Papers+Conferences

2013
Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P.  2013.  Flexible refinement of protein-ligand docking on manifolds. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :1392-1397. Download: PDF (384.37 KB)
Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC.  2013.  A new distributed algorithm for side-chain positioning in the process of protein docking. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :739-744. Download: PDF (334.84 KB)
2010
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
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)