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1

Cover Picture: ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function / JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia (Isr. J. Chem. 3-4/2013)

Celniker, Gershon, Nimrod, Guy, Ashkenazy, Haim, Glaser, Fabian, Martz, Eric, Mayrose, Itay, Pupko, Tal, Ben-Tal, Nir, Hanson, Robert M., Prilusky, Jaime, Renjian, Zhou, Nakane, Takanori, Sussman, Joe

Journal:

Israel Journal of Chemistry

Year:

2013

Language:

english

File:

PDF, 747 KB

english, 2013

2

BcXYG1, a Secreted Xyloglucanase from Botrytis cinerea induces Cell Death and Triggers Plant Defense

Zhu, Wenjun, Ronen, Mordechi, Gur, Yonatan, Minz-Dub, Anna, Masrati, Gal, Ben-Tal, Nir, Sharon, Itai, Savidor, Alon, Eizner, Elad, Valerius, Oliver, Braus, Gerhard, Bowler, Kyle, Bar-Peled, Maor, Shar

Journal:

PLANT PHYSIOLOGY

Year:

2017

Language:

english

File:

PDF, 2.43 MB

english, 2017

3

Residue frequencies and pairing preferences at protein–protein interfaces

Fabian Glaser, David M. Steinberg, Ilya A. Vakser, Nir Ben-Tal

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 1.09 MB

english, 2001

4

The Effect of Electrostatic Shielding on H Tunneling in R67 Dihydrofolate Reductase

Atsushi Yahashiri, Guy Nimrod, Nir Ben-Tal, Elizabeth E. Howell, Amnon Kohen

Journal:

Year:

2009

Language:

english

File:

PDF, 460 KB

english, 2009

5

In silico identification of functional protein interfaces

Rachel E. Bell, Nir Ben-Tal

Journal:

Comparative and Functional Genomics

Year:

2003

Language:

english

File:

PDF, 182 KB

english, 2003

6

Free Energy Determinants of Peptide Association with Lipid Bilayers.

Amit Kessel, Nir Ben-Tal

Journal:

Year:

2002

File:

PDF, 24 KB

2002

7

Hormone concentrations in tobacco roots change during arbuscular mycorrhizal colonization with Glomus intraradices

Orna Shaul-Keinan, Vijay Gadkar, Idit Ginzberg, José M. Grünzweig, Ilan Chet, Yigal Elad, Smadar Wininger, Edi Belausov, Yuval Eshed, Nir Atzmon, Yossi Ben-Tal, Yoram Kapulnik

Journal:

New Phytologist

Year:

2002

Language:

english

File:

PDF, 342 KB

english, 2002

8

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

Sharon Ebner, Nathan Sharon, Nir Ben-Tal

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 526 KB

english, 2003

9

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

Fabian Glaser, Yossi Rosenberg, Amit Kessel, Tal Pupko, Nir Ben-Tal

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 262 KB

english, 2005

10

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

Amit Kessel, D.Peter Tieleman, Nir Ben-Tal

Journal:

European Biophysics Journal

Year:

2004

Language:

english

File:

PDF, 1.07 MB

english, 2004

11

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

Rambold, Angelika S, Müller, Veronika, Ron, Uri, Ben-Tal, Nir, Winklhofer, Konstanze F, Tatzelt, Jörg

Journal:

The EMBO Journal

Year:

2008

Language:

english

File:

PDF, 1.57 MB

english, 2008

12

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

Delmaghani, Sedigheh, del Castillo, Francisco J, Michel, Vincent, Leibovici, Michel, Aghaie, Asadollah, Ron, Uri, Van Laer, Lut, Ben-Tal, Nir, Van Camp, Guy, Weil, Dominique

Journal:

Nature Genetics

Year:

2006

Language:

english

File:

PDF, 638 KB

english, 2006

13

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

Meytal Landau, Nir Ben-Tal

Journal:

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer

Year:

2008

Language:

english

File:

PDF, 1.66 MB

english, 2008

14

Progress in structure prediction of α-helical membrane proteins

Sarel J Fleishman, Nir Ben-Tal

Journal:

Current Opinion in Structural Biology

Year:

2006

Language:

english

File:

PDF, 321 KB

english, 2006

15

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

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

Journal:

Year:

2004

Language:

english

File:

PDF, 496 KB

english, 2004

16

Detection of Functionally Important Regions in “Hypothetical Proteins” of Known Structure

Guy Nimrod, Maya Schushan, David M. Steinberg, Nir Ben-Tal

Journal:

Year:

2008

Language:

english

File:

PDF, 750 KB

english, 2008

17

Structural Determinants of Transmembrane Helical Proteins

Susan E. Harrington, Nir Ben-Tal

Journal:

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

18

Transmembrane protein structures without X-rays

Sarel J. Fleishman, Vinzenz M. Unger, Nir Ben-Tal

Journal:

Trends in Biochemical Sciences

Year:

2006

Language:

english

File:

PDF, 451 KB

english, 2006

19

Has the code for protein translocation been broken?

Dalit Shental-Bechor, Sarel J. Fleishman, Nir Ben-Tal

Journal:

Trends in Biochemical Sciences

Year:

2006

Language:

english

File:

PDF, 333 KB

english, 2006

20

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

Diana Murray, Nir Ben-Tal, Barry Honig, Stuart McLaughlin

Journal:

Year:

1997

Language:

english

File:

PDF, 203 KB

english, 1997

21

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

Kalid, Ori, Ben-Tal, Nir

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 361 KB

english, 2009

22

KPROT: A knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction

Yitzhak Pilpel, Nir Ben-Tal, Doron Lancet

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 391 KB

english, 1999

23

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

Aharon Armon, Dan Graur, Nir Ben-Tal

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 1014 KB

english, 2001

24

An Evolutionarily Conserved Network of Amino Acids Mediates Gating in Voltage-dependent Potassium Channels

Sarel J Fleishman, Ofer Yifrach, Nir Ben-Tal

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 347 KB

english, 2004

25

Quasi-symmetry in the Cryo-EM Structure of EmrE Provides the Key to Modeling its Transmembrane Domain

Sarel J. Fleishman, Susan E. Harrington, Angela Enosh, Dan Halperin, Christopher G. Tate, Nir Ben-Tal

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.32 MB

english, 2006

26

Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features

Guy Nimrod, András Szilágyi, Christina Leslie, Nir Ben-Tal

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.12 MB

english, 2009

27

Model-Guided Mutagenesis Drives Functional Studies of Human NHA2, Implicated in Hypertension

Maya Schushan, Minghui Xiang, Pavel Bogomiakov, Etana Padan, Rajini Rao, Nir Ben-Tal

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 2.15 MB

english, 2010

28

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

Sarel J. Fleishman, Vinzenz M. Unger, Mark Yeager, Nir Ben-Tal

Journal:

Year:

2004

Language:

english

File:

PDF, 603 KB

english, 2004

29

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

Yana Gofman, Simona Shats, Bernard Attali, Turkan Haliloglu, Nir Ben-Tal

Journal:

Year:

2012

Language:

english

File:

PDF, 1.77 MB

english, 2012

30

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

Nir Ben-Tal, Doree Sitkoff, Sharron Bransburg-Zabary, Esther Nachliel, Menachem Gutman

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2000

Language:

english

File:

PDF, 3.39 MB

english, 2000

31

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

Dalit Shental-Bechor, Tsafi Danieli, Yoav I Henis, Nir Ben-Tal

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2002

Language:

english

File:

PDF, 405 KB

english, 2002

32

Type I chaperonins: not all are created equal

Galit Levy-Rimler, Rachel E Bell, Nir Ben-Tal, Abdussalam Azem

Journal:

Year:

2002

Language:

english

File:

PDF, 226 KB

english, 2002

33

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

Sarel J. Fleishman, Nir Ben-Tal

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 462 KB

english, 2002

34

On the regulatory role of dipeptidyl peptidase IV (CD26adenosine deaminase complexing protein) on adenosine deaminase activity

