2020

Klara Papouskova, Michaela Moravcova, Gal Masrati, Nir Ben-Tal, Hana Sychrova, Olga Zimmermannova.

C5 conserved region of hydrophilic C-terminal part of Saccharomyces cerevisiae Nha1 antiporter determines its requirement of Erv14 COPII cargo receptor for plasma-membrane targeting

Molecular Microbiology, DOI: 10.1111/mmi.14595, 2020.

Yaniv Lustig, Shlomit Keler, Rachel Kolodny, Nir Ben-Tal, Danit Atias-Varon, Ekaterina Shlush, Motti Gerlic, Ariel Munitz , Ram Doolman, Keren Asraf , Liran I. Shlush and Asaf Vivante 

Potential antigenic cross-reactivity between SARS-CoV-2 and Dengue viruses

Clinical Infectious Diseases, ciaa1207, https://doi.org/10.1093/cid/ciaa1207, 2020.

 

Burcin Acar, Jessica Rose,Burcu Aykac Fas, Nir Ben-Tal,Oded Lewinson, Turkan Haliloglu
Distinct Allosteric Networks Underlie Mechanistic Speciation of ABC Transporters
Structure https://doi.org/10.1016/j.str.2020.03.014, 2020.


 

Siwar Sabrialabed, Janet G. Yang, Elon Yariv, Nir Ben-Tal, and Oded Lewinson
Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY
J. Biol. Chem. https://www.jbc.org/cgi/doi/10.1074/jbc.RA119.012063, 2020.

 

Aya Narunsky, Amit Kessel, Ron Solan, Vikram Alva, Rachel Kolodny and Nir Ben-Tal
On the evolution of protein–adenine binding
PNAS https://doi.org/10.1073/pnas.1911349117, 2020.​

T. C. Marcink, E. Yariv, K. Rybkina, V. Más, F. T. Bovier, A. des Georges, A. L. Greninger, C. A. Alabi, M. Porotto, N. Ben-Tal, A. Moscona
Hijacking the Fusion Complex of Human Parainfluenza Virus as an Antiviral Strategy
mBio . DOI: 10.1128/mBio.03203-19, 2020.


Maria Littmann, Katharina Selig, Liel Cohen-Lavi, Yotam Frank, Peter Hönigschmid, Evans Kataka, Anja Mösch, Kun Qian, Avihai Ron, Sebastian Schmid, Adam Sorbie, Liran Szlak, Ayana Dagan-Wiener, Nir Ben-Tal, Masha Y. Niv, Daniel Razansky, Björn W. Schuller, Donna Ankerst, Tomer Hertz & Burkhard Rost
Validity of machine learning in biology and medicine increased through collaborations across fields of expertise
Nature Machine Intelligence,https://doi.org/10.1038/s42256-019-0139-8, 2020

 

Adi Ben Chorin, Gal Masrati, Amit Kessel, Aya Narunsky, Josef Sprinzak, Shlomtzion Lahav, Haim Ashkenazy, Nir Ben-Tal

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

Protein Science, 29:258–267, 2020.

2019

 

 

 

 

 

Aya Narunsky, Nir Ben-Tal, and Rachel Kolodny
Navigating Among Known Structures in Protein Space
Computational Methods in Protein Evolution, Methods in Molecular Biology, vol. 1851, https://doi.org/10.1007/978-1-4939-8736-8_12, 2019.


 

Michal Lisnyansky, Elon Yariv, Omri Segal, Milit Marom, Anat Loewenstein, Nir Ben-Tal, Moshe Giladi and Yoni Haitin
Metal coordination is crucial for GGPPS-bisphosphonates interactions: A crystallographic and computational analysis
Molecular Pharmacology, mol.119.117499; DOI: https://doi.org/10.1124/mol.119.117499, 2019.

 


Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal and Piero Fariselli
DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations
BMC Bioinformatics,20(Suppl 14):335,https://doi.org/10.1186/s12859-019-2923-1, 2019.

2018

Meghan Whitney Franklin, Sergey Nepomnyachyi, Ryan Feehan, Nir Ben-Tal, Rachel Kolodny and Joanna SG Slusky
Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins
eLife 7:e40308, DOI: https://doi.org/10.7554/eLife.40308, 2018.

 


Ludovica Montanucci, Pier Luigi Martelli, Nir Ben-Tal and Piero Fariselli
A natural upper bound to the accuracy of predicting protein stability changes upon mutations
Bioinformatics, 35(9),1513–1517 doi: 10.1093/bioinformatics/bty880 ,2018.


 

Gal Masrati, Manish Dwivedi, Abraham Rimon, Yael Gluck-Margolin, Amit Kessel, Haim Ashkenazy, Itay Mayrose, Etana Padan & Nir Ben-Tal
Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants
NATURE COMMUNICATIONS, DOI: 10.1038/s41467-018-06770-5,2018.

