Learning MHC I - peptide binding. - Nebojsa Jojic; Manuel Reyes-Gomez; David Heckerman; Carl Myers Kadie; Ora Schueler-Furman (ISMB (Supplement of Bioinformatics), 2006)

Minimizing and Learning Energy Functions for Side-Chain Prediction. - Chen Yanover; Ora Schueler-Furman; Yair Weiss (J. Comput. Biol., 2008)

Rapid Sampling of Molecular Motions with Prior Information Constraints. - Barak Raveh; Angela Enosh; Ora Schueler-Furman; Dan Halperin (PLoS Comput. Biol., 2009)

Rosetta FlexPepDock web server - high resolution modeling of peptide-protein interactions. - Nir London; Barak Raveh; Eyal Cohen; Guy Fathi; Ora Schueler-Furman (Nucleic Acids Res., 2011)

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity. - Nir London; Corissa L. Lamphear; James L. Hougland; Carol A. Fierke; Ora Schueler-Furman (PLoS Comput. Biol., 2011)

Application of asymmetric statistical potentials to antibody-protein docking. - Ryan Brenke; David R. Hall; Gwo-Yu Chuang; Stephen R. Comeau; Tanggis Bohnuud; Dmitri Beglov; Ora Schueler-Furman; Sandor Vajda; Dima Kozakov (Bioinform., 2012)

Peptiderive server: derive peptide inhibitors from protein-protein interactions. - Yuval Sedan; Orly Marcu; Sergey Lyskov; Ora Schueler-Furman (Nucleic Acids Res., 2016)

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. - Kathryn A. Porter; Bing Xia; Dmitri Beglov; Tanggis Bohnuud; Nawsad Alam; Ora Schueler-Furman; Dima Kozakov (Bioinform., 2017)

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. - Nawsad Alam; Oriel Goldstein; Bing Xia; Kathryn A. Porter; Dima Kozakov; Ora Schueler-Furman (PLoS Comput. Biol., 2017)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

Protein language models can capture protein quaternary state. - Orly Avraham; Tomer Tsaban; Ziv Ben-Aharon; Linoy Tsaban; Ora Schueler-Furman (BMC Bioinform., 2023)