Multiple Alignment of protein structures and sequences for VMD. - John Eargle; Dan Wright; Zaida Luthey-Schulten (Bioinform., 2006)

MultiSeq: unifying sequence and structure data for evolutionary analysis. - Elijah Roberts; John Eargle; Dan Wright; Zaida Luthey-Schulten (BMC Bioinform., 2006)

Visualizing the dual space of biological molecules. - John Eargle; Zaida Luthey-Schulten (Comput. Biol. Chem., 2006)

NetworkView: 3D display and analysis of protein·RNA interaction networks. - John Eargle; Zaida Luthey-Schulten (Bioinform., 2012)

MetaBase - the wiki-database of biological databases. - Dan M. Bolser; Pierre-Yves Chibon; Nicolas Palopoli; Sungsam Gong; Daniel Jacob; Victoria Dominguez Del Angel; Daniel Swan; Sebastian Bassi; Virginia González; Prashanth Suravajhala; Seungwoo Hwang; Paolo Romano 001; et al. (Nucleic Acids Res., 2012)