Meghan Whitney Franklin, Sergey Nepomnyachiy, Ryan Feehan, Nir Ben-Tal, Rachel Kolodny, and Joanna S.G. Slusky
Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold BtuCD
Structure,https://doi.org/10.1016/j.str.2018.06.007,2018.


 

Min Yang  , Nurit Livnat Levanon, Burçin Acar, Burcu Aykac Fas , Gal Masrati,Jessica Rose, Nir Ben-Tal , Turkan Haliloglu, Yongfang Zhao and Oded Lewinson
Single-molecule probing of the conformational homogeneity of the ABC transporter BtuCD
Nature Chemical Biology, volume 14, pages715–722,2018.

 

2017

Wenjun Zhu, Mordechi Ronen, Yonatan Gur, Anna Minz-Dub, Gal Masrati, Nir Ben-Tal, Itai Sharon, Alon Savidor, Elad Eizner, Oliver Valerius, Gerhard Braus, Kyle Bowler, Maor Bar-Peled, Amir Sharon
BcXYG1, a Secreted Xyloglucanase from Botrytis cinerea induces Cell Death and Triggers Plant Defense
Plant Physiology,https://doi.org/10.1104/pp.17.00375 2017.

 

Sergey Nepomnyachiya, Nir Ben-Tal, and Rachel Kolodny
Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths
www.pnas.org/cgi/doi/10.1073/pnas.1707642114, 2017.

 


Hila Sameach, Aya Narunsky, Salome Azoulay-Ginsburg, Lada Gevorkyan-Aiapetov, Yonathan Zehavi, Yoni Moskovitz, Tamar Juven-Gershon, Nir Ben-Tal and Sharon Ruthstein
Structural and Dynamics Characterization of the MerR Family Metalloregulator CueR in its Repression and Activation States
Structure 25, 988–996, 2017.

 

Amit Kessel, Rachel Kolodny and Nir Ben-Tal
Similarity between the Usher Plug and the Repeating Domain of an Ice-adhesin: Evolution via Surface Reshaping
Isr. J. Chem. 57, 1 – 5, 2017.

2016

Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko and Nir Ben-Tal
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
Nucleic Acids Research DOI:10.1093/nar/gkw408 ,2016.

 

Nurit Livnat-Levanon, Amy I. Gilson, Nir Ben-Tal & Oded Lewinson
The uncoupled ATPase activity of the ABC transporter BtuC2D2 leads to a hysteretic conformational change, conformational memory, and improved activity
Sci Rep. 6:21696 | DOI: 10.1038/srep21696 ,2016.

 

Matthew A. Oberhardt, Raphy Zarecki, Leah Reshef, Fangfang Xia, Miquel Duran-Frigola, Rachel Schreiber, Christopher S. Henry, Nir Ben-Tal, Daniel J. Dwyer, Uri Gophna, and Eytan Ruppin
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
PLOS Computational Biology DOI:10.1371/journal.pcbi.1004705 ,2016.

2015

Padan E, Danieli T, Keren Y, Alkoby D, Masrati G, Haliloglu T, Ben-Tal N, Rimon A
NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability
Proc Natl Acad Sci U S A. 112(41):E5575-82. doi: 10.1073/pnas.1510964112. Epub, 2015.

 

Seren Soner, Pemra Ozbek, Jose Ignacio Garzon, Nir Ben-Tal, Turkan Haliloglu
DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex’s Dynamics
PLoS Comput Biol.11(10):e1004461. doi: 10.1371/journal.pcbi.1004461. eCollection, 2015.

 

Aya Narunsky, Sergey Nepomnyachiy, Haim Ashkenazy, Rachel Kolodny, Nir Ben-Tal
ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure
Structure 23, 2162–2170,2015.

 

Yoon SW, Chen N, Ducatez MF, McBride R, Barman S, Fabrizio TP, Webster RG, Haliloglu T, Paulson JC, Russell CJ, Hertz T, Ben-Tal N, Webby RJ
Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus
Sci Rep. 5:12828. doi: 10.1038/srep12828,2015.

 

Vigonsky E, Fish I, Livnat-Levanon N, Ovcharenko E, Ben-Tal N, Lewinson O
Metal binding spectrum and model structure of the Bacillus anthracis virulence determinant MntA
Metallomics, Advance Article DOI: 10.1039/C5MT00100E, 2015.

 

Sergey Nepomnyachiy, Nir Ben-Tal,Rachel Kolodny
CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers
Structure 23(5):941-8. doi: 10.1016/j.str.2015.02.013. Epub, 2015.

 

Aya Narunsky, Haim Ashkenazy, Rachel Kolodny, Nir Ben-Tal
Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations
BMC Bioinformatics 16(Suppl 3):A3, 2015.

2014

Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N
Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel
PLoS Comput Biol 10(12):e1003976. doi: 10.1371/journal.pcbi.1003976 eCollection ,2014.

