I. Bahar

发表

Anisotropy of fluctuation dynamics of proteins with an elastic network model.

R. Jernigan, A. Atilgan, S. Durell, 2001, Biophysical journal.

Folding core predictions from network models of proteins

I. Bahar, A. Rader, 2004 .

Structure-derived potentials and protein simulations.

R. Jernigan, I. Bahar, 1996, Current opinion in structural biology.

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

I. Bahar, T. Lezon, A. Bakan, 2010, Chemical reviews.

Coarse-grained normal mode analysis in structural biology.

I. Bahar, A. Rader, AJ Rader, 2005, Current opinion in structural biology.

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.

A. Atilgan, I. Bahar, B. Erman, 1997, Folding & design.

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

C. Chennubhotla, I. Bahar, 2006, Molecular systems biology.

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL.

C. Chennubhotla, I. Bahar, Zheng Yang, 2008, Molecular bioSystems.

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

R. Jernigan, I. Bahar, 1997, Journal of molecular biology.

Residue coordination in proteins conforms to the closest packing of spheres

R. Jernigan, I. Bahar, Zerrin Bagci, 2002 .

Residue packing in proteins: Uniform distribution on a coarse-grained scale

R. Jernigan, I. Bahar, Zerrin Bagci, 2002 .

Normal mode analysis : theory and applications to biological and chemical systems

I. Bahar, Q. Cui, 2005 .

Gaussian Dynamics of Folded Proteins

I. Bahar, B. Erman, T. Haliloglu, 1997 .

Sequence Evolution Correlates with Structural Dynamics

I. Bahar, Y. Liu, 2012, Molecular biology and evolution.

Global dynamics of proteins: bridging between structure and function.

I. Bahar, T. Lezon, Lee-Wei Yang, 2010, Annual review of biophysics.

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions.

I. Bahar, M. Gur, E. Zomot, 2013, The Journal of chemical physics.

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

J. Madura, I. Bahar, M. Gur, 2013, Biophysical journal.

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

I. Bahar, E. Prochownik, G. Mustata, 2009, Journal of medicinal chemistry.

Equilibrium states of rigid bodies with multiple interaction sites: Application to protein helices

R. Jernigan, I. Bahar, B. Erman, 1997 .

Empirical solvent‐mediated potentials hold for both intra‐molecular and inter‐molecular inter‐residue interactions

O. Ptitsyn, R. Jernigan, A. Y. Badretdinov, 1998, Protein science : a publication of the Protein Society.

Allostery as Structure‐Encoded Collective Dynamics

I. Bahar, A. Bakan, I. Shrivastava, 2020 .

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

C. Chennubhotla, I. Bahar, D. Tobi, 2007, Current opinion in structural biology.

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.

Hongchun Li, I. Bahar, P. Doruker, 2019, Current opinion in structural biology.

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

Ivet Bahar, N. A. Temiz, I. Bahar, 2002, Proteins.

Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain.

I. Bahar, J. García-Nafría, Anindita Dutta, 2019, Structure.

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

I. Bahar, James M. Krieger, I. Greger, 2015, Biophysical journal.

Dynamics and allosteric potential of the AMPA receptor N‐terminal domain

B. Reinhart, D. Bartel, I. Bahar, 2011, The EMBO journal.

A hierarchical elastic network model for unsupervised electron density map segmentation

Virginia M. Burger, C. Chennubhotla, I. Bahar, 2011 .

Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores.

G B Ermentrout, G. Ermentrout, I. Bahar, 2006, Biophysical journal.

Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis

Ivet Bahar, Bard Ermentrout, Yoram Vodovotz, 2008, PloS one.

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

Ivet Bahar, Pemra Doruker, I. Bahar, 2002, Biophysical journal.

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

Ivet Bahar, I. Bahar, E. Zomot, 2010, Molecular bioSystems.

A Conformational Switch in a Partially Unwound Helix Selectively Determines the Pathway for Substrate Release from the Carnitine/γ-Butyrobetaine Antiporter CaiT*

Ivet Bahar, I. Bahar, E. Zomot, 2012, The Journal of Biological Chemistry.

Microseconds Simulations Reveal a New Sodium-binding Site and the Mechanism of Sodium-coupled Substrate Uptake by LeuT*

Ivet Bahar, Mert Gur, I. Bahar, 2014, The Journal of Biological Chemistry.

Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter.

M. H. Cheng, I. Bahar, 2015, Structure.

Mechanisms of CFTR Functional Variants That Impair Regulated Bicarbonate Permeation and Increase Risk for Pancreatitis but Not for Cystic Fibrosis

Ivet Bahar, Michelle L. Kienholz, Randall E. Brand, 2014, PLoS genetics.

Molecular mechanisms of chaperonin GroEL-GroES function.

R L Jernigan, D. Covell, R. Jernigan, 2002, Biochemistry.

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

Ivet Bahar, K. Dill, I. Bahar, 2002, Protein science : a publication of the Protein Society.

Understanding the recognition of protein structural classes by amino acid composition

R. Jernigan, A. Atilgan, I. Bahar, 1997, Proteins.

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

I. Bahar, A. Bakan, 2009, Proceedings of the National Academy of Sciences.

Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis.

Simon C Watkins, J. Klein-Seetharaman, B. Liu, 2017, Nature chemical biology.

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

A. Atilgan, M. Demirel, I. Bahar, 1998 .

Proteins with similar architecture exhibit similar large-scale dynamic behavior.

R. Jernigan, O. Keskin, I. Bahar, 2000, Biophysical journal.

Global ribosome motions revealed with elastic network model.

R. Jernigan, I. Bahar, A. Rader, 2004, Journal of structural biology.

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

C. Chennubhotla, A. Gronenborn, I. Bahar, 2007, Structure.

Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model.

D. Covell, R. Jernigan, I. Bahar, 1998, Biochemistry.

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

Lucy J. Colwell, Johan A. Grahnen, Nimrod D. Rubinstein, 2012, Protein science : a publication of the Protein Society.

