Nir Ben-Tal

发表

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

Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny, 2015, Structure.

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

Itay Mayrose, Tal Pupko, Fabian Glaser, 2005, Nucleic Acids Res..

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

Seren Soner, Nir Ben-Tal, José Ignacio Garzón, 2015, PLoS Comput. Biol..

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

Nir Ben-Tal, Aya Narunsky, 2014, BMC Bioinformatics.

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

Itay Mayrose, Tal Pupko, Fabian Glaser, 2002, ISMB.

Quality assessment of protein model-structures using evolutionary conservation

Nir Ben-Tal, Matan Kalman, N. Ben-Tal, 2010, Bioinform..

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

Nir Ben-Tal, Ofir Goldenberg, Elana Erez, 2008, Nucleic Acids Res..

Modeling and Validation of Transmembrane Protein Structures

Nir Ben-Tal, Maya Schushan, N. Ben-Tal, 2010 .

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

Nir Ben-Tal, N. Ben-Tal, 2013, Bioinformatics.

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

Piero Fariselli, Tal Pupko, Rita Casadio, 2004, Bioinform..

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

Nir Ben-Tal, Turkan Haliloglu, Yana Gofman, 2012, Nucleic Acids Res..

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

Itay Mayrose, Tal Pupko, Shiran Abadi, 2016, Nucleic Acids Res..

In silico identification of functional regions in proteins

Tal Pupko, Fabian Glaser, Nir Ben-Tal, 2005, ISMB.

Navigating Among Known Structures in Protein Space.

Nir Ben-Tal, Aya Narunsky, Rachel Kolodny, 2018, Methods in molecular biology.

Supplementary text Final

Tomer Hertz, Nir Ben-Tal, Daphna Meroz, 2012 .

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

Nir Ben-Tal, Lior Wolf, Haim Ashkenazy, 2011, Bioinform..

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

Dan Halperin, Nir Ben-Tal, Angela Enosh, 2007, Bioinform..

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations

Piero Fariselli, Emidio Capriotti, Nir Ben-Tal, 2019, BMC Bioinformatics.

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

Christina S. Leslie, Nir Ben-Tal, Guy Nimrod, 2010, Bioinform..

PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You

Matthias Bethge, Gunnar Blohm, Kevin Bretonnel Cohen, 2017, PLoS Comput. Biol..

Co-evolving residues in membrane proteins

Dmitrij Frishman, Nir Ben-Tal, Matan Kalman, 2007, Bioinform..

Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design

Nir Ben-Tal, Ori Kalid, N. Ben-Tal, 2009, J. Chem. Inf. Model..

Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel

Debora S. Marks, Nir Ben-Tal, Turkan Haliloglu, 2014, PLoS Comput. Biol..

Comment on "Network Motifs: Simple Building Blocks of Complex Networks" and "Superfamilies of Evolved and Designed Networks"

Sarel J Fleishman, Lewi Stone, Nir Ben-Tal, 2004, Science.

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

Nir Ben-Tal, Yossi Rosenberg, Roy Wollman, 2005, Nucleic Acids Res..

New Model of Cystic Fibrosis Transmembrane Conductance Regulator Proposes Active Channel-like Conformation

Jordi Villà-Freixa, Nir Ben-Tal, Maya Schushan, 2012, J. Chem. Inf. Model..

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

Nir Ben-Tal, Haim Ashkenazy, Aya Narunsky, 2015, BMC Bioinformatics.

A natural upper bound to the accuracy of predicting protein stability changes upon mutations

Piero Fariselli, Pier Luigi Martelli, Nir Ben-Tal, 2018, Bioinform..

Assigning transmembrane segments to helices in intermediate-resolution structures

Nir Ben-Tal, Angela Enosh, Dan Halperin, 2004, ISMB/ECCB.

Editorial

Nir Ben-Tal, N. Ben-Tal, 2013, Bioinform..

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

Tal Pupko, Nir Ben-Tal, Haim Ashkenazy, 2010, Nucleic Acids Res..

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

Fangfang Xia, Eytan Ruppin, Daniel J. Dwyer, 2016, PLoS Comput. Biol..

Structural Genomics

Tal Pupko, Inbal Paz, Fabian Glaser, 2005 .

Cooperative Transition between Open and Closed Conformations in Potassium Channels

Nir Ben-Tal, Turkan Haliloglu, 2008, PLoS Comput. Biol..

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

Burkhard Rost, Eytan Ruppin, Nir Ben-Tal, 2010, Nucleic Acids Res..

Global view of the protein universe

Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny, 2014, Proceedings of the National Academy of Sciences.

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

Nir Ben-Tal, Yana Gofman, N. Ben-Tal, 2010, Proceedings of the National Academy of Sciences.

Membrane interactions of novicidin, a novel antimicrobial peptide: phosphatidylglycerol promotes bilayer insertion.

Raz Jelinek, Nir Ben-Tal, Yana Gofman, 2010, The journal of physical chemistry. B.

Stability of an ion channel in lipid bilayers: implicit solvent model calculations with gramicidin.

Nir Ben-Tal, Menachem Gutman, Amit Kessel, 2002, Biochemistry.

A putative mechanism for downregulation of the catalytic activity of the EGF receptor via direct contact between its kinase and C-terminal domains.

Sarel J Fleishman, Nir Ben-Tal, Meytal Landau, 2004, Structure.

Introduction to Proteins: Structure, Function, and Motion

Nir Ben-Tal, Amit Kessel, 2010 .