 

Han Remaut and Nir Ben-Tal
Lifting the lid on pilus assembly
eLife 2014;3:e04997. DOI: 10.7554/eLife.04997, 2014.

 

Nir Ben-Tal and Rachel Kolodny
Representation of the Protein Universe using Classifications, Maps, and Networks
Isr. J. Chem., 54: 1286–1292. doi: 10.1002/ijch.201400001,2014.

 

Sergey Nepomnyachiy, Nir Ben-Tal and Rachel Kolodny
Global view of the protein universe
PNAS,vol. 111,no. 321 1691–11696,2014.


 

Kenneth A. Stapleford, Lark L. Coffey,Sreyrath Lay, Antonio V. Borderı´a, Veasna Duong, Ofer Isakov, Kathryn Rozen-Gagnon, Camilo Arias-Goeta, Herve´ Blanc, Ste´phanie Beaucourt, Turkan Haliloglu, Christine Schmitt,Isabelle Bonne, Nir Ben-Tal, Noam Shomron, Anna-Bella Failloux,Philippe Buchy, and Marco Vignuzzi
Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential

Cell Host & Microbe 15,Elsevier Inc, 706–716, 2014.

Guy Yachdav, Edda Kloppmann, Laszlo Kajan, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, Lothar Richter, Haim Ashkenazy, Marco Punta, Avner Schlessinger, Yana Bromberg, Reinhard Schneider, Gerrit Vriend, Chris Sander, Nir Ben-Tal and Burkhard Rost
PredictProtein—an open resource for online prediction of protein structural and functional features
Nucleic Acids Research, doi:10.1093/nar/gku366,2014.

 

Chen Shochat, Noa Tal, Vitalina Gryshkova, Yehudit Birger, Obul R. Bandapalli, Giovanni Cazzaniga, Nava Gershman, Andreas E. Kulozik, Andrea Biondi, Marc R. Mansour, Jean-Claude Twizere, Martina U. Muckenthaler, Nir Ben-Tal, Stefan N. Constantinescu, Dani Bercovich, and Shai Izraeli
Novel activating mutations lacking cysteine in type I cytokine receptors in acute lymphoblastic leukemia
Blood first edition paper doi:10.1182/blood-2014-10-529685, prepublished online,2014.

 

Aya Narunsky, Nir Ben-Tal
ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure
BMC Bioinformatics, 15(Suppl 3):A5, 2014.

 

Leitman J, Shenkman M, Gofman Y, Shtern NO, Ben-Tal N, Hendershot LM, Lederkremer GZ
Herp coordinates compartmentalization and recruitment of HRD1 and misfolded proteins for ERAD
Mol Biol Cell 25(7):1050-60. doi: 10.1091/mbc.E13-06-0350. Epub ,2014.

2013

Kondapalli KC, Hack A, Schushan M, Landau M, Ben-Tal N, Rao R,
Functional evaluation of autism-associated mutations in NHE9
Nat Commun. 4:2510. doi: 10.1038/ncomms3510 PMID: 24065030,2013.

 

Nir Ben-Tal,
Editorial for the ISMB/ECCB 2013 Proceedings
ISMB/ECCB doi:10.1093/bioinformatics/btt282, 2013.

 

Gershon Celniker, Guy Nimrod, Haim Ashkenazy, Fabian Glaser, Eric Martz, Itay Mayrose, Tal Pupko, and Nir Ben-Tal,
ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function
Isr.J.Chem. doi: 10.1002/ijch.201200096, 2013.

 

Daniela Dirndorfer, Ralf P. Seidel, Guy Nimrod, Margit Miesbauer, Nir Ben-Tal, Martin Engelhard, Richard Zimmermann, Konstanze F. Winklhofer and Jörg Tatzelt
The alpha-helical structure of prodomains promotes translocation of intrinsically disordered neuropeptide hormones into the endoplasmic reticulum
J Biol Chem. doi: 10.1074/jbc.M112.430264, 2013.

2012

Shai Saroussi, Maya Schushan, Nir Ben-Tal, Wolfgang Junge, Nathan Nelson
Structure and Flexibility of the C-Ring in the Electromotor of Rotary FoF1-ATPase of Pea Chloroplasts
PLoS ONE doi:10.1371/journal.pone.0043045,2012.

 

Yana Gofman, Simona Shats, Bernard Attali, Turkan Haliloglu, and Nir Ben-Tal
How Does KCNE1 Regulate the Kv7.1 Potassium Channel? Model-Structure, Mutations, and Dynamics of the Kv7.1-KCNE1 Complex
Structure DOI: 10.1016/j.str.2012.05.016,2012.

 

James Dalton, Ori Kalid, Maya Schushan, Nir Ben-Tal, and Jordi Villà-Freixa
New model of CFTR proposes active channel-like conformation
J. Chem. Inf. DOI: 10.1021/ci2005884, 2012.


 

Yana Gofman,Turkan Haliloglu, and Nir Ben-Tal
The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation
J. Chem. Theory Comput, DOI: 10.1021/ct300128x,2012.

