PredictProtein - Predicting Protein Structure and Function for 29 Years.

Nir Ben-Tal https://scholar.google.com/citations?user=hkg5fMkAAAAJ https://en.wikipedia.org/wiki/Nir_Ben-Tal https://orcid.org/0000-0001-6901-832X https://www.wikidata.org/entity/Q47333803 https://id.loc.gov/authorities/names/n2010182937 https://d-nb.info/gnd/1162077182

Michael Bernhofer Christian Dallago Timothy Karl Venkata P. Satagopam Michael Heinzinger Maria Littmann Tobias Olenyi Jiajun Qiu Konstantin Schütze Guy Yachdav Haim Ashkenazy Nir Ben-Tal Yana Bromberg Tatyana Goldberg László Kaján Seán I. O'Donoghue Chris Sander Andrea Schafferhans Avner Schlessinger Gerrit Vriend Milot Mirdita Piotr Gawron Wei Gu Yohan Jarosz Christophe Trefois Martin Steinegger Reinhard Schneider 0002 Burkhard Rost PredictProtein - Predicting Protein Structure and Function for 29 Years. 535-540 2021 49 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkab354 https://www.wikidata.org/entity/Q111440852 db/journals/nar/nar49.html#BernhoferDKSHLO21

Maria Littmann Katharina Selig Liel Cohen-Lavi Yotam Frank Peter Hönigschmid Evans Kataka Anja Mösch Kun Qian 0003 Avihai Ron Sebastian Schmid 0002 Adam Sorbie Liran Szlak Ayana Dagan-Wiener Nir Ben-Tal Masha Y. Niv Daniel Razansky Björn W. Schuller Donna P. Ankerst Tomer Hertz Burkhard Rost Validity of machine learning in biology and medicine increased through collaborations across fields of expertise. 18-24 2020 2 Nat. Mach. Intell. 1 https://doi.org/10.1038/s42256-019-0139-8 https://www.wikidata.org/entity/Q126379776 db/journals/natmi/natmi2.html#LittmannSCFHKMQ20

Ludovica Montanucci Pier Luigi Martelli Nir Ben-Tal Piero Fariselli A natural upper bound to the accuracy of predicting protein stability changes upon mutations. 1513-1517 2019 35 Bioinform. 9 https://doi.org/10.1093/bioinformatics/bty880 https://www.wikidata.org/entity/Q62654557 db/journals/bioinformatics/bioinformatics35.html#MontanucciMBF19

Ludovica Montanucci Emidio Capriotti Yotam Frank Nir Ben-Tal Piero Fariselli DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations. 335:1-335:10 2019 20-S BMC Bioinform. 14 https://doi.org/10.1186/s12859-019-2923-1 https://www.wikidata.org/entity/Q91560858 db/journals/bmcbi/bmcbi20S.html#MontanucciCFBF19

Haim Ashkenazy Shiran Abadi Eric Martz Ofer Chay Itay Mayrose Tal Pupko Nir Ben-Tal ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. W344-W350 2016 44 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkw408 https://www.wikidata.org/entity/Q39776544 db/journals/nar/nar44.html#AshkenazyAMCMPB16

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 Eytan Ruppin Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. 2016 12 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.1004705 https://www.wikidata.org/entity/Q35907320 db/journals/ploscb/ploscb12.html#OberhardtZRXDSH16

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. A3 2015 16 BMC Bioinform. S-3 https://doi.org/10.1186/1471-2105-16-S3-A3 https://www.wikidata.org/entity/Q46389159 db/journals/bmcbi/bmcbi16S.html#NarunskyAKB15

Seren Soner Pemra Ozbek José Ignacio Garzón Nir Ben-Tal Turkan Haliloglu DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. 2015 11 PLoS Comput. Biol. 10 https://doi.org/10.1371/journal.pcbi.1004461 https://www.wikidata.org/entity/Q35822949 db/journals/ploscb/ploscb11.html#SonerOGBH15

Aya Narunsky Nir Ben-Tal ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure. A5 2014 15 BMC Bioinform. S-3 https://doi.org/10.1186/1471-2105-15-S3-A5 https://www.wikidata.org/entity/Q57207059 db/journals/bmcbi/bmcbi15S.html#NarunskyB14

Guy Yachdav Edda Kloppmann László Kaján 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 0002 Gerrit Vriend Chris Sander Nir Ben-Tal Burkhard Rost PredictProtein - an open resource for online prediction of protein structural and functional features. 337-343 2014 42 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gku366 https://www.wikidata.org/entity/Q34418986 db/journals/nar/nar42.html#YachdavKKHGHHSRBRAPSB0VSBR14

