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

Ben Chorin A, Masrati G, Kessel A, Narunsky A, Sprinzak J, Lahav S, Ashkenazy H, Ben-Tal N.

Protein Sci. 2019 Nov 8. doi: 10.1002/pro.3779. [Epub ahead of print]


Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase-Bisphosphonate Interactions: A Crystallographic and Computational Analysis.

Lisnyansky M, Yariv E, Segal O, Marom M, Loewenstein A, Ben-Tal N, Giladi M, Haitin Y.

Mol Pharmacol. 2019 Nov;96(5):580-588. doi: 10.1124/mol.119.117499. Epub 2019 Aug 19.


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

Montanucci L, Capriotti E, Frank Y, Ben-Tal N, Fariselli P.

BMC Bioinformatics. 2019 Jul 3;20(Suppl 14):335. doi: 10.1186/s12859-019-2923-1.


Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins.

Franklin MW, Nepomnyachyi S, Feehan R, Ben-Tal N, Kolodny R, Slusky JS.

Elife. 2018 Nov 29;7. pii: e40308. doi: 10.7554/eLife.40308.


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

Montanucci L, Martelli PL, Ben-Tal N, Fariselli P.

Bioinformatics. 2019 May 1;35(9):1513-1517. doi: 10.1093/bioinformatics/bty880.


Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants.

Masrati G, Dwivedi M, Rimon A, Gluck-Margolin Y, Kessel A, Ashkenazy H, Mayrose I, Padan E, Ben-Tal N.

Nat Commun. 2018 Oct 11;9(1):4205. doi: 10.1038/s41467-018-06770-5.


Navigating Among Known Structures in Protein Space.

Narunsky A, Ben-Tal N, Kolodny R.

Methods Mol Biol. 2019;1851:233-249. doi: 10.1007/978-1-4939-8736-8_12.


Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold.

Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG.

Structure. 2018 Sep 4;26(9):1266-1274.e2. doi: 10.1016/j.str.2018.06.007. Epub 2018 Jul 26.


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

Yang M, Livnat Levanon N, Acar B, Aykac Fas B, Masrati G, Rose J, Ben-Tal N, Haliloglu T, Zhao Y, Lewinson O.

Nat Chem Biol. 2018 Jul;14(7):715-722. doi: 10.1038/s41589-018-0088-2. Epub 2018 Jun 18.


Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths.

Nepomnyachiy S, Ben-Tal N, Kolodny R.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11703-11708. doi: 10.1073/pnas.1707642114. Epub 2017 Oct 19. Erratum in: Proc Natl Acad Sci U S A. 2018 Jun 5;115(23 ):E5430.


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

Zhu W, Ronen M, Gur Y, Minz-Dub A, Masrati G, Ben-Tal N, Savidor A, Sharon I, Eizner E, Valerius O, Braus GH, Bowler K, Bar-Peled M, Sharon A.

Plant Physiol. 2017 Sep;175(1):438-456. doi: 10.1104/pp.17.00375. Epub 2017 Jul 14.


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

Sameach H, Narunsky A, Azoulay-Ginsburg S, Gevorkyan-Aiapetov L, Zehavi Y, Moskovitz Y, Juven-Gershon T, Ben-Tal N, Ruthstein S.

Structure. 2017 Jul 5;25(7):988-996.e3. doi: 10.1016/j.str.2017.05.004. Epub 2017 Jun 1.


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

Ashkenazy H, Abadi S, Martz E, Chay O, Mayrose I, Pupko T, Ben-Tal N.

Nucleic Acids Res. 2016 Jul 8;44(W1):W344-50. doi: 10.1093/nar/gkw408. Epub 2016 May 10.


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

Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U, Ruppin E.

PLoS Comput Biol. 2016 Jan 28;12(1):e1004705. doi: 10.1371/journal.pcbi.1004705. eCollection 2016 Jan.


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

Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T.

PLoS Comput Biol. 2015 Oct 27;11(10):e1004461. doi: 10.1371/journal.pcbi.1004461. eCollection 2015 Oct.