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

I. Bahar, D. Tobi, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Identification of kinetically hot residues in proteins

R. Jernigan, A. Atilgan, M. Demirel, 1998, Protein science : a publication of the Protein Society.

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

I. Bahar, Lee-Wei Yang, 2005, Structure.

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

K. Schulten, E. Tajkhorshid, I. Bahar, 2008, Biophysical journal.

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

I. Bahar, Anindita Dutta, 2010, Structure.

Cooperative dynamics of proteins unraveled by network models

I. Bahar, E. Eyal, Anindita Dutta, 2011, Wiley interdisciplinary reviews. Computational molecular science.

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

I. Bahar, A. Bakan, Neysa Nevins, 2013, Journal of chemical theory and computation.

Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.

Hongchun Li, I. Bahar, P. Doruker, 2020, Biophysical journal.

Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity

Hongchun Li, I. Bahar, She Zhang, 2019, Molecular biology and evolution.

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

M. H. Cheng, I. Bahar, J. Y. Lee, 2015, Biophysical journal.

Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure.

E. Sausville, D. Covell, R. Jernigan, 2000, Anti-cancer drug design.

Coordination geometry of nonbonded residues in globular proteins.

R L Jernigan, R. Jernigan, I. Bahar, 1996, Folding & design.

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α‐amylase inhibitor

Ivet Bahar, Pemra Doruker, A. Atilgan, 2000, Proteins.

Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences.

Ivet Bahar, James Krieger, I. Bahar, 2015, Structure.

Pseudomonas aeruginosa utilizes host polyunsaturated phosphatidylethanolamines to trigger theft-ferroptosis in bronchial epithelium

Simon C Watkins, Janet S. Lee, I. Bahar, 2018, The Journal of clinical investigation.

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

R L Jernigan, D. Covell, R. Jernigan, 1999, Journal of molecular biology.

Cooperative fluctuations and subunit communication in tryptophan synthase.

R L Jernigan, R. Jernigan, I. Bahar, 1999, Biochemistry.

Identification of motions in membrane proteins by elastic network models and their experimental validation.

Kalyan C. Tirupula, Z. Oltvai, J. Klein-Seetharaman, 2012, Methods in molecular biology.

9.3 In Silico Coarse-Grained Approaches to Structural Dynamics and Function of Proteins and their Assemblies

I. Bahar, P. Doruker, Y. Liu, 2012 .

Predisposition of the dark state of rhodopsin to functional changes in structure

Judith Klein-Seetharaman, Ivet Bahar, J. Klein-Seetharaman, 2006, Proteins.

Common mechanism of pore opening shared by five different potassium channels.

Ivet Bahar, I. Bahar, I. Shrivastava, 2006, Biophysical journal.

Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

Dror Tobi, I. Bahar, D. Tobi, 2003, Journal of molecular biology.

Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation

I. Bahar, She Zhang, Fangyuan Chen, 2019, Nucleic acids research.

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

Bing Liu, Ivet Bahar, Zoltán N. Oltvai, 2014, Scientific Reports.

Stochastic modeling of p53-regulated apoptosis upon radiation damage

Z. Oltvai, I. Bahar, D. Bhatt, 2011, 1109.0743.

Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency

Terrence J. Sejnowski, Ivet Bahar, James R. Faeder, 2018, eNeuro.

Structurally Unique Inhibitors of Human Mitogen-Activated Protein Kinase Phosphatase-1 Identified in a Pyrrole Carboxamide Library

I. Bahar, A. Bakan, J. Lazo, 2007, Journal of Pharmacology and Experimental Therapeutics.

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

I. Bahar, J. Y. Lee, James M. Krieger, 2019, Neuroscience Letters.

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

M. H. Cheng, I. Bahar, J. Y. Lee, 2019, Neuropharmacology.

Monoamine transporters: structure, intrinsic dynamics and allosteric regulation

M. H. Cheng, I. Bahar, 2019, Nature Structural & Molecular Biology.

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

M. H. Cheng, I. Bahar, She Zhang, 2018, Philosophical Transactions of the Royal Society B: Biological Sciences.

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

M. H. Cheng, I. Bahar, A. Newman, 2017, Scientific Reports.

Allosteric modulation of human dopamine transporter activity under conditions promoting its dimerization

M. H. Cheng, S. Wasserman, I. Bahar, 2017, The Journal of Biological Chemistry.

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

M. H. Cheng, I. Bahar, A. Sorkin, 2015, Front. Neurol..

Sodium-coupled Secondary Transporters: Insights from Structure-based Computations

Ivet Bahar, Ahmet Bakan, Timothy R. Lezon, 2011 .

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

I. Bahar, I. Shrivastava, Zhihua Liu, 2016, EBioMedicine.

HiDeF: identifying persistent structures in multiscale ‘omics data

T. Ideker, I. Bahar, Christopher Churas, 2021, Genome Biology.

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

I. Bahar, A. Bakan, M. Gur, 2011, Protein science : a publication of the Protein Society.

State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps

I. Bahar, J. Carazo, C. Sorzano, 2020, Progress in biophysics and molecular biology.

Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling.

Hongchun Li, I. Bahar, G. Schreiber, 2017, Journal of molecular biology.

Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters

M. H. Cheng, I. Bahar, M. Gur, 2017, The journal of physical chemistry. B.

Elastic Network Models For Biomolecular Dynamics: Theory and Application to Membrane Proteins and Viruses

I. Bahar, T. Lezon, I. Shrivastava, 2009 .

Allosteric Modulation of Intact γ-Secretase Structural Dynamics.

Ji Young Lee, I. Bahar, X. Xie, 2017, Biophysical journal.

An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z

I. Bahar, G. Silverman, Yan Wang, 2019, PloS one.

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

I. Bahar, P. Doruker, Z. Kurkcuoglu, 2016, Journal of chemical theory and computation.

Quantitative systems pharmacological analysis of drugs of abuse reveals the pleiotropy of their targets and the effector role of mTORC1

Hongchun Li, I. Bahar, Fen Pei, 2018, bioRxiv.

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

M. H. Cheng, I. Bahar, Cihan Kaya, 2017, The journal of physical chemistry. B.

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

M. H. Cheng, I. Bahar, S. Amara, 2017, eLife.

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

I. Bahar, She Zhang, Carl Kingsford, 2016, bioRxiv.

Impact of South African 501.V2 Variant on SARS-CoV-2 Spike Infectivity and Neutralization: A Structure-based Computational Assessment

M. H. Cheng, I. Bahar, B. Kaynak, 2021, bioRxiv.

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

Hongchun Li, D. L. Taylor, I. Bahar, 2017, Scientific Reports.