Yana Gofman Charlotta Schärfe Debora S. Marks Turkan Haliloglu Nir Ben-Tal Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel. 2014 10 PLoS Comput. Biol. 12 https://doi.org/10.1371/journal.pcbi.1003976 https://www.wikidata.org/entity/Q28542474 db/journals/ploscb/ploscb10.html#GofmanSMHB14

Nir Ben-Tal Editorial. 1-2 2013 29 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btt282 https://www.wikidata.org/entity/Q43113612 db/journals/bioinformatics/bioinformatics29.html#Ben-Tal13

James A. R. Dalton Ori Kalid Maya Schushan Nir Ben-Tal Jordi Villà-Freixa New Model of Cystic Fibrosis Transmembrane Conductance Regulator Proposes Active Channel-like Conformation. 1842-1853 2012 52 J. Chem. Inf. Model. 7 https://doi.org/10.1021/ci2005884 https://www.wikidata.org/entity/Q42656147 db/journals/jcisd/jcisd52.html#DaltonKSBV12

Yana Gofman Turkan Haliloglu Nir Ben-Tal Monte Carlo simulations of peptide-membrane interactions with the MCPep web server. 358-363 2012 40 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gks577 https://www.wikidata.org/entity/Q42232921 db/journals/nar/nar40.html#GofmanHB12

Gilad Wainreb Lior Wolf Haim Ashkenazy Yves Dehouck Nir Ben-Tal Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. 3286-3292 2011 27 Bioinform. 23 https://doi.org/10.1093/bioinformatics/btr576 https://www.wikidata.org/entity/Q39348278 db/journals/bioinformatics/bioinformatics27.html#WainrebWADB11

Guy Nimrod Maya Schushan András Szilágyi 0002 Christina S. Leslie Nir Ben-Tal iDBPs: a web server for the identification of DNA binding proteins. 692-693 2010 26 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btq019 https://www.wikidata.org/entity/Q39256732 db/journals/bioinformatics/bioinformatics26.html#NimrodSSLB10

Matan Kalman Nir Ben-Tal Quality assessment of protein model-structures using evolutionary conservation. 1299-1307 2010 26 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btq114 https://www.wikidata.org/entity/Q40408638 db/journals/bioinformatics/bioinformatics26.html#KalmanB10

Gilad Wainreb Haim Ashkenazy Yana Bromberg Alina Starovolsky-Shitrit Turkan Haliloglu Eytan Ruppin Karen B. Avraham Burkhard Rost Nir Ben-Tal MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. 523-528 2010 38 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkq528 https://www.wikidata.org/entity/Q33602676 db/journals/nar/nar38.html#WainrebABSHRARB10

Haim Ashkenazy Elana Erez Eric Martz Tal Pupko Nir Ben-Tal ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. 529-533 2010 38 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkq399 https://www.wikidata.org/entity/Q27860850 db/journals/nar/nar38.html#AshkenazyEMPB10

Ori Kalid Nir Ben-Tal Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design. 865-876 2009 49 J. Chem. Inf. Model. 4 https://doi.org/10.1021/ci800352c https://www.wikidata.org/entity/Q46073790 db/journals/jcisd/jcisd49.html#KalidB09

Ofir Goldenberg Elana Erez Guy Nimrod Nir Ben-Tal The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. 323-327 2009 37 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkn822 https://www.wikidata.org/entity/Q42849173 db/journals/nar/nar37.html#GoldenbergENB09

Turkan Haliloglu Nir Ben-Tal Cooperative Transition between Open and Closed Conformations in Potassium Channels. 2008 4 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1000164 https://www.wikidata.org/entity/Q28473610 db/journals/ploscb/ploscb4.html#HalilogluB08

Angela Enosh Sarel Jacob Fleishman Nir Ben-Tal Dan Halperin Prediction and simulation of motion in pairs of transmembrane alpha-helices. 212-218 2007 23 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btl325 https://www.wikidata.org/entity/Q48417035 db/journals/bioinformatics/bioinformatics23.html#EnoshFBH07

Angelika Fuchs Antonio J. Martin-Galiano Matan Kalman Sarel Jacob Fleishman Nir Ben-Tal Dmitrij Frishman Co-evolving residues in membrane proteins. 3312-3319 2007 23 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btm515 https://www.wikidata.org/entity/Q48371316 db/journals/bioinformatics/bioinformatics23.html#FuchsMKFBF07

Roee Gutman Carine Berezin Roy Wollman Yossi Rosenberg Nir Ben-Tal QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns. 255-261 2005 33 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gki496 https://www.wikidata.org/entity/Q24813515 db/journals/nar/nar33.html#GutmanBWRB05

