Shotgun: getting more from sequence similarity searches. - Scott C.-H. Pegg; Patricia C. Babbitt (Bioinform., 1999)

A genetic algorithm for structure-based de novo design. - Scott C.-H. Pegg; Jose J. Haresco; Irwin D. Kuntz (J. Comput. Aided Mol. Des., 2001)

Intersect: identification and visualization of overlaps in database search results. - Scott C.-H. Pegg; Walter R. P. Novak; Patricia C. Babbitt (Bioinform., 2003)

SitePrint: Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design. - James R. Arnold; Keith W. Burdick; Scott C.-H. Pegg; Samuel Toba; Michelle L. Lamb; Irwin D. Kuntz (J. Chem. Inf. Model., 2004)

Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies. - Scott C.-H. Pegg; Shoshana D. Brown; Sunil Ojha; Conrad C. Huang; Thomas E. Ferrin; Patricia C. Babbitt (Pacific Symposium on Biocomputing, 2005)

Development and validation of a modular, extensible docking program: DOCK 5. - Demetri Moustakas; P. Therese Lang; Scott C.-H. Pegg; Eric Pettersen; Irwin D. Kuntz; Natasja Brooijmans; Robert C. Rizzo (J. Comput. Aided Mol. Des., 2006)

Biocuration in the structure-function linkage database: the anatomy of a superfamily. - Gemma L. Holliday; Shoshana D. Brown; Eyal Akiva; David Mischel; Michael A. Hicks 002; John H. Morris; Conrad C. Huang; Elaine C. Meng; Scott C.-H. Pegg; Thomas E. Ferrin; Patricia C. Babbitt (Database J. Biol. Databases Curation, 2017)