VISTRAJ: exploring protein conformational space. - John J. Salama; Howard J. Feldman; Christopher W. V. Hogue (Bioinform., 2001)

The Biomolecular Interaction Network Database and related tools 2005 update. - C. Alfarano; C. E. Andrade; K. Anthony; N. Bahroos; Martha Bajec; K. Bantoft; Doron Betel; B. Bobechko; K. Boutilier; E. Burgess; K. Buzadzija; R. Cavero; et al. (Nucleic Acids Res., 2005)

Domain-based small molecule binding site annotation. - Kevin A. Snyder; Howard J. Feldman; Michel Dumontier; John J. Salama; Christopher W. V. Hogue (BMC Bioinform., 2006)

Pocket Similarity: Are α Carbons Enough? - Howard J. Feldman; Paul Labute (J. Chem. Inf. Model., 2010)

Identifying structural domains of proteins using clustering. - Howard J. Feldman (BMC Bioinform., 2012)