Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (RECOMB, 2006)

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. - Brian Y. Chen; Drew H. Bryant; Viacheslav Fofanov; David M. Kristensen; Amanda E. Cruess; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Bioinform. Comput. Biol., 2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Comput. Biol., 2007)

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. - Drew H. Bryant; Mark Moll; Brian Y. Chen; Viacheslav Fofanov; Lydia E. Kavraki (BMC Bioinform., 2010)

The LabelHash Algorithm for Substructure Matching. - Mark Moll; Drew H. Bryant; Lydia E. Kavraki (BMC Bioinform., 2010)

The LabelHash Server and Tools for substructure-based functional annotation. - Mark Moll; Drew H. Bryant; Lydia E. Kavraki (Bioinform., 2011)

Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome. - Drew H. Bryant; Mark Moll; Paul W. Finn; Lydia E. Kavraki (PLoS Comput. Biol., 2013)