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

Narunsky A, Nepomnyachiy S, Ashkenazy H, Kolodny R, Ben-Tal N.

Structure. 2015 Nov 3;23(11):2162-70. doi: 10.1016/j.str.2015.08.018. Epub 2015 Oct 9.


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

Padan E, Danieli T, Keren Y, Alkoby D, Masrati G, Haliloglu T, Ben-Tal N, Rimon A.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):E5575-82. doi: 10.1073/pnas.1510964112. Epub 2015 Sep 28.


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

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.

Sci Rep. 2015 Aug 13;5:12828. doi: 10.1038/srep12828.


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

Vigonsky E, Fish I, Livnat-Levanon N, Ovcharenko E, Ben-Tal N, Lewinson O.

Metallomics. 2015 Oct;7(10):1407-19. doi: 10.1039/c5mt00100e. Epub 2015 Jun 24.


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

Nepomnyachiy S, Ben-Tal N, Kolodny R.

Structure. 2015 May 5;23(5):941-948. doi: 10.1016/j.str.2015.02.013. Epub 2015 Apr 9.


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

Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003976. doi: 10.1371/journal.pcbi.1003976. eCollection 2014 Dec.


Lifting the lid on pilus assembly.

Remaut H, Ben-Tal N.

Elife. 2014 Oct 28;3. doi: 10.7554/eLife.04997.


Global view of the protein universe.

Nepomnyachiy S, Ben-Tal N, Kolodny R.

Proc Natl Acad Sci U S A. 2014 Aug 12;111(32):11691-6. doi: 10.1073/pnas.1403395111. Epub 2014 Jul 28.


Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential.

Stapleford KA, Coffey LL, Lay S, Bordería AV, Duong V, Isakov O, Rozen-Gagnon K, Arias-Goeta C, Blanc H, Beaucourt S, Haliloğlu T, Schmitt C, Bonne I, Ben-Tal N, Shomron N, Failloux AB, Buchy P, Vignuzzi M.

Cell Host Microbe. 2014 Jun 11;15(6):706-16. doi: 10.1016/j.chom.2014.05.008.


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

Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W337-43. doi: 10.1093/nar/gku366. Epub 2014 May 5.


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

Shochat C, Tal N, Gryshkova V, Birger Y, Bandapalli OR, Cazzaniga G, Gershman N, Kulozik AE, Biondi A, Mansour MR, Twizere JC, Muckenthaler MU, Ben-Tal N, Constantinescu SN, Bercovich D, Izraeli S.

Blood. 2014 Jul 3;124(1):106-10. doi: 10.1182/blood-2013-10-529685. Epub 2014 May 1.


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

Leitman J, Shenkman M, Gofman Y, Shtern NO, Ben-Tal N, Hendershot LM, Lederkremer GZ.

Mol Biol Cell. 2014 Apr;25(7):1050-60. doi: 10.1091/mbc.E13-06-0350. Epub 2014 Jan 29.


Functional evaluation of autism-associated mutations in NHE9.

Kondapalli KC, Hack A, Schushan M, Landau M, Ben-Tal N, Rao R.

Nat Commun. 2013;4:2510. doi: 10.1038/ncomms3510.


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

Ben-Tal N.

Bioinformatics. 2013 Jul 1;29(13):i1-2. doi: 10.1093/bioinformatics/btt282. No abstract available.


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

Dirndorfer D, Seidel RP, Nimrod G, Miesbauer M, Ben-Tal N, Engelhard M, Zimmermann R, Winklhofer KF, Tatzelt J.

J Biol Chem. 2013 May 17;288(20):13961-73. doi: 10.1074/jbc.M112.430264. Epub 2013 Mar 26.


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

Saroussi S, Schushan M, Ben-Tal N, Junge W, Nelson N.

PLoS One. 2012;7(9):e43045. doi: 10.1371/journal.pone.0043045. Epub 2012 Sep 25.