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

M. H. Cheng, I. Bahar, James M. Krieger, 2020, bioRxiv.

Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1

Hongchun Li, I. Bahar, Fen Pei, 2018, bioRxiv.

Coupling between different modes in local chain dynamics: a modal correlation analysis

A. Atilgan, I. Bahar, B. Erman, 1995 .

Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh.

Ivet Bahar, Timothy R Lezon, I. Bahar, 2012, Biophysical journal.

Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger.

M. H. Cheng, I. Bahar, M. Giladi, 2018, Cell calcium.

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

I. Bahar, 2014, Biophysical journal.

Iron catalysis of lipid peroxidation in ferroptosis: Regulated enzymatic or random free radical reaction?

I. Bahar, H. Bayır, I. Shrivastava, 2019, Free radical biology & medicine.

Decoding of persistent multiscale structures in complex biological networks.

T. Ideker, I. Bahar, Christopher Churas, 2020, bioRxiv : the preprint server for biology.

Identifying persistent structures in multiscale ‘omics data

T. Ideker, I. Bahar, Christopher Churas, 2020, bioRxiv.

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

M. H. Cheng, I. Bahar, C. Chu, 2018, eNeuro.

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

Hassan A. Karimi, Ivet Bahar, Xiong Liu, 2006, Nucleic Acids Res..

A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for targeted therapy

I. Bahar, W. Gradishar, X. Xie, 2019, EBioMedicine.

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

I. Bahar, W. Nowak, C. Benadiba, 2017, Scientific Reports.

A Quantitative Systems Pharmacology Platform Reveals NAFLD Pathophysiological States and Targeting Strategies

Daniel E. Lefever, D. L. Taylor, I. Bahar, 2022, Metabolites.

In Vivo Structure–Activity Relationship Studies Support Allosteric Targeting of a Dual Specificity Phosphatase

Karl T. Debiec, I. Bahar, A. Bakan, 2014, Chembiochem : a European journal of chemical biology.

Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis

I. Bahar, G. Silverman, D. Perlmutter, 2020, bioRxiv.

Multisystem In ﬂ ammatory Syndrome in Children and Long COVID: The SARS-CoV-2 Viral Superantigen Hypothesis

M. H. Cheng, I. Bahar, M. Noval Rivas, 2022 .

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

B. Liu, I. Bahar, Hong Wang, 2017, Radiation Research.

Quantitative assessment of cell fate decision between autophagy and apoptosis

Z. Oltvai, I. Bahar, H. Bayır, 2017, bioRxiv.

Stress-strain relations and molecular orientation in highly crosslinked cis-polyisoprene networks

I. Bahar, B. Erman, C. Kanberoglu, 1993 .

Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain.

I. Bahar, J. García-Nafría, Anindita Dutta, 2019, Structure.

HLA class I-associated expansion of TRBV11-2 T cells in Multisystem Inflammatory Syndrome in Children.

M. H. Cheng, I. Bahar, J. McCormick, 2021, The Journal of clinical investigation.

Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions

I. Bahar, P. Doruker, B. Kaynak, 2020, Computational and structural biotechnology journal.

Activation and Speciation Mechanisms in Class A GPCRs

I. Bahar, P. Doruker, B. Wingert, 2022, Journal of molecular biology.

Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation

I. Bahar, C. Eng, James M. Krieger, 2021, bioRxiv.

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

Simon C Watkins, I. Bahar, H. Bayır, 2020, Proceedings of the National Academy of Sciences.

Correction: Mechanisms of CFTR Functional Variants That Impair Regulated Bicarbonate Permeation and Increase Risk for Pancreatitis but Not for Cystic Fibrosis

Min Goo Lee, Michelle A. Anderson, J. Larusch, 2014, PLoS Genetics.

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

I. Bahar, H. Bayır, I. Shrivastava, 2020, Nature Chemical Biology.

Resolving the paradox of ferroptotic cell death: Ferrostatin-1 binds to 15LOX/PEBP1 complex, suppresses generation of peroxidized ETE-PE, and protects against ferroptosis

B. Stockwell, I. Bahar, H. Bayır, 2020, Redox biology.

"Only a Life Lived for Others Is Worth Living": Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions.

Simon C Watkins, I. Bahar, H. Bayır, 2017, Antioxidants & redox signaling.

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

I. Bahar, H. Bayır, I. Shrivastava, 2018, Journal of the American Chemical Society.

PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals

Simon C Watkins, I. Bahar, H. Bayır, 2017, Cell.

GPCR kinases generate an APH1A phosphorylation barcode to regulate amyloid-β generation

I. Bahar, P. Doruker, James M. Krieger, 2022, Cell reports.

Potent and broad neutralization of SARS-CoV-2 variants of concern (VOCs) including omicron sub-lineages BA.1 and BA.2 by biparatopic human VH domains

Michele D. Sobolewski, M. H. Cheng, I. Bahar, 2022, iScience.

Mathematical Modeling Reveals a Synergistic Mechanism of Toll-like Receptor Pathways

J. L. Ding, I. Bahar, P. Thiagarajan, 2014 .

Phospholipase iPLA 2  Averts Ferroptosis by Eliminating Death Signal, 15HpETE-PE: Relevance to Parkinson’s Disease

I. Bahar, H. Bayır, I. Shrivastava, 2021 .

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

I. Bahar, H. Bayır, A. Bakan, 2015, Molecular Pharmacology.

Metal-Binding Residues are Distinguished by their Lower Mobilities and Efficient Signal Propagation Properties

I. Bahar, Anindita Dutta, 2010 .

Allosteric Modulator KM822 Attenuates Behavioral Actions of Amphetamine in Caenorhabditis elegans through Interactions with the Dopamine Transporter DAT-1

M. H. Cheng, R. Blakely, I. Bahar, 2021, Molecular Pharmacology.

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

I. Bahar, E. Ahrens, P. Morel, 2011, Journal of leukocyte biology.

Tenascin cytotactin epidermal growth factor‐like repeat binds epidermal growth factor receptor with low affinity

I. Bahar, C. Camacho, M. Cascio, 2007, Journal of cellular physiology.

Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets

Eric P. Xing, Fen Pei, Wei Wu, 2018, bioRxiv.

