Papers+Conferences

2009
Landon, MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JMM, Orwig SD, Kozakov D, Brenke R, Chuang G-Y, Beglov D et al..  2009.  Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. Journal of Computer-Aided Molecular Design. 23(8):491-500. Download: PDF (574.15 KB)
Vajda, S, Kozakov D.  2009.  Convergence and combination of methods in protein–protein docking. Current Opinion in Structural Biology. 19(2):164-170. Download: PDF (250.8 KB)
Brenke, R, Kozakov D, Chuang G-Y, Beglov D, Hall D, Landon MR, Mattos C, Vajda S.  2009.  Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics. 25(5):621-627. Download: PDF (412.04 KB)
Beglov, D, Brenke R, Chuang G-Y, Hall D, Landon M, Ngan C H, Shen Y, Thiel S, Zerbe B, Kozakov D et al..  2009.  Identification of Druggable Hot Spots on Proteins and in Protein Protein Interfaces. Computational Protein-Protein Interactions.
2008
Kozakov, D, Schueler‐Furman O, Vajda S.  2008.  Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima. Proteins: Structure, Function, and Bioinformatics. 72(3):993-1004. Download: PDF (328.1 KB)
2007
Comeau, SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S.  2007.  ClusPro: Performance in CAPRI rounds 6–11 and the new server. Proteins: Structure, Function, and Bioinformatics. 69(4):781-785. Download: PDF (213.15 KB)
Shen, Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S.  2007.  Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI. Proteins: Structure, Function, and Bioinformatics. 69(4):734-742. Download: PDF (274.39 KB)
2006
Kozakov, D, Brenke R, Comeau SR, Vajda S.  2006.  PIPER: An FFT-based protein docking program with pairwise potentials. Proteins: Structure, Function, and Bioinformatics. 65(2):392-406. Download: PDF (385.54 KB)
2005
Kozakov, D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformations in Protein Docking. Biophysical Journal. 89(2):867-875. Download: PDF (326.16 KB)
Kozakov, D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformation in Protein Docking. CAPRI Meeting.  Download: PPT (5.34 MB)