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

Gofman Y, Haliloglu T, Ben-Tal N.

J Chem Theory Comput. 2012 Aug 14;8(8):2896-2904. Epub 2012 Jun 6.


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

Gofman Y, Shats S, Attali B, Haliloglu T, Ben-Tal N.

Structure. 2012 Aug 8;20(8):1343-52. doi: 10.1016/j.str.2012.05.016. Epub 2012 Jul 5.


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

Dalton J, Kalid O, Schushan M, Ben-Tal N, Villà-Freixa J.

J Chem Inf Model. 2012 Jul 23;52(7):1842-53. doi: 10.1021/ci2005884. Epub 2012 Jul 12.


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

Gofman Y, Haliloglu T, Ben-Tal N.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W358-63. doi: 10.1093/nar/gks577. Epub 2012 Jun 13.


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

Schushan M, Bhattacharjee A, Ben-Tal N, Lutsenko S.

Metallomics. 2012 Jul;4(7):669-78. doi: 10.1039/c2mt20025b. Epub 2012 Jun 13.


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

Schushan M, Rimon A, Haliloglu T, Forrest LR, Padan E, Ben-Tal N.

J Biol Chem. 2012 May 25;287(22):18249-61. doi: 10.1074/jbc.M111.336446. Epub 2012 Mar 19.


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

Merklinger E, Gofman Y, Kedrov A, Driessen AJ, Ben-Tal N, Shai Y, Rapaport D.

Biochem J. 2012 Mar 1;442(2):381-9. doi: 10.1042/BJ20111363.


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

Wainreb G, Wolf L, Ashkenazy H, Dehouck Y, Ben-Tal N.

Bioinformatics. 2011 Dec 1;27(23):3286-92. doi: 10.1093/bioinformatics/btr576. Epub 2011 Oct 13.


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

Meroz D, Yoon SW, Ducatez MF, Fabrizio TP, Webby RJ, Hertz T, Ben-Tal N.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13522-7. doi: 10.1073/pnas.1014854108. Epub 2011 Aug 1.


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

Schushan M, Landau M, Padan E, Ben-Tal N.

J Biol Chem. 2011 May 27;286(21):le9; author reply Ie10. doi: 10.1074/jbc.L110.159202. No abstract available.


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

Williams AL, Bielopolski N, Meroz D, Lam AD, Passmore DR, Ben-Tal N, Ernst SA, Ashery U, Stuenkel EL.

J Biol Chem. 2011 Apr 22;286(16):14542-53. doi: 10.1074/jbc.M110.215624. Epub 2011 Feb 17.


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

Peretz A, Pell L, Gofman Y, Haitin Y, Shamgar L, Patrich E, Kornilov P, Gourgy-Hacohen O, Ben-Tal N, Attali B.

Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15637-42. doi: 10.1073/pnas.0911294107. Epub 2010 Aug 16.


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

Dorosz J, Gofman Y, Kolusheva S, Otzen D, Ben-Tal N, Nielsen NC, Jelinek R.

J Phys Chem B. 2010 Sep 2;114(34):11053-60. doi: 10.1021/jp1052248.


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

Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W523-8. doi: 10.1093/nar/gkq528. Epub 2010 Jun 11. Erratum in: Nucleic Acids Res. 2010 Nov 1;38(21):7869.


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

Schushan M, Barkan Y, Haliloglu T, Ben-Tal N.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10908-13. doi: 10.1073/pnas.0914717107. Epub 2010 Jun 1.


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

Yeheskel A, Haliloglu T, Ben-Tal N.

Biophys J. 2010 May 19;98(10):2179-88. doi: 10.1016/j.bpj.2010.01.049.


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

Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W529-33. doi: 10.1093/nar/gkq399. Epub 2010 May 16.


Quality assessment of protein model-structures using evolutionary conservation.

Kalman M, Ben-Tal N.

Bioinformatics. 2010 May 15;26(10):1299-307. doi: 10.1093/bioinformatics/btq114. Epub 2010 Apr 12.

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