Discovery of (R)-N-Benzyl-2-(2,5-dioxopyrrolidin-1-yl)propanamide [(R)-AS-1], a Novel Orally Bioavailable EAAT2 Modulator with Drug-like Properties and Potent Antiseizure Activity In Vivo

M. H. Cheng, I. Bahar, P. Wlaź, 2022, Journal of medicinal chemistry.

Microsoft Word-43957320-file00.docx

I. Bahar, H. Bayır, A. Bakan, 2015 .

Radioresistance of Serpinb3a-/- Mice and Derived Hematopoietic and Marrow Stromal Cell Lines.

B. Liu, I. Bahar, Hong Wang, 2019, Radiation research.

Mechanical properties and transition temperatures of crosslinked-oriented gelatin

J. E. Mark, I. Bahar, A. Kloczkowski, 1997 .

Identification of core amino acids stabilizing rhodopsin.

Judith Klein-Seetharaman, Ivet Bahar, H Gobind Khorana, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Local Dynamics of Polymer Chains in Restrictive Environment

I. Bahar, B. Erman, 1992 .

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

I. Bahar, F. Sutterwala, R. Gottlieb, 2020, Proceedings of the National Academy of Sciences.

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

Simon C Watkins, J. Klein-Seetharaman, I. Bahar, 2013, Nature Cell Biology.

Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods

I. Bahar, Lee-Wei Yang, Anupam Banerjee, 2022, Current opinion in structural biology.

Syntaxin 1 Ser14 phosphorylation is required for nonvesicular dopamine release

M. H. Cheng, I. Bahar, A. Carter, 2023, Science advances.

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.

J M Carazo, C O S Sorzano, R Marabini, 2019, Acta crystallographica. Section F, Structural biology communications.

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

A. Gronenborn, I. Bahar, Lin Liu, 2012, Journal of the American Chemical Society.

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

I. Bahar, H. Bayır, A. Bakan, 2014, Free radical biology & medicine.

A Sequence Alignment-Independent Method for Protein Classification

Judith Klein-Seetharaman, Ivet Bahar, Panayiotis V. Benos, 2004, Applied bioinformatics.

Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins.

R. Jernigan, I. Bahar, 1994, Biophysical journal.

Pore dilatation increases the bicarbonate permeability of CFTR, ANO1 and glycine receptor anion channels

Min Goo Lee, M. H. Cheng, I. Bahar, 2016, Journal of Physiology.

Make tough plastic films from gelatin

J. E. Mark, I. Bahar, B. Erman, 1996 .

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

Ivet Bahar, Gengkon Lum, I. Bahar, 2015, Bioinform..

ProDy: Protein Dynamics Inferred from Theory and Experiments

Ivet Bahar, Ahmet Bakan, Lidio M. Meireles, 2011, Bioinform..

The center for causal discovery of biomedical knowledge from big data

Richard Scheines, Gregory F. Cooper, Clark Glymour, 2015, J. Am. Medical Informatics Assoc..

Effect of Molecular Structure on Local Chain Dynamics: Analytical Approaches and Computational Methods

I. Bahar, B. Erman, L. Monnerie, 1994 .

A closed form solution for the internal dynamics of polymer chains. I. Bonds with independent rotational potentials

J. E. Mark, I. Bahar, B. Erman, 1990 .

Dynamics of large proteins through hierarchical levels of coarse‐grained structures

Robert L. Jernigan, Ivet Bahar, Pemra Doruker, 2002, J. Comput. Chem..

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

Ivet Bahar, Eran Eyal, Akio Kitao, 2009, Bioinform..

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

M. H. Cheng, I. Bahar, J. V. Van Eyk, 2020, bioRxiv.

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

M. H. Cheng, I. Bahar, She Zhang, 2020, Proceedings of the National Academy of Sciences.

Modeling the deamidation of asparagine residues via succinimide intermediates

I. Bahar, T. Sen, V. Aviyente, 2001 .

Dynamic mechanical study of amorphous phases in poly(ethylene terephthalate) /nylon-6 blends

Ivet Bahar, Burak Erman, I. Bahar, 1995 .

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

Ivet Bahar, Michael Tsang, Ahmet Bakan, 2009, Nature chemical biology.

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

I. Bahar, H. Bayır, I. Shrivastava, 2021, International journal of molecular sciences.

Novel orientation techniques for the preparation of high-performance materials from semi-flexible polymers such as the cellulosics

J. E. Mark, I. Bahar, A. Kloczkowski, 1992 .

Isotropic-nematic phase transitions in polymer networks deformed in the dry and swollen states

J. E. Mark, I. Bahar, B. Erman, 1992 .

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

Ivet Bahar, I. Bahar, N. Sluis-Cremer, 2004, Current HIV research.

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

James Krieger, Ivet Bahar, Valerian E Kagan, 2019, J. Chem. Inf. Model..

DynOmics: dynamics of structural proteome and beyond

Ivet Bahar, Ji Young Lee, Lee-Wei Yang, 2017, Nucleic Acids Res..

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

Luca Ponzoni, Nga H Nguyen, Ivet Bahar, 2020, PLoS Comput. Biol..

Rhapsody: predicting the pathogenicity of human missense variants

Luca Ponzoni, Ivet Bahar, Zoltán N Oltvai, 2020, Bioinform..

Rhapsody: Pathogenicity prediction of human missense variants based on protein sequence, structure and dynamics

Luca Ponzoni, Ivet Bahar, Zoltán N. Oltvai, 2019, bioRxiv.

Intramolecular Contributions to Stretched-Exponential Relaxation Behavior in Polymers

I. Bahar, B. Erman, G. Fytas, 1994 .

Quantitative assessment of cell fate decision between autophagy and apoptosis

Z. Oltvai, I. Bahar, H. Bayır, 2017, bioRxiv.

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

Kelsey P. Pendleton, G. Mills, L. Garraway, 2014, Proceedings of the National Academy of Sciences.

