Papers+Conferences

2012
Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D.  2012.  Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. :120821123549006. Download: PDF (317.26 KB)
2010
Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis IC et al..  2010.  Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins: Structure, Function, and Bioinformatics. 78(15):3124-3130. Download: PDF (297.68 KB)
2008
Shen Y, Paschalidis IC, Vakili P, Vajda S.  2008.  Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Computational Biology. 4(10):e1000191. Download: PDF (497.62 KB)
2007
Paschalidis IC, Shen Y, Vakili P, Vajda S.  2007.  SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Transactions on Automatic Control. 52(4):664-676. Download: PDF (1.13 MB)
2006
Paschalidis IC, Shen Y, Vakili P, Vajda S.  2006.  Protein Docking by Exploiting Multi-dimensional Energy Funnels. IEEE 2006 International Conference of EMBS.  Download: PDF (1.25 MB); ZIP (8.05 MB)
Paschalidis IC, Shen Y, Vakili P, Vajda S.  2006.  Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. :5330-5333. Download: PDF (295.9 KB)