CoMFA 3D-QSAR analysis of HIV-1 RT nonnucleoside inhibitors, TIBO derivatives based on docking conformation and alignment.
Zhou Z, Madura JD, J Chem Inf Comput Sci, 2004 Nov-Dec - link

Kinetic and docking studies of the interaction of quinones with the quinone reductase active site.
Zhou Z, Fisher D, Spidel J, Greenfield J, Patson B, Fazal A, Wigal C, Moe OA, Madura JD, Biochemistry, 2003 Feb 25 - link

Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase.
Zhou Z, Madrid M, Madura JD, Proteins, 2002 Dec 1 - link

Docking of sulfonamides to carbonic anhydrase II and IV.
Esposito EX, Baran K, Kelly K, Madura JD, J Mol Graph Model, 2000 Jun - link