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

Nir Ben-Tal, Rachel Kolodny, R. Kolodny, 2014 .

A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices.

Sarel J Fleishman, Nir Ben-Tal, N. Ben-Tal, 2002, Journal of molecular biology.

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

Nir Ben-Tal, Meytal Landau, N. Ben-Tal, 2008, Biochimica et biophysica acta.

Has the code for protein translocation been broken?

Sarel J Fleishman, Nir Ben-Tal, N. Ben-Tal, 2006, Trends in biochemical sciences.

Transmembrane protein structures without X-rays.

Sarel J Fleishman, Nir Ben-Tal, Vinzenz M Unger, 2006, Trends in biochemical sciences.

A Calpha model for the transmembrane alpha helices of gap junction intercellular channels.

Sarel J Fleishman, Nir Ben-Tal, Mark Yeager, 2004, Molecular cell.

Structural determinants of transmembrane helical proteins.

Nir Ben-Tal, N. Ben-Tal, Susan E. Harrington, 2009, Structure.

Progress in structure prediction of alpha-helical membrane proteins.

Sarel J Fleishman, Nir Ben-Tal, N. Ben-Tal, 2006, Current opinion in structural biology.

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

Sarel J Fleishman, Nir Ben-Tal, Ofer Yifrach, 2004, Journal of molecular biology.

FUNCTIONAL EVALUATION OF AUTISM-ASSOCIATED MUTATIONS IN NHE9

Nir Ben-Tal, Meytal Landau, Maya Schushan, 2013, Nature Communications.

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

Nir Ben-Tal, Turkan Haliloglu, N. Ben-Tal, 2005, Biophysical journal.

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

Nir Ben-Tal, Yana Gofman, Daniella Goldfarb, 2009, The journal of physical chemistry. B.

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

Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny, 2015, Structure.

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

Itay Mayrose, Tal Pupko, Fabian Glaser, 2013 .

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

Eytan Ruppin, Nir Ben-Tal, Haim Ashkenazy, 2010, Nucleic Acids Research.

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

Nir Ben-Tal, Guy Nimrod, Maya Schushan, 2008, Structure.

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

Sarel J Fleishman, Nir Ben-Tal, Amit Kessel, 2004, Biophysical journal.

The Conserved Carboxy Terminus of the Capsid Domain of Human Immunodeficiency Virus Type 1 Gag Protein Is Important for Virion Assembly and Release

Eran Bacharach, Tal Pupko, Fabian Glaser, 2004, Journal of Virology.

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

Tomer Hertz, Nir Ben-Tal, Daphna Meroz, 2011, Proceedings of the National Academy of Sciences.

Free Energy Determinants of Peptide Association with Lipid Bilayers.

Nir Ben-Tal, Amit Kessel, 2002 .

Free energy determinants of peptide association with lipid bilayers

Nir Ben-Tal, Amit Kessel, N. Ben-Tal, 2002 .

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

Sarel J. Fleishman, Nir Ben-Tal, Ofer Yifrach, 2004 .

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

Sebastian Linser, Nir Ben-Tal, Yana Gofman, 2010, The journal of physical chemistry. B.

Model Structure of the Na+/H+ Exchanger 1 (NHE1)

Nir Ben-Tal, Meytal Landau, N. Ben-Tal, 2007, Journal of Biological Chemistry.

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

Dan Halperin, Sarel J Fleishman, Nir Ben-Tal, 2006, Journal of molecular biology.

Cα-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications

Nir Ben-Tal, Turkan Haliloglu, Maya Schushan, 2010, Proceedings of the National Academy of Sciences.

A Cα model for the transmembrane α helices of gap junction intercellular channels

Sarel J. Fleishman, Nir Ben-Tal, Mark Yeager, 2004 .

How does KCNE1 regulate the Kv7.1 potassium channel? Model-structure, mutations, and dynamics of the Kv7.1-KCNE1 complex.

Nir Ben-Tal, Turkan Haliloglu, Yana Gofman, 2012, Structure.

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

Nir Ben-Tal, Turkan Haliloglu, Oded Lewinson, 2018, Nature Chemical Biology.

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

Sarel J. Fleishman, Nir Ben-Tal, Joseph Schlessinger, 2002, Proceedings of the National Academy of Sciences of the United States of America.

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

Nir Ben-Tal, Emir Haleva, Haim Diamant, 2003, Biophysical journal.

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

Nir Ben-Tal, Yana Gofman, Doron Rapaport, 2012, The Biochemical journal.

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

Nir Ben-Tal, Turkan Haliloglu, Adva Yeheskel, 2010, Biophysical journal.

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

D. Peter Tieleman, Nir Ben-Tal, Amit Kessel, 2004, European Biophysics Journal.

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

Nir Ben-Tal, Turkan Haliloglu, Amit Kessel, 2003, Biophysical journal.

Statistical mechanics of a Coulomb gas with finite size particles: A lattice field theory approach

Nir Ben-Tal, Rob D. Coalson, N. Ben-Tal, 1995 .

An Automatic Method for Predicting Transmembrane Protein Structures Using Cryo-em and Evolutionary Data

Richard A Friesner, Sarel J Fleishman, Nir Ben-Tal, 2004 .

In Silico Identification of Functional Protein Interfaces

Nir Ben-Tal, Rachel E. Bell, N. Ben-Tal, 2003, Comparative and functional genomics.

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

Nir Ben-Tal, Turkan Haliloglu, N. Ben-Tal, 2007, Biophysical journal.