published on 22 November 2011

Markov methods for hierarchical coarse-graining of large protein dynamics.

scientific article

Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES.

scientific article published on 4 July 2006

Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes

scientific article published on 4 April 2008

Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis

scientific article

Metal-binding sites are designed to achieve optimal mechanical and signaling properties

scientific article published on September 2010

Microseconds simulations reveal a new sodium-binding site and the mechanism of sodium-coupled substrate uptake by LeuT

scientific article

Mining frequent patterns in protein structures: a study of protease families.

scientific article

Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter

scientific article

Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter

scientific article

NO Represses the Oxygenation of Arachidonoyl PE by 15LOX/PEBP1: Mechanism and Role in Ferroptosis

scientific article

Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD.

scientific article

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

scientific article

On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

scientific article

On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

scientific article published on June 2010

Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis

scientific article

PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals.

scientific article

PEBP1 acts as a rheostat between prosurvival autophagy and ferroptotic death in asthmatic epithelial cells

scientific article published on 08 June 2020

PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons

scientific article published on 10 January 2018

Pharmacological suppression of B7-H4 glycosylation restores antitumor immunity in immune-cold breast cancers

scientific article published on 16 September 2020

Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations

scientific article published on 04 December 2019

Phospholipase iPLA<sub>2</sub>β averts ferroptosis by eliminating a redox lipid death signal

scientific article published on 04 February 2021

Precise druggability of the PTH type 1 receptor

scientific article published on 23 December 2021

Predicting drug-target interactions using probabilistic matrix factorization

scientific article published on 10 December 2013

Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins ⬇️

scientific article published on September 9, 2011

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

scientific article

ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python

ProDy: Protein Dynamics Inferred from Theory and Experiments ⬇️

scientific article published on April 5, 2011

Protonation of Glutamate 208 Induces the Release of Agmatine in an Outward-facing Conformation of an Arginine/Agmatine Antiporter ⬇️

scientific article published on April 12, 2011

Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter

scientific article published on 12 December 2017

Quantitative assessment of cell fate decision between autophagy and apoptosis

scientific article

Recruitment of pro-IL-1α to mitochondrial cardiolipin, via shared LC3 binding domain, inhibits mitophagy and drives maximal NLRP3 activation

scientific article published on 01 January 2021

Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity?

scientific article

Redox lipid reprogramming commands susceptibility of macrophages and microglia to ferroptotic death

scientific article published on 17 February 2020

Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis

scientific article published on 23 December 2016

Relating molecular flexibility to function: a case study of tubulin

scientific article

Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs ⬇️

scientific article published on September 16, 2010

Sequence Evolution Correlates with Structural Dynamics ⬇️

scientific article published on March 16, 2012

Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization.

scientific article published in June 2018

Signal propagation in proteins and relation to equilibrium fluctuations

scientific article

Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies

scientific article published on September 2014

Spatial bias in cAMP generation determines biological responses to PTH type 1 receptor activation

scientific article published on 05 October 2021

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

scholarly article

Structural dynamics is a determinant of the functional significance of missense variants.

scientific article published on 2 April 2018

Structurally unique inhibitors of human mitogen-activated protein kinase phosphatase-1 identified in a pyrrole carboxamide library

scientific article

Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains

scientific article

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

scientific article published on 02 July 2015

Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters.

scientific article

Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation

scientific article published on 28 September 2020

Targeting of dopamine transporter to filopodia requires an outward-facing conformation of the transporter

scientific article

The anisotropic network model web server at 2015 (ANM 2.0).

scientific article

The center for causal discovery of biomedical knowledge from big data

scientific article

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

scientific article

The mechanism of substrate release by the aspartate transporter GltPh: insights from simulations ⬇️

scientific article published on December 15, 2010

The relationship between n-gram patterns and protein secondary structure

scientific article published on September 2007

The sodium/galactose symporter crystal structure is a dynamic, not so occluded state

scientific article published on 31 March 2010

Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter

scientific article

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae

scientific article

Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models

scientific article published on 25 January 2008

Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening

scientific article

Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones

scientific article published on January 2010

Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations

scientific article published on 20 June 2019

Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology

scientific article

Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity

scientific article published on June 2009

Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages

scientific article

iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics

scientific article

iGNM: a database of protein functional motions based on Gaussian Network Model.

scientific article

oGNM: online computation of structural dynamics using the Gaussian Network Model

scientific article published on July 2006

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