Solvent effect on translational diffusivity and orientational mobility of polymers in solution: A molecular dynamics study

I. Bahar, P. Doruker, B. Badur, 1993 .

Theoretical and experimental study of dissolution of inhomogeneities formed during spinodal decomposition in polymer mixtures

I. Bahar, B. Erman, A. Akcasu, 1992 .

Local Orientational Motions in Flexible Polymeric Chains

I. Bahar, B. Erman, L. Monnerie, 1990 .

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

I. Bahar, M. Hung, M. Gur, 2015, Nature Communications.

Development of small-molecule PUMA inhibitors for mitigating radiation-induced cell death.

Ivet Bahar, Ahmet Bakan, Michael Epperly, 2011, Current topics in medicinal chemistry.

Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.

Pemra Doruker, Ivet Bahar, David Perahia, 2020, Current opinion in structural biology.

Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology.

Daniel E. Lefever, Ivet Bahar, D Lansing Taylor, 2019, Handbook of experimental pharmacology.

Mapping Transcriptomic Vector Fields of Single Cells

J. Weissman, Xiaojie Qiu, Li Wang, 2022, Cell.

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

Ivet Bahar, Carl Kingsford, Natalie Sauerwald, 2016, bioRxiv.

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

P. S. Thiagarajan, Ivet Bahar, Bing Liu, 2016, Science Signaling.

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

I. Bahar, Lee-Wei Yang, R. Wood, 2004, The EMBO journal.

A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection

M. H. Cheng, D. L. Taylor, I. Bahar, 2021, Molecular systems biology.

Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets

E. Xing, I. Bahar, Haohan Wang, 2018, BMC Bioinformatics.

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

Ivet Bahar, Timothy R Billiar, Yoram Vodovotz, 2004, Current molecular medicine.

A novel strategy to block mitotic progression for targeted therapy

Hongchun Li, I. Bahar, Xinghua Lu, 2019, EBioMedicine.

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

Ivet Bahar, Luca Ponzoni, I. Bahar, 2018, Proceedings of the National Academy of Sciences.

A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine

Ivet Bahar, D Lansing Taylor, Mark E Schurdak, 2016, Journal of biomolecular screening.

Conformational statistics of poly(dimethylsiloxane). 1. Probability distribution of rotational isomers from molecular dynamics simulations

I. Bahar, I. Zúñiga, W. Mattice, 1991 .

Structure and dynamic regulation of Src-family kinases

I. Bahar, S. Banu Ozkan, T. Smithgall, 2008, Cellular and Molecular Life Sciences.

Allostery in Its Many Disguises: From Theory to Applications.

Ruth Nussinov, Ivet Bahar, Dima Kozakov, 2019, Structure.

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

Illés J. Farkas, Chakra Chennubhotla, Ivet Bahar, 2006, BMC Bioinformatics.

Discovery and Characterization of Novel Small Molecule Inhibitors of Human Cdc25B Dual Specificity Phosphatase

Ivet Bahar, Peter Wipf, Dror Tobi, 2004, Molecular Pharmacology.

Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia

M. H. Cheng, I. Bahar, J. Meiler, 2021, bioRxiv.

Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations

C. Chennubhotla, I. Bahar, 2007, PLoS Comput. Biol..

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations

C. Chennubhotla, I. Bahar, 2007, PLoS Comput. Biol..

EIF3H Orchestrates Hippo Pathway–Mediated Oncogenesis via Catalytic Control of YAP Stability

I. Bahar, Zhihua Liu, K. Guan, 2020, Cancer Research.

Precise druggability of the PTH type 1 receptor

Hongchun Li, I. Bahar, P. Doruker, 2021, Nature Chemical Biology.

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

I. Bahar, S. Gellman, J. Y. Lee, 2021, Science Signaling.

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

Ivet Bahar, Wenzhi Mao, Anindita Dutta, 2015, Bioinform..

On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm

Ivet Bahar, Enrique Marcos, Ramon Crehuet, 2010, PLoS Comput. Biol..

Evol and ProDy for bridging protein sequence evolution and structural dynamics

Ying Liu, Chakra Chennubhotla, Ivet Bahar, 2014, Bioinform..

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python

Ivet Bahar, Pemra Doruker, Hongchun Li, 2021, Bioinform..

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

M. H. Cheng, I. Bahar, James M. Krieger, 2021, Structure.

COVID-19–associated multisystem inflammatory syndrome in children (MIS-C): A novel disease that mimics toxic shock syndrome—the superantigen hypothesis

M. H. Cheng, I. Bahar, M. Noval Rivas, 2020, Journal of Allergy and Clinical Immunology.

A network of phosphatidylinositol (4,5)-bisphosphate (PIP2) binding sites on the dopamine transporter regulates amphetamine behavior in Drosophila Melanogaster

M. H. Cheng, I. Bahar, Heinrich J.G. Matthies, 2019, Molecular Psychiatry.

Optimal design of protein docking potentials: Efficiency and limitations

Ivet Bahar, Dror Tobi, I. Bahar, 2005, Proteins.

Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models

Ivet Bahar, Andrej Sali, Timothy R. Lezon, 2009, PLoS Comput. Biol..

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

Ivet Bahar, I. Bahar, E. Zomot, 2011, The Journal of Biological Chemistry.

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

I. Bahar, Anne-Ruxandra Carvunis, She Zhang, 2021, bioRxiv.

Structure‐based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X‐ray diffraction and NMR relaxation data

I. Bahar, T. Haliloglu, I Bahar, 1999, Proteins.

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

Ivet Bahar, I. Bahar, E. Zomot, 2013, The Journal of Biological Chemistry.

Time-resolved Mechanism of Extracellular Gate Opening and Substrate Binding in a Glutamate Transporter*S⃞

Ivet Bahar, Susan G. Amara, I. Bahar, 2008, Journal of Biological Chemistry.

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

M. H. Cheng, I. Bahar, B. Kaynak, 2022, iScience.

Potent Neutralization of Omicron and other SARS-CoV-2 Variants of Concern by Biparatopic Human VH Domains

M. H. Cheng, S. Subramaniam, I. Bahar, 2022, bioRxiv.

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

Ivet Bahar, A. Gronenborn, I. Bahar, 2012, Proteins.

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

Ivet Bahar, Angela M Gronenborn, A. Gronenborn, 2009, Proteins.

Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode‐coupling 15N‐NMR relaxation data

Ivet Bahar, E. Meirovitch, I. Bahar, 2004, Proteins.

