Our Servers

Our lab maintains multiple servers to provide the community with tools for using our methods. If you would like additional information on any of the servers, please contact us, choosing the appropriate server under category.


  1. Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S.  2017.  The ClusPro web server for protein–protein docking. Nature Protocols. 12(2):255-278.
  2. Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S.  2013.  How good is automated protein docking? Proteins: Structure, Function, and Bioinformatics.
  3. 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.
  4. Comeau SR, Gatchell DW, Vajda S, Camacho CJ.  2004.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 20(1):45-50.
  5. Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S.  2017.  ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking. Journal of Molecular Biology. 429(3):372-381.
  6. Porter KA, Xia B, Beglov D, Bohnuud T, Alam N, Schueler-Furman O, Kozakov D.  2017.  ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. Bioinformatics.
  7. Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE, Luo L, Xia B, Beglov D, Vajda S.  2015.  The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nature Protocols. 10(5):733-755.
  8. 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.
  9. 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.
  10. 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.
  11. Bohnuud T, Beglov D, Ngan CH, Zerbe BS, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, Kozakov D.  2012.  Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. Nucleic Acids Research. 40(16):7644-7652.
  12. Ngan CH, Hall DR, Zerbe BS, Grove LE, Kozakov D, Vajda S.  2012.  FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics. 28(2):286-287.
  13. 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.
  14. Bohnuud T, Kozakov D, Vajda S.  2014.  Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces. PLoS Computational Biology. 10(10):e1003872.