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)

Prediction of Substrates for Glutathione Transferases by Covalent Docking. - Guang Qiang Dong; Sara Calhoun; Hao Fan 002; Chakrapani Kalyanaraman; Megan C. Branch; Susan T. Mashiyama; Nir London; Matthew P. Jacobson; Patricia C. Babbitt; Brian K. Shoichet; Richard N. Armstrong; Andrej Sali (J. Chem. Inf. Model., 2014)

Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. - Chimno I. Nnadi; Meredith L. Jenkins; Daniel R. Gentile; Leslie A. Bateman; Daniel Zaidman; Trent E. Balius; Daniel K. Nomura; John E. Burke; Kevan M. Shokat; Nir London (J. Chem. Inf. Model., 2018)

PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes. - Daniel Zaidman; Jaime Prilusky; Nir London (J. Chem. Inf. Model., 2020)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

Computational Design of Lysine Targeting Covalent Binders Using Rosetta. - Barr Tivon; Jan Wiese; Matthias P. Müller; Ronen Gabizon; Daniel Rauh; Nir London (J. Chem. Inf. Model., 2025)