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List of works by Nir Ben-Tal

A Cα Model for the Transmembrane α Helices of Gap Junction Intercellular Channels

article

A Myo6 mutation destroys coordination between the myosin heads, revealing new functions of myosin VI in the stereocilia of mammalian inner ear hair cells

scientific article

A Novel Scoring Function for Predicting the Conformations of Tightly Packed Pairs of Transmembrane α-Helices

scientific article published on 01 August 2002

A Putative Mechanism for Downregulation of the Catalytic Activity of the EGF Receptor via Direct Contact between Its Kinase and C-Terminal Domains

scientific article published on 01 December 2004

A combined pulse EPR and Monte Carlo simulation study provides molecular insight on peptide-membrane interactions

scientific article published in September 2009

A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes

scientific article

A mutation in GJB3 is associated with recessive erythrokeratodermia variabilis (EKV) and leads to defective trafficking of the connexin 31 protein

scientific article (publication date: 15 May 2002)

A putative molecular-activation switch in the transmembrane domain of erbB2.

scientific article

A structural model of the copper ATPase ATP7B to facilitate analysis of Wilson disease-causing mutations and studies of the transport mechanism.

scientific article

An angular motion of a conserved four-helix bundle facilitates alternating access transport in the TtNapA and EcNhaA transporters

scientific article published on 30 November 2020

An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data

scientific article

An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels

scientific article published in July 2004

Assigning transmembrane segments to helices in intermediate-resolution structures

scientific article published on August 2004

Association entropy in adsorption processes.

scientific article published on September 2000

BcXYG1, a Secreted Xyloglucanase from Botrytis cinerea, Triggers Both Cell Death and Plant Immune Responses

scientific article published on 14 July 2017

Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results

scientific article

Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants

scientific article published in Nature Communications

C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications

scientific article

Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models

article

Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus

scientific article

Co-evolving residues in membrane proteins

scientific article published in December 2007

Comment on "Network motifs: simple building blocks of complex networks" and "Superfamilies of evolved and designed networks".

scientific article published in August 2004

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

scientific article published on 16 June 2004

ConSeq: the identification of functionally and structurally important residues in protein sequences

scientific article published on 10 February 2004

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

scientific article

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

scientific article (publication date: July 2010)

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

scientific article

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins

scientific article published on 22 November 2019

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

article by Gershon Celniker et al published April 2013 in Israel Journal of Chemistry

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

scientific article (publication date: 2003)

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

scientific article

ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure

Continuum solvent model studies of the interactions of an anticonvulsant drug with a lipid bilayer.

scientific article

Cooperative transition between open and closed conformations in potassium channels

scientific article

CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers

scientific article published on 9 April 2015

Detection of functionally important regions in "hypothetical proteins" of known structure

scientific article published in December 2008

Dimeric and high-resolution structures of Chlamydomonas Photosystem I from a temperature-sensitive Photosystem II mutant

scientific article published on 09 December 2021

Disruption of the Aspergillus fumigatus ECM33 homologue results in rapid conidial germination, antifungal resistance and hypervirulence

scientific article published in July 2006

DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics

scientific article published on 27 October 2015

Dynamic equilibrium between multiple active and inactive conformations explains regulation and oncogenic mutations in ErbB receptors

scientific article published on 22 August 2007

Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles

scientific article

Electrostatic interaction of myristoylated proteins with membranes: simple physics, complicated biology ⬇️

scientific article published on August 15, 1997

Electrostatic properties of membranes containing acidic lipids and adsorbed basic peptides: theory and experiment

scientific article

Electrostatics and the Membrane Association of Src: Theory and Experiment ⬇️

scientific article published on February 24, 1998

Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential

scientific article published on June 2014

Energetics of Colloids: Do Oppositely Charged Particles Necessarily Attract Each Other?

Evolutionary analysis reveals collective properties and specificity in the C-type lectin and lectin-like domain superfamily

scientific article (publication date: October 2003)

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

scientific article published on 29 November 2018

Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution

Free diffusion of steroid hormones across biomembranes: a simplex search with implicit solvent model calculations

scientific article

Free-energy determinants of alpha-helix insertion into lipid bilayers

scientific article

Functional evaluation of autism-associated mutations in NHE9.

scientific article published on January 2013

Generation, comparison, and merging of pathways between protein conformations: gating in K-channels

scientific article

Global view of the protein universe

scientific article

Harmonic generation in ionizing systems by the complex scaled adiabatic-switch method

article

Harmonic generation in ionizing systems by the time-dependent complex coordinate Floquet method

Has the code for protein translocation been broken?

scientific article

Helix-helix interactions in lipid bilayers

scientific article

Herp coordinates compartmentalization and recruitment of HRD1 and misfolded proteins for ERAD.

scientific article published on 29 January 2014

How Does KCNE1 Regulate the Kv7.1 Potassium Channel? Model-Structure, Mutations, and Dynamics of the Kv7.1-KCNE1 Complex

article

Identification of DNA-binding proteins using structural, electrostatic and evolutionary features

scientific article published on 20 February 2009

Implicit solvent model estimates of the stability of model structures of the alamethicin channel

scientific article published on 17 September 2003

In silico identification of functional protein interfaces

scientific article

In silico identification of functional regions in proteins

scientific article published in June 2005

Increased concentration of polyvalent phospholipids in the adsorption domain of a charged protein

scientific article published on April 2004

Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating

scientific article published on May 2010

Interaction of an antimicrobial peptide with membranes: experiments and simulations with NKCS.

