Convergence and combination of methods in protein-protein docking.
Vajda S, Kozakov D, Curr Opin Struct Biol, 2009 Apr - link

Protein docking by the underestimation of free energy funnels in the space of encounter complexes.
Shen Y, Paschalidis ICh, Vakili P, Vajda S, PLoS Comput Biol, 2008 Oct - link

DARS (Decoys As the Reference State) potentials for protein-protein docking.
Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S, Biophys J, 2008 Nov 1 - link

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.
Ritchie DW, Kozakov D, Vajda S, Bioinformatics, 2008 Sep 1 - link

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima.
Kozakov D, Schueler-Furman O, Vajda S, Proteins, 2008 Aug 15 - link

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.
Paschalidis ICh, Shen Y, Vakili P, Vajda S, Conf Proc IEEE Eng Med Biol Soc, 2006 - link

Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.
Shen Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S, Proteins, 2007 Dec 1 - link

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.
Paschalidis IC, Shen Y, Vakili P, Vajda S, IEEE Trans Automat Contr, 2007 Apr 1 - link

PIPER: an FFT-based protein docking program with pairwise potentials.
Kozakov D, Brenke R, Comeau SR, Vajda S, Proteins, 2006 Nov 1 - link

Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.
Comeau SR, Vajda S, Camacho CJ, Proteins, 2005 Aug 1 - link

Classification of protein complexes based on docking difficulty.
Vajda S, Proteins, 2005 Aug 1 - link

Optimal clustering for detecting near-native conformations in protein docking.
Kozakov D, Clodfelter KH, Vajda S, Camacho CJ, Biophys J, 2005 Aug - link

ClusPro: a fully automated algorithm for protein-protein docking.
Comeau SR, Gatchell DW, Vajda S, Camacho CJ, Nucleic Acids Res, 2004 Jul 1 - link

Protein-protein docking: is the glass half-full or half-empty?
Vajda S, Camacho CJ, Trends Biotechnol, 2004 Mar - link

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
Comeau SR, Gatchell DW, Vajda S, Camacho CJ, Bioinformatics, 2004 Jan 1 - link

Combination of scoring functions improves discrimination in protein-protein docking.
Murphy J, Gatchell DW, Prasad JC, Vajda S, Proteins, 2003 Dec 1 - link

Protein-protein association kinetics and protein docking.
Camacho CJ, Vajda S, Curr Opin Struct Biol, 2002 Feb - link

Protein docking along smooth association pathways.
Camacho CJ, Vajda S, Proc Natl Acad Sci U S A, 2001 Sep 11 - link

Scoring docked conformations generated by rigid-body protein-protein docking.
Camacho CJ, Gatchell DW, Kimura SR, Vajda S, Proteins, 2000 Aug 15 - link

Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors.
King BL, Vajda S, DeLisi C, FEBS Lett, 1996 Apr 8 - link

Flexible docking of peptides to class I major-histocompatibility-complex receptors.
Rosenfeld R, Zheng Q, Vajda S, DeLisi C, Genet Anal, 1995 Mar - link

Flexible docking and design.
Rosenfeld R, Vajda S, DeLisi C, Annu Rev Biophys Biomol Struct, 1995 - link