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Guy Yanai, Gabriel Axel, Liam M. Longo, Nir Ben-Tal & Rachel Kolodny

Contrastive learning unites sequence and structure in a globalrepresentation of protein space

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PNAS 2026. https://doi.org/10.1073/pnas.2532702123

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Arne Elofsson & Nir Ben-Tal

What will be the future of computational biology for macromolecules in the era of AI?

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PLOS Computational Biology 2026. https://doi.org/10.1371/journal.pcbi.1014467

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​Daniel Maman-Shinar, Shachar Vanmak, David Bern, Nir Ben-Tal, Amit Rosemarin, Dotan Moskovich, Noi Haim, Ulrich Schweizer, Marietta Fabiano, Avivit Weisz, Aviva Katzav, Debora Kidron, Mario Beiner, Aula Asali, Yael Hants, Maya Gottfried & Osnat Ashur-Fabian

DIO3 associates with sorting nexins and endosomal trafficking networks in ovarian cancer

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Cellular Oncology 2026. https://doi. org/10.1007/s13402-026-01236-z

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Karolína Kacovska, Klara Papou  skov Λ‡ a, Gal Masrati, Paul Rosas-Santiago, Tereza Przeczkova, Veronika ZΛ‡ arska ,Nir Ben-Tal, Olga Zimmermannova

Trafficking of the human Na+/H+ antiporter NHA2 to the plasma membrane requires cornichon COPII cargo receptors

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Protein Science. 2026;35:e70492, https://doi.org/10.1002/pro.70492, 2026.

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2026

2025

Claudèle Lemay-St-Denis, Stella Cellier-Goetghebeur, Maxime St-Aubin, Keigo Ide, Janine N Copp, Soichiro Tsuda, Nir Ben-Tal, Rachel Kolodny, Joelle N Pelletier

From binding to catalysis: emergence of a rudimentary enzyme conferring intrinsic antibiotic resistance

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Molecular Biology and Evolution, msaf215, https://doi.org/10.1093/molbev/msaf215, 2025.

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Yishi Ezerzer , Moran Frenkel-Pinter, Rachel Kolodny and Nir Ben-Tal

A building blocks perspective on protein emergence and evolution

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Current Opinion in Structural Biology 2025, 91:102996, 2025.

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Ozge Duman, Anastasiya Kuznetsova, Nurit Livnat Levanon, Moti Grupper, Akarun Ayca Ersoy, Burcin Acar, Amit Kessel, Nir Ben-Tal, Oded Lewinson, Turkan Haliloglu

Computational and experimental mapping of the allosteric network of two manganese ABC transporters

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Protein Science. ;34:e70039. wileyonlinelibrary.com/journal/pro 1 of 16https://doi.org/10.1002/pro.70039, 2025.

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Gilad Mechtinger,  Gabriel Axel, Rachel Kolodny and Nir Ben-Tal

Interpretable prediction of zinc ion location in proteins with ZincSight

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Protein Science. 2025;34:e70350., https://doi.org/10.1002/pro.70350, 2025.

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2024

Yiğit Kutlu, Gabriel Axel, Rachel Kolodny3, Nir Ben-Tal, Turkan Haliloglu

Reused Protein Segments Linked to Functional Dynamics

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Molecular Biology and Evolution, Volume 41, Issue 9,  msae184, https://doi.org/10.1093/molbev/msae184, 2024.

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Roth, O., Yechezkel, S., Serero, O., Eliyahu, A., Vints, I., Tzeela, P., Carignano, A., Janacek, D. P., Peters, V., Kessel, A., Dwivedi, V., Carmeli-Weissberg, M., Shaya, F., Faigenboim-Doron, A., Ung, K. L., Pedersen, B. P., Riov, J., Klavins, E., Dawid, C., Hammes, U. Z., & 4 others

Slow release of a synthetic auxin induces formation of adventitious roots in recalcitrant woody plants

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Nat Biotechnol . https://doi.org/10.1038/s41587-023-02065-3, 2024.