 

Yana Gofman, Turkan Haliloglu and Nir Ben-Tal
Monte Carlo simulations of peptide–membrane interactions with the MCPep web server
Nucleic Acids Research 40(W1):W358-W363, 2012.

 

Maya Schushan, Ashima Bhattacharjee, Nir Ben-Tal and Svetlana Lutsenko
A structural model of the copper ATPase ATP7B to facilitate analysis of Wilson disease-causing mutations and studies of the transport mechanism
Metallomics 669-678. DOI: 10.1039/C2MT20025B, 2012.

 

Maya Schushan, Abraham Rimon, Turkan Haliloglu, Lucy R. Forrest, Etana Padan and Nir Ben-Tal
A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes
JBC 287(22):18249-61,2012.

2011

Elisa Merklinger, Yana Gofman, Alexej Kedrov, A. J.M. Driessen, Nir Ben-Tal, Yechiel Shai and Doron Rapaport
Membrane-integration of a mitochondrial signal-anchored protein does not require additional proteinaceous factors
Biochem. J. 442, 381–389, DOI: 10.1042,2012.

 

Gilad Wainreb, Lior Wolf, Haim Ashkenazy, Yves Dehouck and Nir Ben-Tal
Protein stability: A single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
Bioinformatics vol. 27 no. 23 3286-3292,2011.

 

Sarel J Fleishman, Timothy A Whitehead, Eva-Maria Strauch, Jacob E Corn, Sanbo Qin, Huan-Xiang Zhou, Julie C Mitchell, Omar N A Demerdash, Mayuko Takeda-Shitaka, Genki Terashi, Iain H Moal, Xiaofan Li, Paul A Bates, Martin Zacharias, Hahnbeom Park, Jun-Su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jérôme Azé, Seren Soner, Sefik Kerem Ovalı, Pemra Ozbek, Nir Ben Tal, Türkan Haliloglu, Howook Hwang, Thom Vreven, Brian G Pierce, Zhiping Weng, Laura Pérez-Cano, Carles Pons, Juan Fernández-Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Patapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M Standley, Haruki Nakamura, Kengo Kinoshita, Camden M Driggers, Robert G Hall, Jessica L Morgan, Victor L Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L Kastritis, Alexandre M J J Bonvin, Weiyi Zhang, Carlos J Camacho, Krishna P Kilambi, Aroop Sircar, Jeffrey J Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodríguez, Daisuke Kihara, P Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J Wodak, Joel Janin, David Baker
Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
J Mol Biol. ;414(2):289-302. DOI: 10.1016/j.jmb.2011.09.031, 2011.

 

D. Meroz, SW. Yoon, M.F. Ducatez, T.P. Fabrizio, R.J. Webby, T. Hertz, and N. Ben-Tal
Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1)virus in the human population.
PNAS 108(33):13522-13527; DOI: 10.1073/pnas.1014854108; PMID: 21808039, 2011.

 

M. Schushan, M. Landau, E. Padan and N. Ben-Tal
Two Conflicting NHE1 Model Structures: Compatibility with Experimental Data and Implications for the Transport Mechanism.
JBC 286(21):le9; DOI: 10.1074/jbc.L110.159202, 2011.

 

Williams AL, Bielopolski N, Meroz D, Lam AD, Passmore DR, Ben-Tal N, Ernst SA, Ashery U, Stuenkel EL.
Structural and functional analysis of tomosyn identifies domains important in exocytotic regulation.
JBC 286(16):14542-53. Epub ,2011.

2010

S.E. Harrington and N. Ben-Tal
Natural constraints, folding, motion, and structural stability in transmembrane helical proteins
In "Structural Bioinformatics of Membrane Proteins" (Dmitrij Frishman, Editor), Springer.

 

M. Schushan and N. Ben-Tal
Modeling and validation of transmembrane protein structures.
Chapter 17 (pages 369-401) - "Introduction to Protein Structure Prediction: Methods and Algorithms" (Huzefa Rangwala and George Karypis, Eds.), John Wiley and Sons. New Jersey. ISBN: 978-0-470-47059-6, 2010.

 

A. Peretz, L. Pell, Y. Gofman, Y. Haitin, L. Shamgar, E. Patrich, P. Kornilov, O. Gourgy-Hacohen, N. Ben-Tal, B. Attali 
Targeting the voltage sensor of Kv7.2 voltage-gated K+ channels with a new gating-modifier
Proc Natl Acad Sci U S A.107(35):15637-42; DOI: 10.1073/pnas.0911294107; PMID: 20713704, 2010.

 

J. Dorosz, Y. Gofman, S. Kolusheva, D. Otzen, N. Ben-Tal, N.C. Nielsen, R. Jelinek
Membrane interactions of novicidin, a novel antimicrobial peptide: phosphatidylglycerol promotes bilayer insertion
J Phys Chem B. 114(34):11053-60; DOI: 10.1021/jp1052248; PMID: 20690652, 2010.

