Pspace: a program that assesses protein space. - Mihaly Mezei; Ming-Ming Zhou (Source Code Biol. Medicine, 2007)

Dockres: a computer program that analyzes the output of virtual screening of small molecules. - Mihaly Mezei; Ming-Ming Zhou (Source Code Biol. Medicine, 2010)

Labeling watershed algorithm based on morphological reconstruction in color space. - Gui-mei Zhang; Ming-Ming Zhou; Jun Chu; Jun Miao (HAVE, 2011)

ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. - Jamel Meslamani; Steven G. Smith; Roberto Sanchez; Ming-Ming Zhou (Bioinform., 2014)