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Peleg Ragonis-Bachar, Gabriel Axel, Shahar Blau, Nir Ben-Tal, Rachel Kolodny, Meytal Landau

What can AlphaFold do for antimicrobial amyloids?

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Proteins.2024;92:265–281, 2024.

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Ben-Tal, N.  

AI-based view of protein space. An item within Voices on “What can recent methodological advances help us understand about protein and genome evolution?”

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Cell Systems, 15 (3): 205-210, 2024, https://doi.org/10.1016/j.cels.2024.02.006. https://www.sciencedirect.com/science/article/pii/S2405471224000607

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2023

Barak Yariv, Elon Yariv,  Amit Kessel,  Gal Masrati, Adi Ben Chorin,  Eric Martz, Itay Mayrose,  Tal Pupko,  and Nir Ben-Tal

Using evolutionary data to make sense of macromolecules with a ‘face-lifted’ ConSurf

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Protein Science DOI10.1002/pro.4582

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Hila Werner , Ammar Abou Kandil , Zohar Meir, Yehonathan Malis, Yona Shadkchan, Gal Masrati,Nir Ben-Tal, Koret Hirschberg and Nir Osherov

Identification and Analysis of Fungal-Specific Regions in the Aspergillus fumigatus Cu Exporter CrpA That Are Essential for Cu Resistance but Not for Virulence

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Int. J. Mol. Sci. 2023, 24, 3705. https://doi.org/10.3390/ijms24043705, 2023

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Gal Masrati, Amit Kessel and Nir Ben-Tal

Cation/proton antiporters: novel structure-driven pharmaceutical opportunities

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Trends in Pharmacological Sciences https://doi.org/10.1016/j.tips.2023.02.006, 2023

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Natan Nagar, Jérôme Tubiana, Gil Loewenthal, Haim J. Wolfson, Nir Ben Tal, Tal Pupko

EvoRator2: predicting site-specific amino acid substitutions based on protein structural information using deep learning

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JMB 168155, https://doi.org/10.1016/j.jmb.2023.168155 , 2023

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Ayca Ersoy, Bengi Altintel , Nurit Livnat Levanon, Nir Ben-Tal, Turkan Haliloglu, Oded Lewinson

Computational analysis of long-range allosteric communications in CFTR

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SSRN https://dx.doi.org/10.2139/ssrn.4487221 , 2023

Ersoy, Altintel, Livnat Levanon et al. eLife 12:RP88659. DOI: https://doi.org/10.7554/eLife.88659, 2023.​​​

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Diego Velázquez, VojtΔ›ch PrΕ―ša, Gal Masrati, Elon Yariv, Hana Sychrova, Nir Ben-Tal, Olga Zimmermannova

Allosteric links between the hydrophilic N-terminus and transmembrane core of human Na+/H+ antiporter NHA2

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Protein Science. 2022;31:e4460, https://doi.org/10.1002/pro.4460, 2022

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Kaiyu Qiu, Nir Ben-Tal and Rachel Kolodny

​Similar protein segments shared between domains ofdifferent evolutionary lineages

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Protein Science. 31(9):e4407.https://doi.org/10.1002/pro.440710 of 10QIUET AL., 2022

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Nir Ben-Tal  and Rachel Kolodny

Homologues not needed: Structure prediction from a protein language model

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Structure, Volume 30, Issue 8, Pages 1047-1049, https://doi.org/10.1016/j.str.2022.07.002, 2022

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Natan Nagar, Nir Ben-Tal and Tal Pupko

EvoRator: Prediction of Residue-level Evolutionary Rates from Protein Structures Using Machine Learning

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Journal of Molecular Biology, https://doi.org/10.1016/j.jmb.2022.167538, 2022.

