Small molecule inhibitors of histone arginine methyltransferases: homology modeling, molecular docking, binding mode analysis, and biological evaluations.
Ragno R, Simeoni S, Castellano S, Vicidomini C, Mai A, Caroli A, Tramontano A, Bonaccini C, Trojer P, Bauer I, Brosch G, Sbardella G, J Med Chem, 2007 Mar 22 - link

The betaI/betaIII-tubulin isoforms and their complexes with antimitotic agents. Docking and molecular dynamics studies.
Magnani M, Ortuso F, Soro S, Alcaro S, Tramontano A, Botta M, FEBS J, 2006 Jul - link

PUZZLE: a new method for automated protein docking based on surface shape complementarity.
Helmer-Citterich M, Tramontano A, J Mol Biol, 1994 Jan 21 - link