scientific article published in April 2010

Interactions of cationic-hydrophobic peptides with lipid bilayers: a Monte Carlo simulation method

scientific article published on 11 May 2007

Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta

scientific article published in December 2003

Interactions of the M2delta segment of the acetylcholine receptor with lipid bilayers: a continuum-solvent model study

scientific article

Lifting the lid on pilus assembly

scientific article published on 28 October 2014

Long-range effects on the binding of the influenza HA to receptors are mediated by changes in the stability of a metastable HA conformation

scientific article published on 01 September 2002

Membrane Interactions of Novicidin, a Novel Antimicrobial Peptide: Phosphatidylglycerol Promotes Bilayer Insertion

Membrane integration of a mitochondrial signal-anchored protein does not require additional proteinaceous factors

article published in 2012

Metal binding spectrum and model structure of the Bacillus anthracis virulence determinant MntA

article

Model structure of the Na+/H+ exchanger 1 (NHE1): functional and clinical implications

scientific article published on 2 November 2007

Model-guided mutagenesis drives functional studies of human NHA2, implicated in hypertension

scientific article

Modeling and Validation of Transmembrane Protein Structures

Monte Carlo simulations of peptide-membrane interactions with the MCPep web server

scientific article published on 13 June 2012

Monte Carlo studies of folding, dynamics, and stability in alpha-helices

scientific article published on 14 January 2005

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

scientific article

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.

scientific article published on 23 November 2010

Multi-stage regulation, a key to reliable adaptive biochemical pathways

scientific article published on December 2001

Mutations in the gene encoding pejvakin, a newly identified protein of the afferent auditory pathway, cause DFNB59 auditory neuropathy

scientific journal article

New model of cystic fibrosis transmembrane conductance regulator proposes active channel-like conformation.

scientific article published on 12 July 2012

NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability

scientific article

Novel activating mutations lacking cysteine in type I cytokine receptors in acute lymphoblastic leukemia

scientific article published in May 2014

On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment

scientific article published on 09 December 2020

On the evolution of protein-adenine binding

scientific article published on 20 February 2020

On the regulatory role of dipeptidyl peptidase IV (=CD=adenosine deaminase complexing protein) on adenosine deaminase activity.

scientific article published in May 2002

PredictProtein--an open resource for online prediction of protein structural and functional features

scientific article

Prediction and simulation of motion in pairs of transmembrane alpha-helices

scientific article published in January 2007

Progress in structure prediction of alpha-helical membrane proteins.

scientific article

Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site

scientific article published on 13 October 2011

Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population

scientific article

Quality assessment of protein model-structures using evolutionary conservation

scientific article published on 12 April 2010

Quantum versus classical dynamics in a periodically driven anharmonic oscillator

article

Quasi-symmetry in the cryo-EM structure of EmrE provides the key to modeling its transmembrane domain

scientific article published on 30 August 2006

QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns

scientific article

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues

scientific article published in January 2002

Representation of the Protein Universe using Classifications, Maps, and Networks

Residue frequencies and pairing preferences at protein-protein interfaces

scientific article published in May 2001

Similarity between the Usher Plug and the Repeating Domain of an Ice-adhesin: Evolution via Surface Reshaping

Single-molecule probing of the conformational homogeneity of the ABC transporter BtuCD

scientific article published on 18 June 2018

Stability of an Ion Channel in Lipid Bilayers: Implicit Solvent Model Calculations with Gramicidin†

article

Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes

scientific article

Stress-protective signalling of prion protein is corrupted by scrapie prions

scientific article

Structural Determinants of Transmembrane Helical Proteins

Structural and Dynamics Characterization of the MerR Family Metalloregulator CueR in its Repression and Activation States

scientific article published on 26 May 2017

Structural and functional analysis of tomosyn identifies domains important in exocytotic regulation

scientific journal article

Structure and flexibility of the C-ring in the electromotor of rotary F(0)F(1)-ATPase of pea chloroplasts

scientific article (publication date: 2012)

Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel

scientific article (publication date: December 2014)

Study of MDM2 binding to p53-analogues: affinity, helicity, and applicability to drug design

scientific article

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli

scientific article published on 28 January 2016

Targeting the voltage sensor of Kv7.2 voltage-gated K+ channels with a new gating-modifier

scientific article

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

scientific article published on 29 October 2008

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

scientific article

The Structural Context of Disease-causing Mutations in Gap Junctions

scientific article published in Journal of Biological Chemistry

The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation

scientific article published on 6 June 2012

The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release

scientific article published on September 2004

The effect of electrostatic shielding on H tunneling in R67 dihydrofolate reductase

scientific article published on November 2009

The uncoupled ATPase activity of the ABC transporter BtuC2D2 leads to a hysteretic conformational change, conformational memory, and improved activity

scientific article published on 22 February 2016

The α-helical structure of prodomains promotes translocation of intrinsically disordered neuropeptide hormones into the endoplasmic reticulum

scientific article published on 26 March 2013

Theoretical calculations of the permeability of monensin-cation complexes in model bio-membranes

scientific article published in June 2000

Transmembrane protein structures without X-rays.

scientific article

Two conflicting NHE1 model structures: compatibility with experimental data and implications for the transport mechanism

scientific article published on May 2011

Two new areas were defined: "Metabolic Networks" and "RNA Bioinformatics

scientific article published in July 2013

Type I chaperonins: not all are created equal

scientific article

Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations

scientific article

Weak localization in a chaotic periodically driven anharmonic oscillator

scientific article published on 01 March 1993

iDBPs: a web server for the identification of DNA binding proteins

scientific article

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