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Omri Shelef, Sara Gutkin, Daniel Feder, Ariel Ben-Bassat, Michal Mandelboim, Yoni Haitin, Nir Ben-Tal, Eran Bacharach, Doron Shabat

Ultrasensitive chemiluminescent neuraminidase probe for rapid screening and identification of small-molecules with antiviral activity against influenza A virus in mammalian cells

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Chem. Sci., 2022, 13, 12348 ,DOI: 10.1039/d2sc03460c, 2022.​​​​​​​​​

2022

2021

 

 

 

 

 

Liam M. Longo, Jagoda JabΕ‚oΕ„ska, Pratik Vyas, Manil Kanade, Rachel Kolodny, Nir Ben-Tal, Dan S. Tawfik.

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

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eLife ;9:e64415. DOI: https://doi.org/10.7554/eLife.64415, 2020.

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Gal Masrati, Ramakanta Mondal, Abraham Rimon, Amit Kessel, Etana Padan, Erik Lindahl and Nir Ben-Tal.

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

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PNAS, https://www.pnas.org/content/early/2020/11/24/2002710117, 2020.

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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

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

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

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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
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J. Biol. Chem. https://www.jbc.org/cgi/doi/10.1074/jbc.RA119.012063, 2020.

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

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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
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mBio. DOI: 10.1128/mBio.03203-19, 2020.


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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
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Nature Machine Intelligence,https://doi.org/10.1038/s42256-019-0139-8, 2020

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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

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Protein Science, 29:258–267,https://doi.org/10.1002/pro.3779, 2020.

2020

Anastasiya Kuznetsova, Gal Masrati, Elena Vigonsky, Nurit Livnat-Levanon, Jessica Rose, Moti Grupper, Adan Baloum, Janet G. Yang, Douglas C. Rees, Nir Ben-Tal, Oded Lewinson

Titratable transmembrane residues and a hydrophobic plug are essential for manganese import via the Bacillus anthracis ABC transporter MntBC-A

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J. Biol. Chem. https://doi.org/10.1016/j.jbc.2021.101087 297(4) 10108, 2021.

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Nir Ben-Tal, Daisuke Kihara and Arun Prasad Pandurangan

Editorial: Computational Approaches to Study the Impact of Mutations on Disease and Drug Resistance

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Front. Mol. Biosci. 8:813552.https://doi.org/10.3389/fmolb.2021.813552, 2021.

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Rose C. Hadley, Daniel Zhitnitsky, Nurit Livnat-Levanon, Gal Masrati, ElenaVigonsky, Jessica Rose, Nir Ben-Tal, Amy C. Rosenzweig

and Oded Lewinson

The copper-linked E. coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery

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JBC, https://doi.org/10.1016/j.jbc.2021.1014459, 2021.

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Neeraj Sharma, Chaitanya Patel, Marina Shenkman, Amit Kessel, Nir Ben-Tal and Gerardo Z. Lederkremer

The Sigma-1 receptor is an ER-localized type II membrane protein

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JBC, https://doi.org/10.1016/j.jbc.2021.101299, 2021.

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Maya Rubin and Nir Ben-Tal

Using ConSurf to Detect Functionally Important Regions in RNA

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Current Protocols, 1, e270.https://doi.org/10.1002/cpz1.270, 2021.

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Ron Solan, Joana Pereira, Andrei N. Lupas, Rachel Kolodny and Nir Ben-Tal

Gram-negative outer-membrane proteins with multiple β-barrel domains

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PNAS Vol. 118 No. 31 e2104059118,  https://doi.org/10.1073/pnas.2104059118, 2021.

 

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R. Mondal, A. Rimon, G. Masrati, N. Ben-Tal, A. Friedler and E. Padan

Towards Molecular Understanding of thepH Dependence Characterizing NhaA of Which Structural Fold is Shared by Other Transporters

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Journal of Molecular Biology 433 (2021) 1671563, https://doi.org/10.1016/j.jmb.2021.167156, 2021.

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Gal Masarati, Meytal Landau, Nir Ben-Tal, Andrei Lupas, Mickey Kosloff and Jan Kosinsky  

Integrative structural biology in the era of accurate structure prediction

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Journal of Molecular Biology https://doi.org/10.1016/j.jmb.2021.167127,  2021.

