Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. - Tal Pupko; Rachel E. Bell; Itay Mayrose; Fabian Glaser; Nir Ben-Tal (ISMB, 2002)

ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. - Fabian Glaser; Tal Pupko; Inbal Paz; Rachel E. Bell; Dalit Bechor-Shental; Eric Martz; Nir Ben-Tal (Bioinform., 2003)

Assigning transmembrane segments to helices in intermediate-resolution structures. - Angela Enosh; Sarel Jacob Fleishman; Nir Ben-Tal; Dan Halperin (ISMB/ECCB (Supplement of Bioinformatics), 2004)

ConSeq: the identification of functionally and structurally important residues in protein sequences. - Carine Berezin; Fabian Glaser; Josef Rosenberg; Inbal Paz; Tal Pupko; Piero Fariselli; Rita Casadio; Nir Ben-Tal (Bioinform., 2004)

In silico identification of functional regions in proteins. - Guy Nimrod; Fabian Glaser; David Steinberg; Nir Ben-Tal; Tal Pupko (ISMB (Supplement of Bioinformatics), 2005)

QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns. - Roee Gutman; Carine Berezin; Roy Wollman; Yossi Rosenberg; Nir Ben-Tal (Nucleic Acids Res., 2005)

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. - Meytal Landau; Itay Mayrose; Yossi Rosenberg; Fabian Glaser; Eric Martz; Tal Pupko; Nir Ben-Tal (Nucleic Acids Res., 2005)

Prediction and simulation of motion in pairs of transmembrane alpha-helices. - Angela Enosh; Sarel Jacob Fleishman; Nir Ben-Tal; Dan Halperin (Bioinform., 2007)

Co-evolving residues in membrane proteins. - Angelika Fuchs; Antonio J. Martin-Galiano; Matan Kalman; Sarel Jacob Fleishman; Nir Ben-Tal; Dmitrij Frishman (Bioinform., 2007)

Cooperative Transition between Open and Closed Conformations in Potassium Channels. - Turkan Haliloglu; Nir Ben-Tal (PLoS Comput. Biol., 2008)

Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design. - Ori Kalid; Nir Ben-Tal (J. Chem. Inf. Model., 2009)

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. - Ofir Goldenberg; Elana Erez; Guy Nimrod; Nir Ben-Tal (Nucleic Acids Res., 2009)

Quality assessment of protein model-structures using evolutionary conservation. - Matan Kalman; Nir Ben-Tal (Bioinform., 2010)

iDBPs: a web server for the identification of DNA binding proteins. - Guy Nimrod; Maya Schushan; András Szilágyi 002; Christina S. Leslie; Nir Ben-Tal (Bioinform., 2010)

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. - Haim Ashkenazy; Elana Erez; Eric Martz; Tal Pupko; Nir Ben-Tal (Nucleic Acids Res., 2010)

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. - Gilad Wainreb; Haim Ashkenazy; Yana Bromberg; Alina Starovolsky-Shitrit; Turkan Haliloglu; Eytan Ruppin; Karen B. Avraham; Burkhard Rost; Nir Ben-Tal (Nucleic Acids Res., 2010)

Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. - Gilad Wainreb; Lior Wolf; Haim Ashkenazy; Yves Dehouck; Nir Ben-Tal (Bioinform., 2011)

New Model of Cystic Fibrosis Transmembrane Conductance Regulator Proposes Active Channel-like Conformation. - James A. R. Dalton; Ori Kalid; Maya Schushan; Nir Ben-Tal; Jordi Villà-Freixa (J. Chem. Inf. Model., 2012)

Monte Carlo simulations of peptide-membrane interactions with the MCPep web server. - Yana Gofman; Turkan Haliloglu; Nir Ben-Tal (Nucleic Acids Res., 2012)

Editorial. - Nir Ben-Tal (Bioinform., 2013)

ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure. - Aya Narunsky; Nir Ben-Tal (BMC Bioinform., 2014)

PredictProtein - an open resource for online prediction of protein structural and functional features. - Guy Yachdav; Edda Kloppmann; László Kaján; Maximilian Hecht; Tatyana Goldberg; Tobias Hamp; Peter Hönigschmid; Andrea Schafferhans; Manfred Roos; Michael Bernhofer; Lothar Richter; Haim Ashkenazy; et al. (Nucleic Acids Res., 2014)

Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel. - Yana Gofman; Charlotta Schärfe; Debora S. Marks; Turkan Haliloglu; Nir Ben-Tal (PLoS Comput. Biol., 2014)

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

DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. - Seren Soner; Pemra Ozbek; José Ignacio Garzón; Nir Ben-Tal; Turkan Haliloglu (PLoS Comput. Biol., 2015)

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. - Haim Ashkenazy; Shiran Abadi; Eric Martz; Ofer Chay; Itay Mayrose; Tal Pupko; Nir Ben-Tal (Nucleic Acids Res., 2016)

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. - 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 (PLoS Comput. Biol., 2016)

A natural upper bound to the accuracy of predicting protein stability changes upon mutations. - Ludovica Montanucci; Pier Luigi Martelli; Nir Ben-Tal; Piero Fariselli (Bioinform., 2019)

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations. - Ludovica Montanucci; Emidio Capriotti; Yotam Frank; Nir Ben-Tal; Piero Fariselli (BMC Bioinform., 2019)

Validity of machine learning in biology and medicine increased through collaborations across fields of expertise. - Maria Littmann; Katharina Selig; Liel Cohen-Lavi; Yotam Frank; Peter Hönigschmid; Evans Kataka; Anja Mösch; Kun Qian 003; Avihai Ron; Sebastian Schmid 002; Adam Sorbie; Liran Szlak; et al. (Nat. Mach. Intell., 2020)

PredictProtein - Predicting Protein Structure and Function for 29 Years. - 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; et al. (Nucleic Acids Res., 2021)