 

G. Wainreb, H. Ashkenazy, Y. Bromberg, A. Starovolsky-Shitrit, T. Haliloglu, E. Ruppin, K. B. Avraham, B. Rost, N. Ben-Tal
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.
Nucleic Acids Research 38 (Web Server issue):W523-8; DOI: 10.1093/nar/gkq528; PMID: 20542913, 2010.

 

H. Ashkenazy, E. Erez, E. Martz, T. Pupko, N. Ben-Tal
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Nucleic Acids Research 38 (Web Server issue):W529-33; DOI: 10.1093/nar/gkq399; PMID: 20478830, 2010.

 

M. Schushan, Y. Barkan, T. Haliloglu, N. Ben-Tal
Cα-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications
Proc Natl Acad Sci U S A 107(24):10908-13. DOI: 10.1073/pnas.0914717107; PMID: 20534491, 2010.

 

A. Yeheskel, T. Haliloglu, N. Ben-Tal
Independent and Cooperative Motions of the Kv1.2 Channel: Voltage Sensing and Gating
Biophysical Journal 98(10):2179–2188; PMID: 20483326, 2010.

 

M. Kalman and N. Ben-Tal
Quality Assessment of Protein Model-Structures Using Evolutionary Conservation
Bioinformatics 26(10):1299-1307; DOI: 10.1093/bioinformatics/btq114; PMID: 20385730,2010.

 

Y. Gofman, S. Linser, A. Rzeszutek, D. Shental-Bechor, SS Funari, N Ben-Tal, R. Willumeit
Interaction of an antimicrobial peptide with membranes: experiments and simulations with NKCS.
J Phys Chem B. 114(12):4230-7; PMID: 20201501, 2010.

 

M. Schushan, M. Xiang, P. Bogomiakov, E. Padan, R. Rao, N. Ben-Tal
Model-Guided Mutagenesis Drives Functional Studies of Human NHA2, Implicated in Hypertension
J Mol Biol. 396: 1181–1196; DOI: 10.1016/j.jmb.2009.12.055; PMID: 20053353, 2010.

 

G. Nimrod, M. Schushan, A. Szilágyi, C. Leslie, N. Ben-Tal.
iDBPs: a web server for the identification of DNA binding proteins
Bioinformatics.26(5):692-3. PMID: 20089514, 2010.

2009

M. Gordon-Grossman, Y. Gofman, H. Zimmermann, V. Frydman, Y. Shai, N. Ben-Tal, D. Goldfarb
A Combined Pulse EPR and Monte Carlo Simulation Study Provides Molecular Insight on Peptide-Membrane Interactions
J Phys Chem B. 113(38):12687-95; PMID: 19725508, 2009.

 

A. Yahashiri, G. Nimrod, N. Ben-Tal, EE. Howell, A Kohen
The Effect of Electrostatic Shielding on H Tunneling in R67 Dihydrofolate Reductase
Chembiochem.10(16):2620-2623; PMID: 19774544, 2009.

 

S.E. Harrington, N. Ben-Tal .
Structural Determinants of Transmembrane Helical Proteins
Structure 17(8):1092-1103; PMID: 19679087, 2009.

 

O. Kalid and N. Ben-Tal .
Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design
J. Chem. Inf. Model. 49(4):865-76; PMID: 19323449, 2009.

 

G. Nimrod, A. Szilágyi, C. Leslie and N. Ben-Tal .
Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features
Journal of Molecular Biology 387(4):1040-1053; PMID: 19233205, 2009.

 

O. Goldenberg, E. Erez, G. Nimrod and N. Ben-Tal .
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
Nucl. Acids Res. (Database issue), 37:D323-D327; PMID: 18971256, 2009.

2008

R. Hertzano, E. Shalit, A.K. Rzadzinska, A.A. Dror, L. Song, U. Ron, J.T. Tan, A.S. Shitrit, H. Fuchs, T. Hasson, N. Ben-Tal, H.L. Sweeney,M.H. de Angelis, K.P. Steel, K.B. Avraham
A Myo6 mutation destroys coordination between the myosin heads, revealing new functions of myosin VI in the stereocilia of mammalian inner ear hair cells
PLoS Genet. 4(10); DOI:10.1371/journal.pgen.1000207; PMID: 18833301, 2008.

 

G. Nimrod, M. Schushan, D.M. Steinberg, N. Ben-Tal .
Detection of Functionally Important Regions in "Hypothetical Proteins" of Known Structure
Structure, 16:1755–1763, 2008.