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Nir Ben-Tal and Andrei N Lupas

Editorial overview: Sequences and topology: ‘paths from sequence to structure'

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Current Opinion in Structural Biology, 68:vi–viii, https://doi.org/10.1016/j.sbi.2021.05.005,  2021.

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Michael Bernhofer, Christian Dallago, Tim Karl, Venkata Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, Laszlo Kajan, Sean O’Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost

PredictProtein - Predicting Protein Structure and Function for 29 Years

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Nucleic Acids Research, gkab354, https://doi.org/10.1093/nar/gkab354, 2021.

 

 

Yiǧit Kutlu, Nir Ben-Tal, and Turkan Haliloglu

Global Dynamics Renders Protein Sites with High Functional Response

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J. Phys. Chem, https://doi.org/10.1021/acs.jpcb.1c02511, 2021.

 

 

Rachel Kolodny, Sergey Nepomnyachiy, Dan S. Tawfik, Nir Ben-Tal.

Bridging Themes: Short Protein Segments Found in Different Architectures

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Molecular Biology and Evolution, Volume 38, Issue 6, June 2021, Pages 2191–2208, https://doi.org/10.1093/molbev/msab017

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Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA

Structural motifs in protein cores and at protein–protein interfaces are different

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Protein Science, https://doi.org/10.1002/pro.3996 2021.

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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

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Molecular Microbiology, https://doi.org/10.1111/mmi.14595, 2021.

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​​Ido Caspy, Tom Schwartz, Vinzenz Bayro-Kaiser, Mariia Fadeeva, Amit Kessel, Nir Ben-Tal & Nathan Nelson

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

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Commun Biol 4, 1380  https://doi.org/10.1038/s42003-021-02911-7, 2021.

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2019

 
 
 
 
 
Aya Narunsky, Nir Ben-Tal, and Rachel Kolodny
Navigating Among Known Structures in Protein Space
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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
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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
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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
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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
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Bioinformatics, 35(9),1513–1517 https://doi.org/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
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NATURE COMMUNICATIONS, https://doi.org/10.1038/s41467-018-06770-5 5,2018.
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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
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Structure,https://doi.org/10.1016/j.str.2018.06.007,2018.

 
Min Yangβ€Š , Nurit Livnat Levanon, Burçin Acar, Burcu Aykac Fasβ€Š, Gal Masrati,Jessica Rose, Nir Ben-Talβ€Š, Turkan Haliloglu, Yongfang Zhao and Oded Lewinson
Single-molecule probing of the conformational homogeneity of the ABC transporter BtuCD
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Nature Chemical Biology, volume 14, pages715–722,https://doi.org/10.1038/s41589-018-0088-2, 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
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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
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Pnas, https://doi.org/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
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Structure 25, 988–996,https://doi.org/10.1016/j.str.2017.05.004,  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
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Isr. J. Chem. 57, 1 – 5,https://doi.org/10.1002/ijch.201600133,  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
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Nucleic Acids Research DOI:10.1093/nar/gkw408 ,2016.
 
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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
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Sci Rep. 6:21696 | DOI: 10.1038/srep21696 ,2016.
 
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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
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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
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Proc Natl Acad Sci U S A. 112(41):E5575-82. doi: 10.1073/pnas.1510964112. Epub, 2015.
 
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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
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PLoS Comput Biol.11(10):e1004461. doi: 10.1371/journal.pcbi.1004461. eCollection, 2015.
 
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Aya Narunsky, Sergey Nepomnyachiy, Haim Ashkenazy, Rachel Kolodny, Nir Ben-Tal
ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure
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Structure 23, 2162–2170,2015.
 
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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
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Sci Rep. 5:12828. doi: 10.1038/srep12828,2015.
 
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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
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Metallomics, Advance Article DOI: 10.1039/C5MT00100E, 2015.
 
