PUDGE: a flexible, interactive server for protein structure prediction. - Raquel Norel; Donald Petrey; Barry Honig (Nucleic Acids Res., 2010)

MarkUs: a server to navigate sequence-structure-function space. - Markus Fischer; Qiangfeng Cliff Zhang; Fabian Dey; Brian Y. Chen; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

PredUs: a web server for predicting protein interfaces using structural neighbors. - Qiangfeng Cliff Zhang; Lei Deng 002; Markus Fisher; Jihong Guan; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

Using Structure to Explore the Sequence Alignment Space of Remote Homologs. - Andrew Kuziemko; Barry Honig; Donald Petrey (PLoS Comput. Biol., 2011)

PrePPI: a structure-informed database of protein-protein interactions. - Qiangfeng Cliff Zhang; Donald Petrey; José Ignacio Garzón; Lei Deng 002; Barry Honig (Nucleic Acids Res., 2013)

Predicting Peptide-Mediated Interactions on a Genome-Wide Scale. - T. Scott Chen; Donald Petrey; José Ignacio Garzón; Barry Honig (PLoS Comput. Biol., 2015)