 

D. Bercovich, I. Ganmore, L.M Scott, G. Wainreb, Y. Birger, A. Elimelech, C. Shochat, G. Cazzaniga, A. Biondi, G. Basso, G. Cario, M. Schrappe, M. Stanulla, S. Strehl, O. A Haas, G. Mann, V. Binder, A. Borkhardt, H. Kempski, J. Trka, B. Bielorei, S. Avigad, B. Stark, O. Smith, N. Dastugue, J.P. Bourquin, N. Ben-Tal, A.R. Green, S. Izraeli .
Mutations of JAK2 in acute lymphoblastic leukaemias associated with Down’s syndrome
Lancet, 372:1484–92, 2008.

 

A. S. Rambold, V. Mu¨ller, U. Ron, N. Ben-Tal, K. F. Winklhofer and Jo¨rg Tatzelt
Stress-protective signalling of prion protein is corrupted by scrapie prions
EMBO 27:1974–1984, doi:10.1038/emboj.2008.122, 2008.

 

A. Enosh, B. Raveh, O. Furman-Schueler, D. Halperin, N. Ben-Tal
Generation, Comparison, and Merging of Pathways between Protein Conformations: Gating in K-Channels
Biophys. J. 95:3850–3860, 2008.

 

T. Haliloglu, N. Ben-Tal
Cooperative Transition between Open and Closed Conformations in Potassium Channels
PLoS Computational Biology Vol. 4, Issue 8 e1000164, 2008.

 

M. Landau, N. Ben-Tal
Dynamic equilibrium between multiple active and inactive conformations explains regulation and oncogenic mutations in ErbB receptors
BBA 1785:12–31, 2008.

2007

A. Fuchs, A. J. Martin-Galiano, M. Kalman, S. Fleishman, N. Ben-Tal, D. Frishman
Co-evolving residues in membrane proteins
Bioinformatics 23:3312–3319, 2007.

 

M. Landau, K. Herz, E. Padan, and N. Ben-Tal
Model Structure of the Na+/H+ Exchanger 1 (NHE1). FUNCTIONAL AND CLINICAL IMPLICATIONS
Journal of Biological Chemistry, V.282 No.52, 37854–37863, 2007.

 

D. Shental-Bechor, T. Haliloglu and N. Ben-Tal
Interactions of Cationic-Hydrophobic Peptides with Lipid Bilayers: A Monte Carlo Simulation Method
Biophys. J. 93:1858-1871, 2007.

 

A. Enosh, S. J. Fleishman, N. Ben-Tal and D. Halperin
Prediction and simulation of motion in pairs of transmembrane α-helices
Bioinformatics 23:e212–e218, 2007.

2006

S. J. Fleishman, S. E. Harrington, A. Enosh, D. Halperin, C. G. Tate and N. Ben-Tal
Quasi-symmetry in the Cryo-EM Structure of EmrE Provides the Key to Modeling its Transmembrane Domain
Journal of Molecular Biology 364:54-67,2006.

 

S.J. Fleishman, A.D. Sabag, E. Ophir, K.B. Avraham and N. Ben-Tal
The structural context of disease-causing mutations in gap junctions
Journal of Biological Chemistry, V.281 No.39, 28958-28963,2006.

 

S. Delmaghani, F. J del Castillo, V. Michel, M. Leibovici, A. Aghaie, U. Ron, L. Van Laer, N. Ben-Tal, G. Van Camp, D. Weil, F. Langa, M. Lathrop, P. Avan and C. Petit
Mutations in the gene encoding pejvakin, a newly identified protein of the afferent auditory pathway, cause DFNB59 auditory neuropathy
Nat. Genetics. 38:770-778,2006.

 

S. J. Fleishman and N. Ben-Tal
Progress in structure prediction of α-helical membrane proteins
Current Opinion in Structural Biology 16:496-504,2006.

 

Jacob Romano, Guy Nimrod, Nir Ben-Tal, Yona Shadkchan, Koti Baruch, Haim Sharon and Nir Osherov
Disruption of the Aspergillus fumigatus ECM33 homologue results in rapid conidial germination, antifungal resistance and hypervirulence
Microbiology 152:1919-1928,2006.

 

D. Shental-Bechor, S. J. Fleishman, and N. Ben-Tal
Has the code for protein translocation been broken?
TRENDS in Biochemical Sciences 31:192-196,2006.


 

S. J. Fleishman, V. M. Unger, and N. Ben-Tal
Transmembrane protein structures without X-rays
TRENDS in Biochemical Sciences. 31:106-113,2006.

2005

G. Nimrod, F. Glaser, D. Steinberg, N. Ben-Tal, and T. Pupko
In silico identification of functional regions in proteins
Bioinformatics. 21 Suppl. 1:i328-i337, 2005.

 

R. Gutman, C. Berezin, R. Wollman, Y. Rosenberg, N. Ben-Tal
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns
Nucl. Acids Res. 33:W255-W261, 2005.

 

M. Landau, I. Mayrose, Y. Rosenberg, F. Glaser, E. Martz, T. Pupko and N. Ben-Tal
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
Nucl. Acids Res. 33:W299-W302, 2005.