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Sergey Nepomnyachiy, Nir Ben-Tal,Rachel Kolodny
CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers
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Structure 23(5):941-8. doi: 10.1016/j.str.2015.02.013. Epub, 2015.
 
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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
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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
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PLoS Comput Biol 10(12):e1003976. doi: 10.1371/journal.pcbi.1003976 eCollection ,2014.
 
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Han Remaut and Nir Ben-Tal
Lifting the lid on pilus assembly
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eLife 2014;3:e04997. DOI: 10.7554/eLife.04997, 2014.
 
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Nir Ben-Tal and Rachel Kolodny
Representation of the Protein Universe using Classifications, Maps, and Networks
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Isr. J. Chem., 54: 1286–1292. doi: 10.1002/ijch.201400001,2014.
 
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Sergey Nepomnyachiy, Nir Ben-Tal and Rachel Kolodny
Global view of the protein universe
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PNAS,vol. 111,no. 321 1691–11696,2014.

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Kenneth A. Stapleford, Lark L. Coffey,Sreyrath Lay, Antonio V. BorderΔ±´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
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Cell Host & Microbe 15,Elsevier Inc, 706–716, 2014.

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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
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Nucleic Acids Research, doi:10.1093/nar/gku366,2014.
 
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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
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Blood first edition paper doi:10.1182/blood-2014-10-529685, prepublished online,2014.
 
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Aya Narunsky, Nir Ben-Tal
ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure
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BMC Bioinformatics, 15(Suppl 3):A5, 2014.
 
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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
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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
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Nat Commun. 4:2510. doi: 10.1038/ncomms3510 PMID: 24065030,2013.
 
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Nir Ben-Tal,
Editorial for the ISMB/ECCB 2013 Proceedings
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ISMB/ECCB doi:10.1093/bioinformatics/btt282, 2013.
 
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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
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Isr.J.Chem. doi: 10.1002/ijch.201200096, 2013.
 
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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
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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
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PLoS ONE doi:10.1371/journal.pone.0043045,2012.
 
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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
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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
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J. Chem. Inf. DOI: 10.1021/ci2005884, 2012.

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Yana Gofman,Turkan Haliloglu, and Nir Ben-Tal
The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation
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J. Chem. Theory Comput, DOI: 10.1021/ct300128x,2012.
 
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Yana Gofman, Turkan Haliloglu and Nir Ben-Tal
Monte Carlo simulations of peptide–membrane interactions with the MCPep web server
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Nucleic Acids Research 40(W1):W358-W363, 2012.
 
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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
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Metallomics 669-678. DOI: 10.1039/C2MT20025B, 2012.
 
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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
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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
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Biochem. J. 442, 381–389, DOI: 10.1042,2012.

 
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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
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Bioinformatics vol. 27 no. 23 3286-3292,2011.
 
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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 OvalΔ±, 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
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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
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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
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JBC 286(21):le9; DOI: 10.1074/jbc.L110.159202, 2011.
 
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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
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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
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In "Structural Bioinformatics of Membrane Proteins" (Dmitrij Frishman, Editor), Springer.
 
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M. Schushan and N. Ben-Tal
Modeling and validation of transmembrane protein structures
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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.
 
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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
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PNAS.107(35):15637-42; DOI: 10.1073/pnas.0911294107; PMID: 20713704, 2010.
 
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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
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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.
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Nucleic Acids Research 38 (Web Server issue):W523-8; DOI: 10.1093/nar/gkq528; PMID: 20542913, 2010.
 
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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.
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Nucleic Acids Research 38 (Web Server issue):W529-33; DOI: 10.1093/nar/gkq399; PMID: 20478830, 2010.
 
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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
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PNAS 107(24):10908-13. DOI: 10.1073/pnas.0914717107; PMID: 20534491, 2010.
 
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A. Yeheskel, T. Haliloglu, N. Ben-Tal
Independent and Cooperative Motions of the Kv1.2 Channel: Voltage Sensing and Gating
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Biophysical Journal 98(10):2179–2188; PMID: 20483326, 2010.
 
