Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models.
Cotesta S, Giordanetto F, Trosset JY, Crivori P, Kroemer RT, Stouten PF, Vulpetti A, Proteins, 2005 Sep 1 - link

Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations.
Kroemer RT, Vulpetti A, McDonald JJ, Rohrer DC, Trosset JY, Giordanetto F, Cotesta S, McMartin C, Kihlen M, Stouten PF, J Chem Inf Comput Sci, 2004 May-Jun - link

Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking.
Roisman LC, Piehler J, Trosset JY, Scheraga HA, Schreiber G, Proc Natl Acad Sci U S A, 2001 Nov 6 - link

New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen Aalpha-like peptide bound to thrombin (S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program.
Maurer MC, Trosset JY, Lester CC, DiBella EE, Scheraga HA, Proteins, 1999 Jan 1 - link

Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines.
Trosset JY, Scheraga HA, Proc Natl Acad Sci U S A, 1998 Jul 7 - link