A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers. - Roman J. Dorfman; Karl M. Smith; Brian B. Masek; Robert D. Clark (J. Comput. Aided Mol. Des., 2008)

Virtual Screening for R-Groups, including Predicted pIC50 Contributions, within Large Structural Databases, Using Topomer CoMFA. - Richard D. Cramer; Phillip Cruz; Gunther Stahl; William C. Curtiss; Brian Campbell 002; Brian B. Masek; Farhad Soltanshahi (J. Chem. Inf. Model., 2008)

Sharing Chemical Information without Sharing Chemical Structure. - Brian B. Masek; Lingling Shen; Karl M. Smith; Robert S. Pearlman (J. Chem. Inf. Model., 2008)

NovoFLAP: A Ligand-Based De Novo Design Approach for the Generation of Medicinally Relevant Ideas. - James R. Damewood; Charles L. Lerman; Brian B. Masek (J. Chem. Inf. Model., 2010)

Muse+TriposScore: a ligand-based de novo design approach. - Fabian Bös; Ulrike Uhrig; Brian B. Masek; James R. Damewood (J. Cheminformatics, 2011)

Multistep Reaction Based De Novo Drug Design: Generating Synthetically Feasible Design Ideas. - Brian B. Masek; David S. Baker; Roman J. Dorfman; Karen DuBrucq; Victoria C. Francis; Stephan Nagy; Bree L. Richey; Farhad Soltanshahi (J. Chem. Inf. Model., 2016)