E. coli Adenylate Kinase Dynamics: Comparison of Elastic Network Model Modes with Mode-Coupling

E. Meirovitch, I. Bahar, N. Temiz, 2004 .

Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity

Callen T. Wallace, Simon C Watkins, M. H. Cheng, 2021, The Journal of biological chemistry.

Regulation of CFTR Bicarbonate Channel Activity by WNK1: Implications for Pancreatitis and CFTR-Related Disorders

Min Goo Lee, Jihoon G. Yoon, M. H. Cheng, 2019, Cellular and molecular gastroenterology and hepatology.

Syntaxin1 Ser14 Phosphorylation is Required for Non-Vesicular Dopamine Release

I. Bahar, A. Galli, D. Zanella, 2022, bioRxiv.

New insight into the significance of KLF4 PARylation in genome stability, carcinogenesis, and therapy

I. Bahar, I. Shrivastava, Zhihua Liu, 2020, EMBO molecular medicine.

Structural dynamics of nucleosome core particle: Comparison with nucleosomes containing histone variants

Ilya Ioshikhes, Ivet Bahar, Amutha Ramaswamy, 2004, Proteins.

Dynamics of conformational transitions to isomeric states favoring intramolecular excimer formation in aromatic polyesters with methylene or oxyethylene spacers

I. Bahar, W. Mattice, 1989 .

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

Ivet Bahar, Michael Widom, I. Bahar, 2009, Biophysical journal.

Recognition of native structure from complete enumeration of low‐resolution models with constraints

Ivet Bahar, I. Bahar, Banu Özkan, 1998, Proteins.

Short‐range conformational energies, secondary structure propensities, and recognition of correct sequence‐structure matches

R L Jernigan, R. Jernigan, I. Bahar, 1997, Proteins.

Adaptability of protein structures to enable functional interactions and evolutionary implications.

Ivet Bahar, Turkan Haliloglu, I. Bahar, 2015, Current opinion in structural biology.

Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions.

R L Jernigan, R. Jernigan, I. Bahar, 1994, Biophysical journal.

Functional Characterization of the Dopaminergic Psychostimulant Sydnocarb as an Allosteric Modulator of the Human Dopamine Transporter

M. H. Cheng, I. Bahar, O. V. Mortensen, 2021, Biomedicines.

Large collective motions regulate the functional properties of glutamate transporter trimers

Ivet Bahar, Susan G. Amara, I. Bahar, 2011, Proceedings of the National Academy of Sciences.

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

Ying Liu, Ivet Bahar, Lila M. Gierasch, 2010, PLoS Comput. Biol..

Kinematics of polymer chains with freely rotating bonds in a restrictive environment. 1. Theory

I. Bahar, B. Erman, L. Monnerie, 1992 .

Stochastic Treatment of Conformational Transitions of Polymer Chains in the Sub-Rouse Regime

I. Bahar, B. Erman, L. Monnerie, 1991 .

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

Ivet Bahar, Enrique Marcos, Ramon Crehuet, 2011, PLoS Comput. Biol..

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

Ivet Bahar, Timothy R. Lezon, I. Bahar, 2010, PLoS Comput. Biol..

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Ivet Bahar, Sunhwan Jo, Benoît Roux, 2014, PLoS Comput. Biol..

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

Ying Liu, Ivet Bahar, Lila M. Gierasch, 2014, PLoS Comput. Biol..

Anisotropic network model: systematic evaluation and a new web interface

Ivet Bahar, Eran Eyal, Lee-Wei Yang, 2006, Bioinform..

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

Ivet Bahar, Zeynep Kurkcuoglu, Ahmet Bakan, 2012, PLoS Comput. Biol..

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

Ivet Bahar, Lee-Wei Yang, Hongchun Li, 2015, Nucleic Acids Res..

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

I. Bahar, O. Kepp, G. Kroemer, 2020, Cancer discovery.

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

Ivet Bahar, Ahmet Bakan, I. Bahar, 2012, Journal of Chemical Theory and Computation.

Phospholipase iPLA2β Averts Ferroptosis By Eliminating A Redox Lipid Death Signal

I. Bahar, H. Bayır, I. Shrivastava, 2020, Nature Chemical Biology.

Inactivation of RIP3 kinase sensitizes to 15LOX/PEBP1-mediated ferroptotic death

A. A. Kapralov, Simon C Watkins, J. Bertin, 2022, Redox biology.

The Gaussian Network Model: Theory and Applications

Chakra Chennubhotla, Ivet Bahar, Lee-Wei Yang, 2005 .

Relating structure to function through the dominant slow modes of motion of DNA topoisomerase II

Robert L. Jernigan, Ivet Bahar, Melik C. Demirel, 1999 .

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms.

R L Jernigan, R. Jernigan, I. Bahar, 1998, Journal of molecular biology.

Llamanade: an open-source computational pipeline for robust nanobody humanization

I. Bahar, Yi Shi, Yufei Xiang, 2021, bioRxiv.

Llamanade: an open-source computational pipeline for robust nanobody humanization

I. Bahar, Yi Shi, Yufei Xiang, 2021, bioRxiv.

Multisystem Inflammatory Syndrome in Children in the United States.

I. Bahar, M. Arditi, 2020, The New England journal of medicine.

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

Zheng Yang, Ivet Bahar, Peter Májek, 2009, PLoS Comput. Biol..

Allosteric interactions in the parathyroid hormone GPCR–arrestin complex formation

I. Bahar, P. Doruker, James M. Krieger, 2020, Nature Chemical Biology.

Stochastics of rotational isomeric transitions in polymer chains

I. Bahar, 1989 .

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models

Chakra Chennubhotla, Ivet Bahar, Eran Eyal, 2007, ISMB/ECCB.

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

M. H. Cheng, I. Bahar, A. Newman, 2017, Scientific Reports.

CONFORMATIONAL CHARACTERISTICS OF POLY(ETHYL METHACRYLATE). DIPOLE MOMENT MEASUREMENTS AND CALCULATIONS

I. Bahar, B. Baysal, A. Kuntman, 1990 .

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

Zheng Yang, Ivet Bahar, Alberto Perez, 2012, Journal of chemical theory and computation.

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

I. Bahar, Lee-Wei Yang, A. Russell, 2005, Acta biomaterialia.

Maturation dynamics of bacteriophage HK97 capsid.