Itzhak Ben-Shooshan, Amit Kessel, Nir Ben-Tal, Rivka Cohen-Luria, Abraham H Parola

Journal:

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease

Year:

2002

Language:

english

File:

PDF, 162 KB

english, 2002

35

Calculations Suggest a Pathway for the Transverse Diffusion of a Hydrophobic Peptide Across a Lipid Bilayer

Kessel, Amit, Schulten, Klaus, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 266 KB

english, 2000

36

Association Entropy in Adsorption Processes

Ben-Tal, Nir, Honig, Barry, Bagdassarian, Carey K., Ben-Shaul, Avinoam

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 134 KB

english, 2000

37

Continuum Solvent Model Calculations of Alamethicin-Membrane Interactions: Thermodynamic Aspects

Kessel, Amit, Cafiso, David S., Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 575 KB

english, 2000

38

Interactions of Cholesterol with Lipid Bilayers: The Preferred Configuration and Fluctuations

Kessel, Amit, Ben-Tal, Nir, May, Sylvio

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 348 KB

english, 2001

39

Multi-Stage Regulation, a Key to Reliable Adaptive Biochemical Pathways

Almogy, Gal, Stone, Lewi, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 374 KB

english, 2001

40

Implicit Solvent Model Studies of the Interactions of the Influenza Hemagglutinin Fusion Peptide with Lipid Bilayers

Bechor, Dalit, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 1.54 MB

english, 2001

41

Continuum Solvent Model Studies of the Interactions of an Anticonvulsant Drug with a Lipid Bilayer

Kessel, Amit, Musafia, Boaz, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 379 KB

english, 2001

42

Interactions of Hydrophobic Peptides with Lipid Bilayers: Monte Carlo Simulations with M2δ

Kessel, Amit, Shental-Bechor, Dalit, Haliloglu, Turkan, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 321 KB

english, 2003

43

Interactions of the M2δ Segment of the Acetylcholine Receptor with Lipid Bilayers: A Continuum-Solvent Model Study

Kessel, Amit, Haliloglu, Turkan, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 341 KB

english, 2003

44

Increased Concentration of Polyvalent Phospholipids in the Adsorption Domain of a Charged Protein

Haleva, Emir, Ben-Tal, Nir, Diamant, Haim

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 209 KB

english, 2004

45

CTR Structure and Mechanism

De Feo, Christopher J., Aller, Stephen G., Barkan, Yariv, Shcushan, Maya, Siluvai, Gnana, Ben-Tal, Nir, Blackburn, Ninian J., Unger, Vinzenz M.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 95 KB

english, 2009

46

Non-Toxin Gating Modifiers Reveal the Promiscuous Nature of the Voltage Sensor of Kv7.2 and TRPV1 Channels

Kornilov, Polina, Peretz, Asher, Gofman, Yana, Ben-Tal, Nir, Attali, Bernard

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 36 KB

english, 2010

47

Independent and Cooperative Motions of the Kv1.2 Channel: Voltage Sensing and Gating

Yeheskel, Adva, Haliloglu, Turkan, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 1.01 MB

english, 2010

48

Electrostatic Properties of Membranes Containing Acidic Lipids and Adsorbed Basic Peptides: Theory and Experiment

Murray, Diana, Arbuzova, Anna, Hangyás-Mihályné, Gyöngyi, Gambhir, Alok, Ben-Tal, Nir, Honig, Barry, McLaughlin, Stuart

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 743 KB

english, 1999

49

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

Fleishman, Sarel J., Harrington, Susan, Friesner, Richard A., Honig, Barry, Ben-Tal, Nir

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 355 KB

english, 2004

50

Monte Carlo Studies of Folding, Dynamics, and Stability in α-Helices

Shental-Bechor, Dalit, Kirca, Safak, Ben-Tal, Nir, Haliloglu, Turkan

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 228 KB

english, 2005

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