 

D. Shental-Bechor, S. Kirca, N. Ben-Tal and T. Haliloglu
Monte Carlo studies of folding, dynamics, and stability in α-helices
Biophys. J. 88:2391-2402, 2005.

 

F. Glaser, Y. Rosenberg, A. Kessel, T. Pupko, N. Ben-Tal
The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
PROTEINS: Structure, Function, and Bioinformatics 58:610-617,2005.

2004

M. Landau, S. J. Fleishman, and N. Ben-Tal
A Putative Mechanism for Downregulation of the Catalytic Activity of the EGF Receptor via Direct Contact between Its Kinase and C-Terminal Domains
Structure 12: 2265-2275,2004.

 

S.J. Fleishman, S. Harrington, R.A. Friesner, B. Honig, and N. Ben-Tal
An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data
Biophys. J. 87: 3448-3459,2004.

 

S.J. Fleishman, V.M. Unger, M. Yeager and N. Ben-Tal
A C-alpha model for the transmembrane alpha helices of gap junction intercellular channels
Mol. Cell 15: 879-888, 2004.

 

D. Melamed, M. Mark-Danieli, M. Kenan-Eichler, O. Kraus, A. Castiel, N. Laham, T. Pupko, F. Glaser, N. Ben-Tal, and E. Bacharach
The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release
J. Virol. 78: 9675-9688, 2004.

 

Y. Artzy-Randrup, S.J. Fleishman, N. Ben-Tal and L. Stone
Technical Comment on "Network motifs: simple building blocks of complex networks" and "Superfamilies of evolved and designed networks&quot
Science 305: 1107, 2004.

 

Itay Mayrose, Dan Graur, Nir Ben-Tal and Tal Pupko
Comparison of Site - Specific Rate - Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior
Mol. Biol. Evol. 21: 1781-1791, 2004.

 

Idit Oren, Sarel J. Fleishman, Amit Kessel and Nir Ben-Tal
Free Diffusion of Steroid Hormones Across Biomembranes: A Simplex Search with Implicit Solvent Model Calculations
Biophys. J. 87: 768-779, 2004.

 

Angela Enosh, Sarel J. Fleishman, NirBen-Tal and Dan Halperin
Assigning transmembrane segments to helices in intermediate-resolution structures
Bioinformatics 20: i122-i129, 2004.

 

Sarel J. Fleishman, Ofer Yifrach and Nir Ben-Tal
An Evolutionarily Conserved Network of Amino Acids Mediates Gating in Voltage-dependent Potassium Channels
J. Mol. Biol. 340: 307-318, 2004.

 

C. Berezin, F. Glaser, J. Rosenberg, I. Paz, T. Pupko, P. Fariselli, R. Casadio and N. Ben-Tal
ConSeq: the identification of functionally and structurally important residues in protein sequences.
Bioinformatics 20: 1322-1324, 2004.

 

E. Haleva, N. Ben-Tal and H. Diamant
Increased concentration of polyvalent phospholipids in the adsorption domain of a charged protein
Biophys. J. 86: 2165-2178, 2004.

 

Amit Kessel, D. Peter Tieleman, Nir Ben-Tal
Implicit solvent model estimates of the stability of model structures of the alamethicin channel
Eur Biophys, 33: 16-28, 2004.

2003

Amit Kessel, Dalit Shental-Bechor, Turkan Haliloglu and Nir Ben-Tal
Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta
Bioiphys. J. 85: 3431-3444,2003.

 

Amit Kessel, Turkan Haliloglu and Nir Ben-Tal
Interactions of the M2delta segment of the acetylcholine receptor with lipid bilayers: a continuum-solvent model study
Bioiphys. J. 85: 3687-3695, 2003.

 

Rachel E. Bell and Nir Ben-Tal
In silico identification of functional protein interfaces.
Comparative and Functional Genomics, 4: 420-423, 2003.

 

Sharon Ebner, Nathan Sharon and Nir Ben-Tal
Evolutionary Analysis Reveals Collective Properties and Specificity in the C-Type Lectin and Lectin-Like Domain Superfamily
Proteins
 

Structure Function and Genetics 52: 44-55, 2003.
 

Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor, Eric Martz and Nir Ben-Tal
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.
Bioinformatics 19: no. 1, 163-164, 2003.

2002

Sarel J. Fleishman, Joseph Schlessinger and Nir Ben-Tal
A putative molecular-activation switch in the transmembrane domain of erbB2
PNAS 99: no. 25 15937-15940, 2002.

 

S.J. Fleishman and N. Ben-Tal
A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices
J. Mol. Biol. 321(2): 363-78, 2002.

 

Amit Kessel and Nir Ben-Tal
Free Energy Determinants of Peptide Association with Lipid Bilayers. Current Topics in Membranes: Peptide-Lipid Interactions
52: 205-253 (Sydney Simon and Thomas McIntosh, Eds.), Academic Press, San Diego, 2002.