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M. Kalman and N. Ben-Tal
Quality Assessment of Protein Model-Structures Using Evolutionary Conservation
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Bioinformatics 26(10):1299-1307; DOI: 10.1093/bioinformatics/btq114; PMID: 20385730,2010.
 
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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.
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J Phys Chem B. 114(12):4230-7; PMID: 20201501, 2010.

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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
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J Mol Biol. 396: 1181–1196; DOI: 10.1016/j.jmb.2009.12.055; PMID: 20053353, 2010.

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

https://pubmed.ncbi.nlm.nih.gov/20478830/

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
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J Phys Chem B. 113(38):12687-95; PMID: 19725508, 2009.
 
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A. Yahashiri, G. Nimrod, N. Ben-Tal, EE. Howell, A Kohen
The Effect of Electrostatic Shielding on H Tunneling in R67 Dihydrofolate Reductase
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Chembiochem.10(16):2620-2623; PMID: 19774544, 2009.
 
​
S.E. Harrington, N. Ben-Tal .
Structural Determinants of Transmembrane Helical Proteins
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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
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J. Chem. Inf. Model. 49(4):865-76; PMID: 19323449, 2009.
 
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G. Nimrod, A. Szilágyi, C. Leslie and N. Ben-Tal .
Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features
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Journal of Molecular Biology 387(4):1040-1053; PMID: 19233205, 2009.
 
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O. Goldenberg, E. Erez, G. Nimrod and N. Ben-Tal .
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
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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
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PLoS Genetics 4(10); DOI:10.1371/journal.pgen.1000207; PMID: 18833301, 2008.
 
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G. Nimrod, M. Schushan, D.M. Steinberg, N. Ben-Tal .
Detection of Functionally Important Regions in "Hypothetical Proteins" of Known Structure
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Structure, 16:1755–1763, 2008.

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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
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Lancet, 372:1484–92, 2008.
 
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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
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EMBO 27:1974–1984, doi:10.1038/emboj.2008.122, 2008.
 
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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
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Biophys. J. 95:3850–3860, 2008.
 
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T. Haliloglu, N. Ben-Tal
Cooperative Transition between Open and Closed Conformations in Potassium Channels
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PLoS Computational Biology, Vol. 4, Issue 8 e1000164, 2008.
 
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M. Landau, N. Ben-Tal
Dynamic equilibrium between multiple active and inactive conformations explains regulation and oncogenic mutations in ErbB receptors
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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
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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
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Journal of Biological Chemistry, V.282 No.52, 37854–37863, 2007.
 
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D. Shental-Bechor, T. Haliloglu and N. Ben-Tal
Interactions of Cationic-Hydrophobic Peptides with Lipid Bilayers: A Monte Carlo Simulation Method
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Biophys. J. 93:1858-1871, 2007.
 
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A. Enosh, S. J. Fleishman, N. Ben-Tal and D. Halperin
Prediction and simulation of motion in pairs of transmembrane α-helices
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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
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Journal of Molecular Biology 364:54-67,2006.
 
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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
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Journal of Biological Chemistry, V.281 No.39, 28958-28963,2006.
 
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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
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Nat. Genetics. 38:770-778,2006.
 
​
S. J. Fleishman and N. Ben-Tal
Progress in structure prediction of α-helical membrane proteins
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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
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Microbiology 152:1919-1928,2006.
 
​
D. Shental-Bechor, S. J. Fleishman, and N. Ben-Tal
Has the code for protein translocation been broken?
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TRENDS in Biochemical Sciences 31:192-196,2006.
​
 
S. J. Fleishman, V. M. Unger, and N. Ben-Tal
Transmembrane protein structures without X-rays
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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
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Bioinformatics. 21 Suppl. 1:i328-i337, 2005.
 
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R. Gutman, C. Berezin, R. Wollman, Y. Rosenberg, N. Ben-Tal
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns
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Nucl. Acids Res. 33:W255-W261, 2005.
 