Ivet Bahar, I. Bahar, A. Rader, 2005, Structure.

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

Hassan A. Karimi, Ivet Bahar, Xiong Liu, 2005, Bioinform..

QuartataWeb: Integrated Chemical–Protein-Pathway Mapping for Polypharmacology and Chemogenomics

D Lansing Taylor, Fen Pei, Ivet Bahar, 2020, Bioinform..

BalestraWeb: efficient online evaluation of drug–target interactions

Ivet Bahar, Zoltán N. Oltvai, D. Lansing Taylor, 2014, Bioinform..

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

Chang Liu, Ivet Bahar, Zoltán N. Oltvai, 2013, J. Chem. Inf. Model..

Characterization of interactions and metal ion binding sites in proteins

Robert L. Jernigan, Ivet Bahar, R. Jernigan, 1994 .

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

Ivet Bahar, Lee-Wei Yang, Chakra Chennubhotla, 2005, Physical biology.

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

I. Bahar, I. Shrivastava, Jason Dechancie, 2011, Molecular bioSystems.

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

Ivet Bahar, Dror Tobi, I. Bahar, 2007, BMC Bioinformatics.

Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A.

I. Bahar, L. Itzhaki, P. Doruker, 2023, Structure.

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods

I. Bahar, D. Pérahia, P. Doruker, 2022, Frontiers in Molecular Biosciences.

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution

I. Bahar, P. Doruker, B. Kaynak, 2021, bioRxiv.

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

Ivet Bahar, I. Bahar, E. Eyal, 2008, Biophysical journal.

Molecular dynamics analysis of transitions between rotational isomers in polymethylene

I. Bahar, I. Zúñiga, W. Mattice, 1991 .

Energy landscape of LeuT from molecular simulations.

Ivet Bahar, Mert Gur, Mary Hongying Cheng, 2015, The Journal of chemical physics.

An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research

Ivet Bahar, Hagai Meirovitch, G Bard Ermentrout, 2006, Biotechnology progress.

Protein Actions: Principles and Modeling

K. Dill, R. Jernigan, I. Bahar, 2017 .

Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT.

Ivet Bahar, Mary Hongying Cheng, M. H. Cheng, 2013, Biophysical journal.

ISMB 2010 Organization

Roger L. Chang, S. Batzoglou, L. Cowen, 2010, Bioinformatics.

An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations

M. H. Cheng, I. Bahar, She Zhang, 2020, bioRxiv.

Disulfide bridge formation prevents CaMKII/Calmodulin interaction in Parkinson’s disease

I. Bahar, J. C. Ayoob, I. General, 2020, bioRxiv.

Relating molecular flexibility to function: a case study of tubulin.

Ozlem Keskin, Robert L Jernigan, Ivet Bahar, 2002, Biophysical journal.

Formation of protein adducts with Hydroperoxy-PE electrophilic cleavage products during ferroptosis

I. Bahar, H. Bayır, I. Shrivastava, 2023, Redox biology.

Anti-Ferroptosis Drug Enhances Total-Body Irradiation Mitigation by Drugs that Block Apoptosis and Necroptosis

I. Bahar, H. Bayır, Hong Wang, 2020, Radiation Research.

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

I. Bahar, J. Carazo, James M. Krieger, 2021, IUCrJ.

Structural basis of CMKLR1 signaling induced by chemerin9

M. H. Cheng, I. Bahar, Xuan Zhang, 2023, bioRxiv.

Bile Acids Gate Dopamine Transporter Mediated Currents

M. H. Cheng, I. Bahar, A. Carter, 2021, bioRxiv.

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

J. Madura, I. Bahar, Lee-Wei Yang, 2005, Acta biomaterialia.

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

I. Bahar, D. Bhatt, 2012, The Journal of chemical physics.

Role of water on unfolding kinetics of helical peptides studied by molecular dynamics simulations.

I. Bahar, P. Doruker, 1997, Biophysical journal.

Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter

I. Bahar, I. Shrivastava, S. Amara, 2009, Proceedings of the National Academy of Sciences.

Segmental orientation in model networks of poly(dimethylsiloxane): Fourier-transform infrared dichroism measurements and theoretical interpretation

I. Bahar, B. Erman, L. Bokobza, 1992 .

Networks with Semi-Flexible Chains

J. E. Mark, I. Bahar, B. Erman, 1992 .

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

I. Bahar, I. Shrivastava, Anindita Dutta, 2012, Structure.

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

Ivet Bahar, I. Bahar, 2010, The Journal of general physiology.

Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations

Ivet Bahar, Ji Young Lee, Hongchun Li, 2019, Protein science : a publication of the Protein Society.

Continuous heterogeneity analysis of CryoEM images through Zernike polynomials and spherical harmonics

Roy R. Lederman, I. Bahar, J. Carazo, 2021, Microscopy and Microanalysis.

Transition states and the meaning of Φ-values in protein folding kinetics

Ivet Bahar, Ken A. Dill, S. Banu Ozkan, 2001, Nature Structural Biology.

Reply to ‘Comment on elastic network models and proteins’

Chakra Chennubhotla, Ivet Bahar, Burak Erman, 2007 .

Interpretation of segmental orientation in deformed networks in terms of constrained junction model of rubber elasticity

I. Bahar, B. Erman, L. Bokobza, 1993 .

Role of Structural Heterogeneities on Segmental Orientation in Deformed Chains: Application to Alternating Copolymers

I. Bahar, B. Erman, T. Haliloglu, 1994 .

RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access.

R. Jernigan, I. Bahar, B. Lustig, 1998, Nucleic acids research.

Osmotic Compressibility and Mechanical Moduli of Swollen Polymeric Networks

I. Bahar, B. Erman, 1987 .

Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.

I. Bahar, Yan Zhang, She Zhang, 2021, The Journal of chemical physics.

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

Ivet Bahar, Joshua A. Benson, I. Bahar, 2014, Human molecular genetics.

