PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm. - Daniel Zaidman; Haim J. Wolfson (Bioinform., 2016)

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)