 

Tal Pupko, Rachel E. Bell, Itay Mayrose, Fabian Glaser and Nir Ben-Tal
Rate4Site: An Algorithmic Tool for the Identification of Functional Regions in Proteins by Surface Mapping of Evolutionary Determinants within their Homologues Bioinformatics 18 Suppl 1:S71-7, 2002.

 

Dalit Shental-Bechor, Tsafi Danieli, Yoav I. Henis, Nir Ben-Tal
Long-range effects on the binding of the influenza HA to receptors are mediated by changes in the stability of a metastable HA conformation
Biochimica et Biophysica Acta, 1565: 81-90, 2002.

 

Sharron Bransburg-Zabary, Amit Kessel, Menachem Gutman and Nir Ben-Tal
Stability of an Ion Channel in Lipid Bilayers: Implicit Solvent Model Calculations with Gramicidin
Biochemistry, 41: 6946-6954, 2002.

 

Irit Gottfried, Marina Landau, Fabian Glaser, Wei-Li Di, Joseph Ophir, Barukh Mevorah, Nir Ben-Tal, David P. Kelsell and Karen B. Avraham&nbsp
A mutation in GJB3 is associated with recessive erythrokeratodermia variabilis (EKV) and leads to defective trafficking of the connexin 31 protein 
Hum. Mol. Genet. 11: 1311-1316&nbsp, 2002.

2001

Gal Almogy, Lewi Stone, and Nir Ben-Tal
Multi-Stage Regulation, a Key to Reliable Adaptive Biochemical Pathways 
Biophys. J. 81: 3016-3028&nbsp,2001.

 

Amit Kessel, Nir Ben-Tal and Sylvio May
Interactions of Cholesterol with Lipid Bilayers: The Preferred Configuration and Fluctuations
Biophys. J. 81: 643-658&nbsp, 2001.

 

Amit Kessel, Boaz Musafia and Nir Ben-Tal
Continuum Solvent Model Studies of the Interactions of an Anticonvulsant Drug with a Lipid Bilayer
Biophys. J. 80: 2535-2545&nbsp, 2001.

 

Fabian Glaser, David M. Steinberg, Ilya A. Vakser and Nir Ben-Tal
Residue frequencies and pairing preferences at protein-protein interfaces
PROTEINS: Structure, Function and Genetics, 43: 89-102&nbsp, 2001.

 

Aharon Armon, Dan Graur and Nir Ben-Tal
ConSurf: An Algorithmic Tool for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
J. Mol. Biol. 307: 447-463, 2001.

 

Dalit Bechor and Nir Ben-Tal
Implicit Solvent Model Studies of the Interactions of the Influenza Hemagglutinin Fusion Peptide with Lipid Bilayers
Biophys. J. 80: 643-655, 2001.

 

2000

Amit Kessel, Klaus Schulten and Nir Ben-Tal
Calculations Suggest a Pathway for the Transverse Diffusion of a Hydrophobic Peptide
Biophys. J. 79: 2322-2330, 2000.

 

Nir Ben-Tal, Barry Honig, Carey K. Bagdassarian and Avinoam Ben-Shaul
Association entropy in adsorption processes
Biophys. J. 79: 1180-1187&nbsp, 2000.

 

Amit Kessel, David S. Cafiso and Nir Ben-Tal
Continuum Solvent Model Calculations of Alamethicin-Membrane Interactions: Thermodynamic Aspects
Biophys. J. 78: 571-583&nbsp, 2000.

 

Nir Ben-Tal, Doree Sitkoff, Sharron Bransburg-Zabary, Esther Nachliel and Menachem Gutman
Theoretical Calculations of the Permeability of Monensin-Cation Complexes in Model Bio-membranes
Biochimica et Biophysica acta, 1466: 221-233&nbsp, 2000.

1999

Yitzhak Pilpel, Nir Ben Tal and Doron Lancet
kPROT: a knowledge-based scale for the Propensity of Residue Orientation in Transmembrane Segments: Application to membrane protein structure prediction
J. Mol. Biol, 294: 921-935, &nbsp, 1999.


 

Diana Murray, Anna Arbuzova, Gyongyi Hangyas-Mihalyne, Alok Gambhir, Nir Ben-Tal, Barry Honig and Stuart McLaughlin
Electrostatic Properties of Membranes Containing Acidic Lipids and Adsorbed Basic Peptides: Theory and Experiment
Biophys. J. 77: 3176-3188&nbsp, 1999.

1998

Diana Murray, Luz Hermida-Matsumoto, Carolyn A. Buser, James Tsang, Catherine T. Sigal, Nir Ben-Tal, Barry Honig, Marilyn D. Resh and Stuart McLaughlin&nbsp
Electrostatics and the Membrane Association of Src: Theory and Experiment
Biochemistry, 37: 2145-2159&nbsp, 1998.

The George S. Wise Faculty
of Life Sciences
Edmond J. Safra Center for Bioinformatics