Molecular dynamics analysis of coupling between librational motions and isomeric jumps in chain molecules

A. Atilgan, I. Bahar, B. Erman, 1996 .

Dynamic rotational isomeric state approach for segmental motions of cis -polyisoprene in the bulk state

I. Bahar, F. Kremer, B. Erman, 1993 .

A dynamic rotational isomeric state approach for extension of the time scale of the local dynamics observed in fully atomistic molecular dynamics simulations: Application to polybutadiene

I. Bahar, B. Erman, T. Haliloglu, 1996 .

Segmental motions of cis-polyisoprene in the bulk state : interpretation of dielectric relaxation data

I. Bahar, F. Kremer, B. Erman, 1992 .

Investigation of local motions in polymers by the dynamic rotational isomeric state model

I. Bahar, B. Erman, 1987 .

Local dynamics and glass transition

I. Bahar, B. Erman, 1998 .

Orientational and conformational correlations in deformed polymer chains with fixed end-to-end separation: A Brownian dynamics simulation study

I. Bahar, B. Erman, T. Haliloglu, 1992 .

Computing the transition state populations in simple protein models.

S Banu Ozkan, Ivet Bahar, Ken A Dill, 2003, Biopolymers.

Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization

Ivet Bahar, Fen Pei, Qingya Shi, 2021, J. Chem. Inf. Model..

Local solvent effects on configurational characteristics of polymer chains: poly(p-chlorostyrene) in benzene

I. Bahar, B. Erman, B. Baysal, 1986 .

Anisotropy of static and dynamic orientational correlations in N‐alkanes

I. Bahar, B. Erman, 1988 .

Local dynamics of freely rotating polymer chains in dense systems

I. Bahar, B. Erman, 1993 .

The origin and extent of coarse‐grained regularities in protein internal packing

Andrzej Kloczkowski, Robert L Jernigan, Ivet Bahar, 2003, Proteins.

Response of a single grafted polyethylene chain to simple shear flow: A Brownian dynamics simulation study

I. Bahar, B. Erman, T. Haliloglu, 1996 .

Relative contributions of coupled rotations and small-amplitude torsions to conformational relaxation in polymers

I. Bahar, B. Erman, T. Haliloglu, 1996 .

Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments

Ivet Bahar, Ahmet Bakan, I. Bahar, 2011, Pacific Symposium on Biocomputing.

Dynamics and allosteric potential of the AMPA receptor Nterminal domain

I. Bahar, I. Shrivastava, Anindita Dutta, 2011 .

The relationship between N‐gram patterns and protein secondary structure

Ivet Bahar, I. Bahar, Xiong Liu, 2007, Proteins.

Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics

Chakra Chennubhotla, Ivet Bahar, C. Chennubhotla, 2006, RECOMB.

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

I. Bahar, Lee-Wei Yang, R. Wood, 2004, The EMBO journal.

Quantitative assessment of cell fate decision between autophagy and apoptosis

Z. Oltvai, I. Bahar, H. Bayır, 2017, Scientific Reports.

[Epidermal growth factor receptor].

I. Bahar, C. Camacho, M. Cascio, 1994, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

Toward a Molecular Understanding of the Interaction of Dual Specificity Phosphatases with Substrates: Insights from Structure-Based Modeling and High Throughput Screening

Ivet Bahar, Ahmet Bakan, Peter Wipf, 2008, Current medicinal chemistry.

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

Z. Oltvai, I. Bahar, Chang Liu, 2013, J. Chem. Inf. Model..

COVID-19–associated multisystem inflammatory syndrome in children (MIS-C): A novel disease that mimics toxic shock syndrome—the superantigen hypothesis

M. H. Cheng, I. Bahar, M. Noval Rivas, 2020, The Journal of Allergy and Clinical Immunology.

Application of the dynamic rotational isomeric states model to poly(ethylene oxide) and comparison with nuclear magnetic relaxation data

I. Bahar, B. Erman, L. Monnerie, 1989 .

Comparison of Dynamic Rotational Isomeric State Results with Previous Expressions for Local Chain Motion

I. Bahar, B. Erman, L. Monnerie, 1989 .

Coarse‐grained simulations of conformational dynamics of proteins: Application to apomyoglobin

I. Bahar, T. Haliloglu, 1998, Proteins.

A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine

I. Bahar, M. Schurdak, Andrew M. Stern, 2016, Journal of biomolecular screening.

Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis.

Simon C Watkins, J. Klein-Seetharaman, B. Liu, 2017, Nature chemical biology.

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

I. Bahar, S. Iwai, C. Masutani, 2004, The EMBO journal.

Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories

Ivet Bahar, Burak Erman, Pemra Doruker, 2002 .

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

K. Schulten, E. Tajkhorshid, I. Bahar, 2008, Biophysical journal.

Experimental Studies of Elastomeric and Optical Properties, and Strain-Induced Liquid-Crystalline Phase Transitions, in Deformed (Hydroxypropyl)cellulose Networks in the Swollen State

J. E. Mark, I. Bahar, B. Erman, 1995 .

Oriented Gelatin—A New Source for High-Performance Materials

J. E. Mark, I. Bahar, B. Erman, 1996 .

Perspectives on: Molecular dynamics and computational methods: On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

I. Bahar, 2010 .

Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices

Ivet Bahar, Shmuel Pietrokovski, Eran Eyal, 2007, Bioinform..

Conformational Search: Proteins

R. Jernigan, I. Bahar, 2002 .

DYNAMICS OF PROTEINS AND BIOMOLECULAR COMPLEXES: INFERRING FUNCTIONAL MOTIONS FROM STRUCTURE

Ivet Bahar, I. Bahar, 1999 .

The Gaussian Network Model

C. Chennubhotla, I. Bahar, A. Rader, 2005 .

Adaptability and specificity: how do proteins balance opposing needs to achieve function?

Ivet Bahar, Hongchun Li, Bentley Wingert, 2020, Current opinion in structural biology.

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations

Chakra Chennubhotla, Ivet Bahar, C. Chennubhotla, 2007, PLoS Comput. Biol..

Molecular Modeling for Drug Discovery

Robert L. Jernigan, Ken A. Dill, Ivet Bahar, 2017 .

Molecular Mechanisms of PTH/PTHrP class B GPCR Signaling and Pharmacological Implications.

I. Bahar, J. Vilardaga, A. White, 2022, Endocrine reviews.

Dynamics and allosteric potential of the AMPA receptor N‐terminal domain

I. Bahar, I. Shrivastava, I. Greger, 2011, The EMBO journal.

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

M. H. Cheng, I. Bahar, She Zhang, 2015, Biophysical journal.