Papers+Conferences

2013
Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D.  2013.  FTFlex: Accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics.  Download: PDF (321.96 KB)
2012
Hingtgen S, Kasmieh R, Elbayly E, Nesterenko I, Figueiredo J-L, Dash R, Sarkar D, Hall DR, Kozakov D, Vajda S et al..  2012.  A First-Generation Multi-Functional Cytokine for Simultaneous Optical Tracking and Tumor Therapy. PLoS ONE. 7(7):e40234. Download: PDF (1.67 MB)
Zerbe B, Hall DR, Vajda S, Whitty A, Kozakov D.  2012.  Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.. Journal of chemical information and modeling.  Download: PDF (3.75 MB)
Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S.  2012.  FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Research. 40(W1):W271-W275. Download: PDF (1.33 MB)
Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL, Kozakov D, Vajda S.  2012.  Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins: Structure, Function, and Bioinformatics. 80(2):591-601. Download: PDF (1.57 MB)
Ngan CH, Hall DR, Zerbe B, Grove LE, Kozakov D, Vajda S.  2012.  FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics. 28(2):286-287. Download: PDF (268.3 KB)
Hall DR, Ngan CH, Zerbe B, Kozakov D, Vajda S.  2012.  Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. Journal of Chemical Information and Modeling. 52(1):199-209. Download: PDF (1.92 MB)
2011
Hall DR, Grove LE, Yueh C, Ngan CH, Kozakov D, Vajda S.  2011.  Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme. Journal of the American Chemical Society. 133(51):20668-20671. Download: PDF (3.55 MB)
Kozakov D, Hall DR, Chuang G-Y, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S.  2011.  Structural conservation of druggable hot spots in protein-protein interfaces. Proceedings of the National Academy of Sciences. 108(33):13528-13533. Download: PDF (7.25 MB)
Cencic R, Desforges M, Hall DR, Kozakov D, Du Y, Min J, Dingledine R, Fu H, Vajda S, Talbot PJ et al..  2011.  Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication. Journal of Virology. 85(13):6381-6389. Download: PDF (2.21 MB)
Cencic R, Hall DR, Robert F, Du Y, Min J, Li L, Qui M, Lewis I, Kurtkaya S, Dingledine R et al..  2011.  Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F.. Proceedings of the National Academy of Sciences of the United States of America. 108(3):1046-51. Abstract  Download: PDF (2.42 MB)
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)
2009
Brenke R, Kozakov D, Chuang G-Y, Beglov D, Hall DR, 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 DR, Landon MR, Ngan CH, Shen Y, Thiel SC, Zerbe B, Kozakov D et al..  2009.  Identification of Druggable Hot Spots on Proteins and in Protein Protein Interfaces. Computational Protein-Protein Interactions.