Meytal Landau Itay Mayrose Yossi Rosenberg Fabian Glaser Eric Martz Tal Pupko Nir Ben-Tal ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. 299-302 2005 33 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gki370 https://www.wikidata.org/entity/Q24812180 db/journals/nar/nar33.html#LandauMRGMPB05

Guy Nimrod Fabian Glaser David Steinberg Nir Ben-Tal Tal Pupko In silico identification of functional regions in proteins. 328-337 2005 conf/ismb/2005 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bti1023 https://www.wikidata.org/entity/Q48484742 db/conf/ismb/ismb2005.html#NimrodGSBP05

Carine Berezin Fabian Glaser Josef Rosenberg Inbal Paz Tal Pupko Piero Fariselli Rita Casadio Nir Ben-Tal ConSeq: the identification of functionally and structurally important residues in protein sequences. 1322-1324 2004 20 Bioinform. 8 https://doi.org/10.1093/bioinformatics/bth070 https://www.wikidata.org/entity/Q48559824 db/journals/bioinformatics/bioinformatics20.html#BerezinGRPPFCB04

Angela Enosh Sarel Jacob Fleishman Nir Ben-Tal Dan Halperin Assigning transmembrane segments to helices in intermediate-resolution structures. 122-129 2004 conf/ismb/2004 ISMB/ECCB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bth939 https://www.wikidata.org/entity/Q41628229 db/conf/ismb/ismb2004.html#EnoshFBH04

Fabian Glaser Tal Pupko Inbal Paz Rachel E. Bell Dalit Bechor-Shental Eric Martz Nir Ben-Tal ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. 163-164 2003 19 Bioinform. 1 db/journals/bioinformatics/bioinformatics19.html#GlaserPPBBMB03 https://doi.org/10.1093/bioinformatics/19.1.163 https://www.wikidata.org/entity/Q29547192

Tal Pupko Rachel E. Bell Itay Mayrose Fabian Glaser Nir Ben-Tal Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. 71-77 2002 conf/ismb/2002 ISMB db/conf/ismb/ismb2002.html#PupkoBMGB02 https://doi.org/10.1093/bioinformatics/18.suppl_1.s71 Shiran Abadi Donna P. Ankerst Haim Ashkenazy Karen B. Avraham Dalit Bechor-Shental Rachel E. Bell Carine Berezin Michael Bernhofer Yana Bromberg Emidio Capriotti Rita Casadio Ofer Chay Liel Cohen-Lavi Ayana Dagan-Wiener Christian Dallago James A. R. Dalton Yves Dehouck Miquel Duran-Frigola Daniel J. Dwyer Angela Enosh Elana Erez Piero Fariselli Sarel Jacob Fleishman Yotam Frank Dmitrij Frishman Angelika Fuchs José Ignacio Garzón Piotr Gawron Fabian Glaser Yana Gofman Tatyana Goldberg Ofir Goldenberg Uri Gophna Wei Gu Roee Gutman Turkan Haliloglu Dan Halperin Tobias Hamp Maximilian Hecht Michael Heinzinger Christopher S. Henry Tomer Hertz Peter Hönigschmid László Kaján Ori Kalid Matan Kalman Timothy Karl Evans Kataka Edda Kloppmann Rachel Kolodny Meytal Landau Christina S. Leslie Maria Littmann Debora S. Marks Pier Luigi Martelli Antonio J. Martin-Galiano Eric Martz Itay Mayrose Milot Mirdita Ludovica Montanucci Anja Mösch Aya Narunsky Guy Nimrod Masha Y. Niv Matthew A. Oberhardt Seán I. O'Donoghue Tobias Olenyi Pemra Ozbek Inbal Paz Marco Punta Tal Pupko Kun Qian 0003 Jiajun Qiu Daniel Razansky Leah Reshef Lothar Richter Avihai Ron Manfred Roos Josef Rosenberg Yossi Rosenberg Burkhard Rost Eytan Ruppin Chris Sander Venkata P. Satagopam Andrea Schafferhans Charlotta Schärfe Avner Schlessinger Sebastian Schmid 0002 Reinhard Schneider 0002 Rachel Schreiber Björn W. Schuller Maya Schushan Konstantin Schütze Katharina Selig Seren Soner Adam Sorbie Alina Starovolsky-Shitrit David Steinberg Martin Steinegger András Szilágyi 0002 Liran Szlak Christophe Trefois Jordi Villà-Freixa Gert VriendGerrit Vriend Gilad Wainreb Lior Wolf Roy Wollman Fangfang Xia Guy Yachdav Yohan YaroszYohan Jarosz Raphy Zarecki