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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
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Nucl. Acids Res. 33:W299-W302, 2005.
 
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D. Shental-Bechor, S. Kirca, N. Ben-Tal and T. Haliloglu
Monte Carlo studies of folding, dynamics, and stability in α-helices
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Biophys. J. 88:2391-2402, 2005.
 
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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
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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
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Structure 12: 2265-2275,2004.
 
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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
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Biophys. J. 87: 3448-3459,2004.
 
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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
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Mol. Cell 15: 879-888, 2004.
 
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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
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J. Virol. 78: 9675-9688, 2004.
 
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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
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Science 305: 1107, 2004.
 
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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
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Mol. Biol. Evol. 21: 1781-1791, 2004.
 
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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
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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
PDF
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
PDF
J. Mol. Biol. 340: 307-318, 2004.
 
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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
PDF
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
PDF
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
PDF
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
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Bioiphys. J. 85: 3431-3444,2003.
 
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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
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Bioiphys. J. 85: 3687-3695, 2003.
 
​
Rachel E. Bell and Nir Ben-Tal
In silico identification of functional protein interfaces
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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
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Proteins Structure Function and Genetics 52: 44-55, 2003.
 
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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
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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
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PNAS 99: no. 25 15937-15940, 2002.
 
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S.J. Fleishman and N. Ben-Tal
A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices
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J. Mol. Biol. 321(2): 363-78, 2002.
 
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Amit Kessel and Nir Ben-Tal
Free Energy Determinants of Peptide Association with Lipid Bilayers. Current Topics in Membranes: Peptide-Lipid Interactions
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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
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Bioinformatics 18 Suppl 1:S71-7, 2002.

S
 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
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Biochimica et Biophysica Acta, 1565: 81-90, 2002.
 
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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
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Biochemistry, 41: 6946-6954, 2002.
 
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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 
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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 
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Biophys. J. 81: 3016-3028&nbsp,2001.
 
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Amit Kessel, Nir Ben-Tal and Sylvio May
Interactions of Cholesterol with Lipid Bilayers: The Preferred Configuration and Fluctuations
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Biophys. J. 81: 643-658&nbsp, 2001.
 
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Amit Kessel, Boaz Musafia and Nir Ben-Tal
Continuum Solvent Model Studies of the Interactions of an Anticonvulsant Drug with a Lipid Bilayer
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Biophys. J. 80: 2535-2545&nbsp, 2001.
 
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Fabian Glaser, David M. Steinberg, Ilya A. Vakser and Nir Ben-Tal
Residue frequencies and pairing preferences at protein-protein interfaces
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PROTEINS: Structure, Function and Genetics, 43: 89-102&nbsp, 2001.
 
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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
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J. Mol. Biol. 307: 447-463, 2001.
 
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Dalit Bechor and Nir Ben-Tal
Implicit Solvent Model Studies of the Interactions of the Influenza Hemagglutinin Fusion Peptide with Lipid Bilayers
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Biophys. J. 80: 643-655, 2001.
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2000

Amit Kessel, Klaus Schulten and Nir Ben-Tal
Calculations Suggest a Pathway for the Transverse Diffusion of a Hydrophobic Peptide
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Biophys. J. 79: 2322-2330, 2000.
 
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Nir Ben-Tal, Barry Honig, Carey K. Bagdassarian and Avinoam Ben-Shaul
Association entropy in adsorption processes
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Biophys. J. 79: 1180-1187&nbsp, 2000.
 
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Amit Kessel, David S. Cafiso and Nir Ben-Tal
Continuum Solvent Model Calculations of Alamethicin-Membrane Interactions: Thermodynamic Aspects
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Biophys. J. 78: 571-583&nbsp, 2000.
 
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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
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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
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J. Mol. Biol, 294: 921-935, &nbsp, 1999.
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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
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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
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Biochemistry, 37: 2145-2159&nbsp, 1998.

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